From 2b69c9f858b454a69c74c90f8c1453206faad266 Mon Sep 17 00:00:00 2001
From: Andrew Branch <andrew@wheream.io>
Date: Tue, 27 Feb 2024 15:45:04 -0800
Subject: [PATCH] Show synthesized triple slash references in diagnostics for
 analysis

---
 src/compiler/diagnosticMessages.json          |   9 +
 src/compiler/transformers/declarations.ts     |  13 +-
 .../amdLikeInputDeclarationEmit.errors.txt    |  34 ++
 .../reference/amdLikeInputDeclarationEmit.js  |  40 --
 ...lModuleWithSingleExportedModule.errors.txt |  21 +
 ...tExternalModuleWithSingleExportedModule.js |   4 -
 ...EmitBundleWithAmbientReferences.errors.txt |  24 +
 ...ssFileImportTypeOfAmbientModule.errors.txt |  16 +
 ...nEmitCrossFileImportTypeOfAmbientModule.js |   5 -
 ...paceNoTripleSlashTypesReference.errors.txt |  41 ++
 ...nedNamespaceNoTripleSlashTypesReference.js |   5 -
 ...NamespaceNoTripleSlashTypesReference.types |   2 +-
 ...onEmitHasTypesRefOnNamespaceUse.errors.txt |  17 +
 ...eclarationEmitHasTypesRefOnNamespaceUse.js |   6 -
 ...larationEmitPathMappingMonorepo.errors.txt |  32 ++
 .../declarationEmitPathMappingMonorepo.js     |   5 -
 ...ipleSlashReferenceAmbientModule.errors.txt |  28 ++
 ...onEmitTripleSlashReferenceAmbientModule.js |  31 --
 ...arationFilesWithTypeReferences2.errors.txt |  14 +
 .../declarationFilesWithTypeReferences2.js    |   5 -
 .../importAliasFromNamespace.errors.txt       |  25 +
 .../reference/importAliasFromNamespace.js     |   8 -
 .../baselines/reference/importDecl.errors.txt |  85 ++++
 tests/baselines/reference/importDecl.js       |  23 -
 ...peGenericArrowTypeParenthesized.errors.txt |  23 +
 ...importTypeGenericArrowTypeParenthesized.js |  10 -
 .../jsDeclarationsReactComponents.errors.txt  | 102 ++++
 .../jsDeclarationsReactComponents.js          |  25 -
 ...onsWithJsFileReferenceWithNoOut.errors.txt |   5 +-
 ...eclarationsWithJsFileReferenceWithNoOut.js |   3 -
 ...tionsWithJsFileReferenceWithOut.errors.txt |   5 +-
 ...nsWithJsFileReferenceWithOutDir.errors.txt |  17 +
 ...clarationsWithJsFileReferenceWithOutDir.js |   3 -
 .../missingImportAfterModuleImport.errors.txt |  26 +
 .../missingImportAfterModuleImport.js         |   8 -
 .../moduleAugmentationsImports2.errors.txt    |   5 +-
 .../reference/moduleSymbolMerging.errors.txt  |  16 +
 .../reference/moduleSymbolMerging.js          |   6 -
 ...ImportAssignment(module=node16).errors.txt |  15 +-
 ...sAllowJsImportAssignment(module=node16).js |  11 -
 ...portAssignment(module=nodenext).errors.txt |  15 +-
 ...llowJsImportAssignment(module=nodenext).js |  11 -
 ...lpersCollisions2(module=node16).errors.txt |  10 +-
 ...ImportHelpersCollisions2(module=node16).js |  10 -
 ...ersCollisions2(module=nodenext).errors.txt |  10 +-
 ...portHelpersCollisions2(module=nodenext).js |  10 -
 ...mportAssignments(module=node16).errors.txt |  40 ++
 ...ModulesImportAssignments(module=node16).js |  11 -
 ...ortAssignments(module=nodenext).errors.txt |  40 ++
 ...dulesImportAssignments(module=nodenext).js |  11 -
 ...lpersCollisions2(module=node16).errors.txt |  10 +-
 ...ImportHelpersCollisions2(module=node16).js |  10 -
 ...ersCollisions2(module=nodenext).errors.txt |  10 +-
 ...portHelpersCollisions2(module=nodenext).js |  10 -
 ...lpersCollisions3(module=node16).errors.txt |  10 +-
 ...ImportHelpersCollisions3(module=node16).js |   8 -
 ...ersCollisions3(module=nodenext).errors.txt |  10 +-
 ...portHelpersCollisions3(module=nodenext).js |   8 -
 ...DeclarationEmit6(module=node16).errors.txt |  32 ++
 ...enceModeDeclarationEmit6(module=node16).js |   4 -
 ...clarationEmit6(module=nodenext).errors.txt |  32 ++
 ...ceModeDeclarationEmit6(module=nodenext).js |   4 -
 ...DeclarationEmit7(module=node16).errors.txt |  52 ++
 ...enceModeDeclarationEmit7(module=node16).js |   5 -
 ...clarationEmit7(module=nodenext).errors.txt |  52 ++
 ...ceModeDeclarationEmit7(module=nodenext).js |   5 -
 .../outModuleTripleSlashRefs.errors.txt       |  33 ++
 ...ivacyCannotNameAccessorDeclFile.errors.txt | 142 ++++++
 .../privacyCannotNameAccessorDeclFile.js      |  26 -
 ...rivacyCannotNameVarTypeDeclFile.errors.txt | 105 ++++
 .../privacyCannotNameVarTypeDeclFile.js       |  30 --
 ...CannotNameParameterTypeDeclFile.errors.txt | 161 +++++++
 ...FunctionCannotNameParameterTypeDeclFile.js |  46 --
 ...ionCannotNameReturnTypeDeclFile.errors.txt | 168 +++++++
 ...acyFunctionCannotNameReturnTypeDeclFile.js |  30 --
 ...tExternalModuleImportWithExport.errors.txt |   5 +-
 ...elAmbientExternalModuleImportWithExport.js |  11 -
 ...ternalModuleImportWithoutExport.errors.txt |   5 +-
 ...mbientExternalModuleImportWithoutExport.js |  10 -
 ...olutePathMixedSubfolderNoOutdir.errors.txt |  40 ++
 ...ootAbsolutePathMixedSubfolderNoOutdir.json |   3 +-
 ...olutePathMixedSubfolderNoOutdir.errors.txt |  40 ++
 ...ootAbsolutePathMixedSubfolderNoOutdir.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...hMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...hMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...AbsolutePathMultifolderNoOutdir.errors.txt |  40 ++
 ...apRootAbsolutePathMultifolderNoOutdir.json |   3 +-
 ...AbsolutePathMultifolderNoOutdir.errors.txt |  40 ++
 ...apRootAbsolutePathMultifolderNoOutdir.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...PathMultifolderSpecifyOutputDirectory.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...PathMultifolderSpecifyOutputDirectory.json |   3 +-
 ...athMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...athMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...pRootAbsolutePathSimpleNoOutdir.errors.txt |  29 ++
 .../mapRootAbsolutePathSimpleNoOutdir.json    |   3 +-
 ...pRootAbsolutePathSimpleNoOutdir.errors.txt |  29 ++
 .../mapRootAbsolutePathSimpleNoOutdir.json    |   3 +-
 ...athSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...olutePathSimpleSpecifyOutputDirectory.json |   3 +-
 ...athSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...olutePathSimpleSpecifyOutputDirectory.json |   3 +-
 ...lutePathSimpleSpecifyOutputFile.errors.txt |   5 +-
 ...lutePathSimpleSpecifyOutputFile.errors.txt |   5 +-
 ...otAbsolutePathSubfolderNoOutdir.errors.txt |  29 ++
 .../mapRootAbsolutePathSubfolderNoOutdir.json |   3 +-
 ...otAbsolutePathSubfolderNoOutdir.errors.txt |  29 ++
 .../mapRootAbsolutePathSubfolderNoOutdir.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...tePathSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...tePathSubfolderSpecifyOutputDirectory.json |   3 +-
 ...ePathSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ePathSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ativePathMixedSubfolderNoOutdir.errors.txt |  40 ++
 ...ootRelativePathMixedSubfolderNoOutdir.json |   3 +-
 ...ativePathMixedSubfolderNoOutdir.errors.txt |  40 ++
 ...ootRelativePathMixedSubfolderNoOutdir.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...hMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...hMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...RelativePathMultifolderNoOutdir.errors.txt |  40 ++
 ...apRootRelativePathMultifolderNoOutdir.json |   3 +-
 ...RelativePathMultifolderNoOutdir.errors.txt |  40 ++
 ...apRootRelativePathMultifolderNoOutdir.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...PathMultifolderSpecifyOutputDirectory.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...PathMultifolderSpecifyOutputDirectory.json |   3 +-
 ...athMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...athMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...pRootRelativePathSimpleNoOutdir.errors.txt |  29 ++
 .../mapRootRelativePathSimpleNoOutdir.json    |   3 +-
 ...pRootRelativePathSimpleNoOutdir.errors.txt |  29 ++
 .../mapRootRelativePathSimpleNoOutdir.json    |   3 +-
 ...athSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...ativePathSimpleSpecifyOutputDirectory.json |   3 +-
 ...athSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...ativePathSimpleSpecifyOutputDirectory.json |   3 +-
 ...tivePathSimpleSpecifyOutputFile.errors.txt |   5 +-
 ...tivePathSimpleSpecifyOutputFile.errors.txt |   5 +-
 ...otRelativePathSubfolderNoOutdir.errors.txt |  29 ++
 .../mapRootRelativePathSubfolderNoOutdir.json |   3 +-
 ...otRelativePathSubfolderNoOutdir.errors.txt |  29 ++
 .../mapRootRelativePathSubfolderNoOutdir.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...vePathSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...vePathSubfolderSpecifyOutputDirectory.json |   3 +-
 ...ePathSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ePathSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...aprootUrlMixedSubfolderNoOutdir.errors.txt |  40 ++
 .../amd/maprootUrlMixedSubfolderNoOutdir.json |   3 +-
 ...aprootUrlMixedSubfolderNoOutdir.errors.txt |  40 ++
 .../maprootUrlMixedSubfolderNoOutdir.json     |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...lMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...lMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 .../maprootUrlMultifolderNoOutdir.errors.txt  |  40 ++
 .../amd/maprootUrlMultifolderNoOutdir.json    |   3 +-
 .../maprootUrlMultifolderNoOutdir.errors.txt  |  40 ++
 .../node/maprootUrlMultifolderNoOutdir.json   |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...tUrlMultifolderSpecifyOutputDirectory.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...tUrlMultifolderSpecifyOutputDirectory.json |   3 +-
 ...UrlMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...UrlMultifolderSpecifyOutputFile.errors.txt |   5 +-
 .../amd/maprootUrlSimpleNoOutdir.errors.txt   |  29 ++
 .../amd/maprootUrlSimpleNoOutdir.json         |   3 +-
 .../node/maprootUrlSimpleNoOutdir.errors.txt  |  29 ++
 .../node/maprootUrlSimpleNoOutdir.json        |   3 +-
 ...UrlSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...aprootUrlSimpleSpecifyOutputDirectory.json |   3 +-
 ...UrlSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...aprootUrlSimpleSpecifyOutputDirectory.json |   3 +-
 ...prootUrlSimpleSpecifyOutputFile.errors.txt |   5 +-
 ...prootUrlSimpleSpecifyOutputFile.errors.txt |   5 +-
 .../maprootUrlSubfolderNoOutdir.errors.txt    |  29 ++
 .../amd/maprootUrlSubfolderNoOutdir.json      |   3 +-
 .../maprootUrlSubfolderNoOutdir.errors.txt    |  29 ++
 .../node/maprootUrlSubfolderNoOutdir.json     |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...ootUrlSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...ootUrlSubfolderSpecifyOutputDirectory.json |   3 +-
 ...otUrlSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...otUrlSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...cerootUrlMixedSubfolderNoOutdir.errors.txt |  40 ++
 ...rlsourcerootUrlMixedSubfolderNoOutdir.json |   3 +-
 ...cerootUrlMixedSubfolderNoOutdir.errors.txt |  40 ++
 ...rlsourcerootUrlMixedSubfolderNoOutdir.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...lMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...lMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...ourcerootUrlMultifolderNoOutdir.errors.txt |  40 ++
 ...otUrlsourcerootUrlMultifolderNoOutdir.json |   3 +-
 ...ourcerootUrlMultifolderNoOutdir.errors.txt |  40 ++
 ...otUrlsourcerootUrlMultifolderNoOutdir.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...tUrlMultifolderSpecifyOutputDirectory.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...tUrlMultifolderSpecifyOutputDirectory.json |   3 +-
 ...UrlMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...UrlMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...tUrlsourcerootUrlSimpleNoOutdir.errors.txt |  29 ++
 ...maprootUrlsourcerootUrlSimpleNoOutdir.json |   3 +-
 ...tUrlsourcerootUrlSimpleNoOutdir.errors.txt |  29 ++
 ...maprootUrlsourcerootUrlSimpleNoOutdir.json |   3 +-
 ...UrlSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...cerootUrlSimpleSpecifyOutputDirectory.json |   3 +-
 ...UrlSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...cerootUrlSimpleSpecifyOutputDirectory.json |   3 +-
 ...erootUrlSimpleSpecifyOutputFile.errors.txt |   5 +-
 ...erootUrlSimpleSpecifyOutputFile.errors.txt |   5 +-
 ...lsourcerootUrlSubfolderNoOutdir.errors.txt |  29 ++
 ...rootUrlsourcerootUrlSubfolderNoOutdir.json |   3 +-
 ...lsourcerootUrlSubfolderNoOutdir.errors.txt |  29 ++
 ...rootUrlsourcerootUrlSubfolderNoOutdir.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...ootUrlSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...ootUrlSubfolderSpecifyOutputDirectory.json |   3 +-
 ...otUrlSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...otUrlSubfolderSpecifyOutputFile.errors.txt |   5 +-
 .../amd/outMixedSubfolderNoOutdir.errors.txt  |  40 ++
 .../amd/outMixedSubfolderNoOutdir.json        |   3 +-
 .../node/outMixedSubfolderNoOutdir.errors.txt |  40 ++
 .../node/outMixedSubfolderNoOutdir.json       |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...tMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...tMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 .../amd/outMultifolderNoOutdir.errors.txt     |  40 ++
 .../amd/outMultifolderNoOutdir.json           |   3 +-
 .../node/outMultifolderNoOutdir.errors.txt    |  40 ++
 .../node/outMultifolderNoOutdir.json          |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 .../outMultifolderSpecifyOutputDirectory.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 .../outMultifolderSpecifyOutputDirectory.json |   3 +-
 ...outMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...outMultifolderSpecifyOutputFile.errors.txt |   5 +-
 .../amd/outSimpleNoOutdir.errors.txt          |  29 ++
 .../amd/outSimpleNoOutdir.json                |   3 +-
 .../node/outSimpleNoOutdir.errors.txt         |  29 ++
 .../node/outSimpleNoOutdir.json               |   3 +-
 ...outSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 .../amd/outSimpleSpecifyOutputDirectory.json  |   3 +-
 ...outSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 .../node/outSimpleSpecifyOutputDirectory.json |   3 +-
 .../amd/outSimpleSpecifyOutputFile.errors.txt |   5 +-
 .../outSimpleSpecifyOutputFile.errors.txt     |   5 +-
 .../amd/outSubfolderNoOutdir.errors.txt       |  29 ++
 .../amd/outSubfolderNoOutdir.json             |   3 +-
 .../node/outSubfolderNoOutdir.errors.txt      |  29 ++
 .../node/outSubfolderNoOutdir.json            |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 .../outSubfolderSpecifyOutputDirectory.json   |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 .../outSubfolderSpecifyOutputDirectory.json   |   3 +-
 .../outSubfolderSpecifyOutputFile.errors.txt  |   5 +-
 .../outSubfolderSpecifyOutputFile.errors.txt  |   5 +-
 .../quotesInFileAndDirectoryNames.errors.txt  |  20 +
 .../amd/quotesInFileAndDirectoryNames.json    |   3 +-
 .../quotesInFileAndDirectoryNames.errors.txt  |  20 +
 .../node/quotesInFileAndDirectoryNames.json   |   3 +-
 ...eferenceResolutionRelativePaths.errors.txt |  24 +
 .../amd/referenceResolutionRelativePaths.json |   4 +-
 ...eferenceResolutionRelativePaths.errors.txt |  24 +
 .../referenceResolutionRelativePaths.json     |   4 +-
 ...nRelativePathsFromRootDirectory.errors.txt |  24 +
 ...olutionRelativePathsFromRootDirectory.json |   4 +-
 ...nRelativePathsFromRootDirectory.errors.txt |  24 +
 ...olutionRelativePathsFromRootDirectory.json |   4 +-
 ...ivePathsRelativeToRootDirectory.errors.txt |  24 +
 ...nRelativePathsRelativeToRootDirectory.json |   4 +-
 ...ivePathsRelativeToRootDirectory.errors.txt |  24 +
 ...nRelativePathsRelativeToRootDirectory.json |   4 +-
 .../amd/rootDirectory.errors.txt              |  18 +
 .../rootDirectory/amd/rootDirectory.json      |   3 +-
 .../node/rootDirectory.errors.txt             |  18 +
 .../rootDirectory/node/rootDirectory.json     |   3 +-
 .../amd/rootDirectoryErrors.errors.txt        |   8 +-
 .../amd/rootDirectoryErrors.json              |   3 +-
 .../node/rootDirectoryErrors.errors.txt       |   8 +-
 .../node/rootDirectoryErrors.json             |   3 +-
 ...olutePathMixedSubfolderNoOutdir.errors.txt |  40 ++
 ...ootAbsolutePathMixedSubfolderNoOutdir.json |   3 +-
 ...olutePathMixedSubfolderNoOutdir.errors.txt |  40 ++
 ...ootAbsolutePathMixedSubfolderNoOutdir.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...hMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...hMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...AbsolutePathMultifolderNoOutdir.errors.txt |  40 ++
 ...ceRootAbsolutePathMultifolderNoOutdir.json |   3 +-
 ...AbsolutePathMultifolderNoOutdir.errors.txt |  40 ++
 ...ceRootAbsolutePathMultifolderNoOutdir.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...PathMultifolderSpecifyOutputDirectory.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...PathMultifolderSpecifyOutputDirectory.json |   3 +-
 ...athMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...athMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...eRootAbsolutePathSimpleNoOutdir.errors.txt |  29 ++
 .../sourceRootAbsolutePathSimpleNoOutdir.json |   3 +-
 ...eRootAbsolutePathSimpleNoOutdir.errors.txt |  29 ++
 .../sourceRootAbsolutePathSimpleNoOutdir.json |   3 +-
 ...athSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...olutePathSimpleSpecifyOutputDirectory.json |   3 +-
 ...athSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...olutePathSimpleSpecifyOutputDirectory.json |   3 +-
 ...lutePathSimpleSpecifyOutputFile.errors.txt |   5 +-
 ...lutePathSimpleSpecifyOutputFile.errors.txt |   5 +-
 ...otAbsolutePathSubfolderNoOutdir.errors.txt |  29 ++
 ...urceRootAbsolutePathSubfolderNoOutdir.json |   3 +-
 ...otAbsolutePathSubfolderNoOutdir.errors.txt |  29 ++
 ...urceRootAbsolutePathSubfolderNoOutdir.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...tePathSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...tePathSubfolderSpecifyOutputDirectory.json |   3 +-
 ...ePathSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ePathSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ativePathMixedSubfolderNoOutdir.errors.txt |  40 ++
 ...ootRelativePathMixedSubfolderNoOutdir.json |   3 +-
 ...ativePathMixedSubfolderNoOutdir.errors.txt |  40 ++
 ...ootRelativePathMixedSubfolderNoOutdir.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...hMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...hMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...RelativePathMultifolderNoOutdir.errors.txt |  40 ++
 ...ceRootRelativePathMultifolderNoOutdir.json |   3 +-
 ...RelativePathMultifolderNoOutdir.errors.txt |  40 ++
 ...ceRootRelativePathMultifolderNoOutdir.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...PathMultifolderSpecifyOutputDirectory.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...PathMultifolderSpecifyOutputDirectory.json |   3 +-
 ...athMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...athMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...eRootRelativePathSimpleNoOutdir.errors.txt |  29 ++
 .../sourceRootRelativePathSimpleNoOutdir.json |   3 +-
 ...eRootRelativePathSimpleNoOutdir.errors.txt |  29 ++
 .../sourceRootRelativePathSimpleNoOutdir.json |   3 +-
 ...athSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...ativePathSimpleSpecifyOutputDirectory.json |   3 +-
 ...athSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...ativePathSimpleSpecifyOutputDirectory.json |   3 +-
 ...tivePathSimpleSpecifyOutputFile.errors.txt |   5 +-
 ...tivePathSimpleSpecifyOutputFile.errors.txt |   5 +-
 ...otRelativePathSubfolderNoOutdir.errors.txt |  29 ++
 ...urceRootRelativePathSubfolderNoOutdir.json |   3 +-
 ...otRelativePathSubfolderNoOutdir.errors.txt |  29 ++
 ...urceRootRelativePathSubfolderNoOutdir.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...vePathSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...vePathSubfolderSpecifyOutputDirectory.json |   3 +-
 ...ePathSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ePathSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...sourcemapMixedSubfolderNoOutdir.errors.txt |  40 ++
 .../amd/sourcemapMixedSubfolderNoOutdir.json  |   3 +-
 ...sourcemapMixedSubfolderNoOutdir.errors.txt |  40 ++
 .../node/sourcemapMixedSubfolderNoOutdir.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...pMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...pMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 .../sourcemapMultifolderNoOutdir.errors.txt   |  40 ++
 .../amd/sourcemapMultifolderNoOutdir.json     |   3 +-
 .../sourcemapMultifolderNoOutdir.errors.txt   |  40 ++
 .../node/sourcemapMultifolderNoOutdir.json    |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...emapMultifolderSpecifyOutputDirectory.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...emapMultifolderSpecifyOutputDirectory.json |   3 +-
 ...mapMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...mapMultifolderSpecifyOutputFile.errors.txt |   5 +-
 .../amd/sourcemapSimpleNoOutdir.errors.txt    |  29 ++
 .../amd/sourcemapSimpleNoOutdir.json          |   3 +-
 .../node/sourcemapSimpleNoOutdir.errors.txt   |  29 ++
 .../node/sourcemapSimpleNoOutdir.json         |   3 +-
 ...mapSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...sourcemapSimpleSpecifyOutputDirectory.json |   3 +-
 ...mapSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...sourcemapSimpleSpecifyOutputDirectory.json |   3 +-
 ...ourcemapSimpleSpecifyOutputFile.errors.txt |   5 +-
 ...ourcemapSimpleSpecifyOutputFile.errors.txt |   5 +-
 .../amd/sourcemapSubfolderNoOutdir.errors.txt |  29 ++
 .../amd/sourcemapSubfolderNoOutdir.json       |   3 +-
 .../sourcemapSubfolderNoOutdir.errors.txt     |  29 ++
 .../node/sourcemapSubfolderNoOutdir.json      |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...rcemapSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...rcemapSubfolderSpecifyOutputDirectory.json |   3 +-
 ...cemapSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...cemapSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...cerootUrlMixedSubfolderNoOutdir.errors.txt |  40 ++
 .../sourcerootUrlMixedSubfolderNoOutdir.json  |   3 +-
 ...cerootUrlMixedSubfolderNoOutdir.errors.txt |  40 ++
 .../sourcerootUrlMixedSubfolderNoOutdir.json  |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...lMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...lMixedSubfolderSpecifyOutputDirectory.json |   3 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...MixedSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...ifyOutputFileAndOutputDirectory.errors.txt |   5 +-
 ...ourcerootUrlMultifolderNoOutdir.errors.txt |  40 ++
 .../amd/sourcerootUrlMultifolderNoOutdir.json |   3 +-
 ...ourcerootUrlMultifolderNoOutdir.errors.txt |  40 ++
 .../sourcerootUrlMultifolderNoOutdir.json     |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...tUrlMultifolderSpecifyOutputDirectory.json |   3 +-
 ...ltifolderSpecifyOutputDirectory.errors.txt |  40 ++
 ...tUrlMultifolderSpecifyOutputDirectory.json |   3 +-
 ...UrlMultifolderSpecifyOutputFile.errors.txt |   5 +-
 ...UrlMultifolderSpecifyOutputFile.errors.txt |   5 +-
 .../sourcerootUrlSimpleNoOutdir.errors.txt    |  29 ++
 .../amd/sourcerootUrlSimpleNoOutdir.json      |   3 +-
 .../sourcerootUrlSimpleNoOutdir.errors.txt    |  29 ++
 .../node/sourcerootUrlSimpleNoOutdir.json     |   3 +-
 ...UrlSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...cerootUrlSimpleSpecifyOutputDirectory.json |   3 +-
 ...UrlSimpleSpecifyOutputDirectory.errors.txt |  29 ++
 ...cerootUrlSimpleSpecifyOutputDirectory.json |   3 +-
 ...erootUrlSimpleSpecifyOutputFile.errors.txt |   5 +-
 ...erootUrlSimpleSpecifyOutputFile.errors.txt |   5 +-
 .../sourcerootUrlSubfolderNoOutdir.errors.txt |  29 ++
 .../amd/sourcerootUrlSubfolderNoOutdir.json   |   3 +-
 .../sourcerootUrlSubfolderNoOutdir.errors.txt |  29 ++
 .../node/sourcerootUrlSubfolderNoOutdir.json  |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...ootUrlSubfolderSpecifyOutputDirectory.json |   3 +-
 ...SubfolderSpecifyOutputDirectory.errors.txt |  29 ++
 ...ootUrlSubfolderSpecifyOutputDirectory.json |   3 +-
 ...otUrlSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...otUrlSubfolderSpecifyOutputFile.errors.txt |   5 +-
 ...sitiveImportHasValidDeclaration.errors.txt |  38 ++
 ...eactTransitiveImportHasValidDeclaration.js |   6 -
 ...tTransitiveImportHasValidDeclaration.types |   4 +-
 ...ceTypesPreferedToPathIfPossible.errors.txt |  14 +
 .../referenceTypesPreferedToPathIfPossible.js |   5 -
 ...pWithMultipleFilesWithCopyright.errors.txt |   5 +-
 ...t-resolution-options-referenced-project.js |  83 ++--
 ...le-is-added,-the-signatures-are-updated.js | 451 ++++++++++++++----
 .../typeReferenceDirectives11.errors.txt      |  10 +-
 .../typeReferenceDirectives12.errors.txt      |   5 +-
 .../typeReferenceDirectives2.errors.txt       |  12 +
 .../reference/typeReferenceDirectives2.js     |   7 -
 .../typeReferenceDirectives8.errors.txt       |  17 +
 .../reference/typeReferenceDirectives8.js     |   8 -
 .../typeReferenceDirectives9.errors.txt       |  35 ++
 .../reference/typeReferenceDirectives9.js     |   7 -
 .../reference/withImportDecl.errors.txt       |  47 ++
 tests/baselines/reference/withImportDecl.js   |   3 -
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 create mode 100644 tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/node/sourcerootUrlMixedSubfolderNoOutdir.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/amd/sourcerootUrlMultifolderNoOutdir.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/node/sourcerootUrlMultifolderNoOutdir.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/amd/sourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/node/sourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/amd/sourcerootUrlSimpleNoOutdir.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/node/sourcerootUrlSimpleNoOutdir.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/amd/sourcerootUrlSimpleSpecifyOutputDirectory.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/node/sourcerootUrlSimpleSpecifyOutputDirectory.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/amd/sourcerootUrlSubfolderNoOutdir.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/node/sourcerootUrlSubfolderNoOutdir.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/amd/sourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt
 create mode 100644 tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/node/sourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt
 create mode 100644 tests/baselines/reference/reactTransitiveImportHasValidDeclaration.errors.txt
 create mode 100644 tests/baselines/reference/referenceTypesPreferedToPathIfPossible.errors.txt
 create mode 100644 tests/baselines/reference/typeReferenceDirectives2.errors.txt
 create mode 100644 tests/baselines/reference/typeReferenceDirectives8.errors.txt
 create mode 100644 tests/baselines/reference/typeReferenceDirectives9.errors.txt
 create mode 100644 tests/baselines/reference/withImportDecl.errors.txt

diff --git a/src/compiler/diagnosticMessages.json b/src/compiler/diagnosticMessages.json
index 48b25e5864ac2..04f29e83ab891 100644
--- a/src/compiler/diagnosticMessages.json
+++ b/src/compiler/diagnosticMessages.json
@@ -7980,5 +7980,14 @@
     "'await using' statements cannot be used inside a class static block.": {
         "category": "Error",
         "code": 18054
+    },
+
+    "Declaration file contains synthesized type reference directives: '{0}'": {
+        "category": "Error",
+        "code": 18055
+    },
+    "Declaration file contains synthesized file reference directives: '{0}'": {
+        "category": "Error",
+        "code": 18056
     }
 }
diff --git a/src/compiler/transformers/declarations.ts b/src/compiler/transformers/declarations.ts
index 0a9e58c6de3b8..9c82c5bd272a6 100644
--- a/src/compiler/transformers/declarations.ts
+++ b/src/compiler/transformers/declarations.ts
@@ -53,6 +53,7 @@ import {
     FunctionTypeNode,
     GeneratedIdentifierFlags,
     GetAccessorDeclaration,
+    getBaseFileName,
     getCommentRange,
     getDirectoryPath,
     getEffectiveBaseTypeNode,
@@ -63,6 +64,7 @@ import {
     getLineAndCharacterOfPosition,
     getNameOfDeclaration,
     getNormalizedAbsolutePath,
+    getNormalizedAbsolutePathWithoutRoot,
     getOriginalNodeId,
     getOutputPathsFor,
     getParseTreeNode,
@@ -547,7 +549,16 @@ export function transformDeclarations(context: TransformationContext) {
                 combinedStatements = setTextRange(factory.createNodeArray([...combinedStatements, createEmptyExports(factory)]), combinedStatements);
             }
         }
-        const updated = factory.updateSourceFile(node, combinedStatements, /*isDeclarationFile*/ true, references, getFileReferencesForUsedTypeReferences(), node.hasNoDefaultLib, getLibReferences());
+        const typeReferences = getFileReferencesForUsedTypeReferences();
+        const updated = factory.updateSourceFile(node, combinedStatements, /*isDeclarationFile*/ true, references, typeReferences, node.hasNoDefaultLib, getLibReferences());
+        const synthesizedTypeReferences = typeReferences.filter(ref => !node.typeReferenceDirectives.some(d => d.fileName === ref.fileName));
+        const synthesizedFileReferences = references.filter(ref => !node.referencedFiles.some(d => getNormalizedAbsolutePathWithoutRoot(getBaseFileName(d.fileName), "") === getNormalizedAbsolutePathWithoutRoot(getBaseFileName(ref.fileName), "")));
+        if (synthesizedTypeReferences.length) {
+            context.addDiagnostic(createDiagnosticForNode(node, Diagnostics.Declaration_file_contains_synthesized_type_reference_directives_Colon_0, synthesizedTypeReferences.map(ref => `"${ref.fileName}"`).join(", ")));
+        }
+        if (synthesizedFileReferences.length) {
+            context.addDiagnostic(createDiagnosticForNode(node, Diagnostics.Declaration_file_contains_synthesized_file_reference_directives_Colon_0, synthesizedFileReferences.map(ref => `"${ref.fileName}"`).join(", ")));
+        }
         updated.exportedModulesFromDeclarationEmit = exportedModulesFromDeclarationEmit;
         return updated;
 
diff --git a/tests/baselines/reference/amdLikeInputDeclarationEmit.errors.txt b/tests/baselines/reference/amdLikeInputDeclarationEmit.errors.txt
new file mode 100644
index 0000000000000..fba8f47e154c9
--- /dev/null
+++ b/tests/baselines/reference/amdLikeInputDeclarationEmit.errors.txt
@@ -0,0 +1,34 @@
+ExtendedClass.js(1,1): error TS18056: Declaration file contains synthesized file reference directives: '"../deps/BaseClass.d.ts"'
+
+
+==== typing.d.ts (0 errors) ====
+    declare function define<T=unknown>(name: string, modules: string[], ready: (...modules: unknown[]) => T);
+==== deps/BaseClass.d.ts (0 errors) ====
+    declare module "deps/BaseClass" {
+        class BaseClass {
+            static extends<A>(a: A): new () => A & BaseClass;
+        }
+        export = BaseClass;
+    }
+==== ExtendedClass.js (1 errors) ====
+    define("lib/ExtendedClass", ["deps/BaseClass"], 
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../deps/BaseClass.d.ts"'
+    /**
+     * {typeof import("deps/BaseClass")}
+     * @param  {typeof import("deps/BaseClass")} BaseClass 
+     * @returns 
+     */
+    (BaseClass) => {    
+        
+        const ExtendedClass = BaseClass.extends({
+            f: function() {
+                return "something";
+            }
+        });
+    
+        // Exports the module in a way tsc recognize class export 
+        const module = {};
+        module.exports = ExtendedClass
+        return module.exports;
+    });
\ No newline at end of file
diff --git a/tests/baselines/reference/amdLikeInputDeclarationEmit.js b/tests/baselines/reference/amdLikeInputDeclarationEmit.js
deleted file mode 100644
index 584a304216a35..0000000000000
--- a/tests/baselines/reference/amdLikeInputDeclarationEmit.js
+++ /dev/null
@@ -1,40 +0,0 @@
-//// [tests/cases/compiler/amdLikeInputDeclarationEmit.ts] ////
-
-//// [typing.d.ts]
-declare function define<T=unknown>(name: string, modules: string[], ready: (...modules: unknown[]) => T);
-//// [BaseClass.d.ts]
-declare module "deps/BaseClass" {
-    class BaseClass {
-        static extends<A>(a: A): new () => A & BaseClass;
-    }
-    export = BaseClass;
-}
-//// [ExtendedClass.js]
-define("lib/ExtendedClass", ["deps/BaseClass"], 
-/**
- * {typeof import("deps/BaseClass")}
- * @param  {typeof import("deps/BaseClass")} BaseClass 
- * @returns 
- */
-(BaseClass) => {    
-    
-    const ExtendedClass = BaseClass.extends({
-        f: function() {
-            return "something";
-        }
-    });
-
-    // Exports the module in a way tsc recognize class export 
-    const module = {};
-    module.exports = ExtendedClass
-    return module.exports;
-});
-
-
-
-//// [ExtendedClass.d.ts]
-/// <reference path="../deps/BaseClass.d.ts" />
-export = ExtendedClass;
-declare const ExtendedClass: new () => {
-    f: () => "something";
-} & import("deps/BaseClass");
diff --git a/tests/baselines/reference/declFileAmbientExternalModuleWithSingleExportedModule.errors.txt b/tests/baselines/reference/declFileAmbientExternalModuleWithSingleExportedModule.errors.txt
new file mode 100644
index 0000000000000..a510450722912
--- /dev/null
+++ b/tests/baselines/reference/declFileAmbientExternalModuleWithSingleExportedModule.errors.txt
@@ -0,0 +1,21 @@
+declFileAmbientExternalModuleWithSingleExportedModule_1.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"declFileAmbientExternalModuleWithSingleExportedModule_0.d.ts"'
+
+
+==== declFileAmbientExternalModuleWithSingleExportedModule_1.ts (1 errors) ====
+    ///<reference path='declFileAmbientExternalModuleWithSingleExportedModule_0.ts'/>
+    import SubModule = require('SubModule');
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"declFileAmbientExternalModuleWithSingleExportedModule_0.d.ts"'
+    export var x: SubModule.m.m3.c;
+    
+    
+==== declFileAmbientExternalModuleWithSingleExportedModule_0.ts (0 errors) ====
+    declare module "SubModule" {
+        export module m {
+            export module m3 {
+                interface c {
+                }
+            }
+        }
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/declFileAmbientExternalModuleWithSingleExportedModule.js b/tests/baselines/reference/declFileAmbientExternalModuleWithSingleExportedModule.js
index c1279fb02999b..5cd2ae7743ee1 100644
--- a/tests/baselines/reference/declFileAmbientExternalModuleWithSingleExportedModule.js
+++ b/tests/baselines/reference/declFileAmbientExternalModuleWithSingleExportedModule.js
@@ -33,7 +33,3 @@ declare module "SubModule" {
         }
     }
 }
-//// [declFileAmbientExternalModuleWithSingleExportedModule_1.d.ts]
-/// <reference path="declFileAmbientExternalModuleWithSingleExportedModule_0.d.ts" />
-import SubModule = require('SubModule');
-export declare var x: SubModule.m.m3.c;
diff --git a/tests/baselines/reference/declarationEmitBundleWithAmbientReferences.errors.txt b/tests/baselines/reference/declarationEmitBundleWithAmbientReferences.errors.txt
new file mode 100644
index 0000000000000..0e11c419d5de5
--- /dev/null
+++ b/tests/baselines/reference/declarationEmitBundleWithAmbientReferences.errors.txt
@@ -0,0 +1,24 @@
+src/datastore_result.ts(1,1): error TS18056: Declaration file contains synthesized file reference directives: '"../lib/lib.d.ts"'
+
+
+==== lib/lib.d.ts (0 errors) ====
+    declare module "lib/result" {
+        export type Result<E extends Error, T> = (E & Failure<E>) | (T & Success<T>);
+        export interface Failure<E extends Error> { }
+        export interface Success<T> { }
+    }
+    
+==== src/datastore_result.ts (1 errors) ====
+    import { Result } from "lib/result";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../lib/lib.d.ts"'
+    
+    export type T<T> = Result<Error, T>;
+    
+==== src/conditional_directive_field.ts (0 errors) ====
+    import * as DatastoreResult from "src/datastore_result";
+    
+    export const build = (): DatastoreResult.T<string> => {
+    	return null;
+    };
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/declarationEmitCrossFileImportTypeOfAmbientModule.errors.txt b/tests/baselines/reference/declarationEmitCrossFileImportTypeOfAmbientModule.errors.txt
new file mode 100644
index 0000000000000..7c9a8d7c6f4a6
--- /dev/null
+++ b/tests/baselines/reference/declarationEmitCrossFileImportTypeOfAmbientModule.errors.txt
@@ -0,0 +1,16 @@
+packages/secondpackage/index.ts(1,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../types/component.d.ts"'
+
+
+==== types/component.d.ts (0 errors) ====
+    declare module '@namespace/component' {
+        export class Foo {}
+    }
+==== packages/somepackage/index.d.ts (0 errors) ====
+    import { Foo } from "@namespace/component";
+    export declare const item: typeof Foo;
+==== packages/secondpackage/index.ts (1 errors) ====
+    import { item } from "../somepackage";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../types/component.d.ts"'
+    export const reeexported = item;
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/declarationEmitCrossFileImportTypeOfAmbientModule.js b/tests/baselines/reference/declarationEmitCrossFileImportTypeOfAmbientModule.js
index 71fb76c0fc0c9..6beb53b14e4ac 100644
--- a/tests/baselines/reference/declarationEmitCrossFileImportTypeOfAmbientModule.js
+++ b/tests/baselines/reference/declarationEmitCrossFileImportTypeOfAmbientModule.js
@@ -18,8 +18,3 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.reeexported = void 0;
 var somepackage_1 = require("../somepackage");
 exports.reeexported = somepackage_1.item;
-
-
-//// [index.d.ts]
-/// <reference path="../../types/component.d.ts" />
-export declare const reeexported: typeof import("@namespace/component").Foo;
diff --git a/tests/baselines/reference/declarationEmitExportAssignedNamespaceNoTripleSlashTypesReference.errors.txt b/tests/baselines/reference/declarationEmitExportAssignedNamespaceNoTripleSlashTypesReference.errors.txt
new file mode 100644
index 0000000000000..6f85312e6a90c
--- /dev/null
+++ b/tests/baselines/reference/declarationEmitExportAssignedNamespaceNoTripleSlashTypesReference.errors.txt
@@ -0,0 +1,41 @@
+src/inferred-comp-export.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"react"'
+
+
+==== node_modules/@types/react/index.d.ts (0 errors) ====
+    export = React;
+    
+    declare namespace React {
+        export type Component<T = any, U = {}, V = {}> = { x: T, y: U, z: V };
+        export interface DOMAttributes<T> { }
+    }
+==== node_modules/@emotion/core/index.d.ts (0 errors) ====
+    import {
+        Component
+    } from 'react'
+    export {};
+    
+    declare module 'react' {
+        interface DOMAttributes<T> {
+            css?: any
+        }
+    }
+    
+==== src/get-comp.ts (0 errors) ====
+    import {Component} from 'react';
+    
+    export function getComp(): Component {
+        return {} as any as Component
+    }
+==== src/inferred-comp-export.ts (1 errors) ====
+    import { getComp } from "./get-comp";
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"react"'
+    
+    // this shouldn't need any triple-slash references - it should have a direct import to `react` and that's it
+    // This issue (#35343) _only_ reproduces in the test harness when the file in question is in a subfolder
+    export const obj = {
+        comp: getComp()
+    }
+==== src/some-other-file.ts (0 errors) ====
+    export * from '@emotion/core';
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/declarationEmitExportAssignedNamespaceNoTripleSlashTypesReference.js b/tests/baselines/reference/declarationEmitExportAssignedNamespaceNoTripleSlashTypesReference.js
index 4157f352368b9..7540d99a1ddfa 100644
--- a/tests/baselines/reference/declarationEmitExportAssignedNamespaceNoTripleSlashTypesReference.js
+++ b/tests/baselines/reference/declarationEmitExportAssignedNamespaceNoTripleSlashTypesReference.js
@@ -78,10 +78,5 @@ __exportStar(require("@emotion/core"), exports);
 //// [get-comp.d.ts]
 import { Component } from 'react';
 export declare function getComp(): Component;
-//// [inferred-comp-export.d.ts]
-/// <reference types="react" />
-export declare const obj: {
-    comp: import("react").Component;
-};
 //// [some-other-file.d.ts]
 export * from '@emotion/core';
diff --git a/tests/baselines/reference/declarationEmitExportAssignedNamespaceNoTripleSlashTypesReference.types b/tests/baselines/reference/declarationEmitExportAssignedNamespaceNoTripleSlashTypesReference.types
index 1da4618b39301..45d3ee51d3715 100644
--- a/tests/baselines/reference/declarationEmitExportAssignedNamespaceNoTripleSlashTypesReference.types
+++ b/tests/baselines/reference/declarationEmitExportAssignedNamespaceNoTripleSlashTypesReference.types
@@ -22,7 +22,7 @@ import {
 export {};
 
 declare module 'react' {
->'react' : error
+>'react' : any
 
     interface DOMAttributes<T> {
         css?: any
diff --git a/tests/baselines/reference/declarationEmitHasTypesRefOnNamespaceUse.errors.txt b/tests/baselines/reference/declarationEmitHasTypesRefOnNamespaceUse.errors.txt
new file mode 100644
index 0000000000000..5850bc12e1579
--- /dev/null
+++ b/tests/baselines/reference/declarationEmitHasTypesRefOnNamespaceUse.errors.txt
@@ -0,0 +1,17 @@
+/src/index.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"dep"'
+
+
+==== /src/index.ts (1 errors) ====
+    class Src implements NS.Dep { }
+    ~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"dep"'
+    
+==== /deps/dep/dep.d.ts (0 errors) ====
+    declare namespace NS {
+        interface Dep {
+        }
+    }
+==== /deps/dep/package.json (0 errors) ====
+    {
+        "typings": "dep.d.ts"
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/declarationEmitHasTypesRefOnNamespaceUse.js b/tests/baselines/reference/declarationEmitHasTypesRefOnNamespaceUse.js
index 751ca63bebe92..121b10cafbb1e 100644
--- a/tests/baselines/reference/declarationEmitHasTypesRefOnNamespaceUse.js
+++ b/tests/baselines/reference/declarationEmitHasTypesRefOnNamespaceUse.js
@@ -19,9 +19,3 @@ var Src = /** @class */ (function () {
     }
     return Src;
 }());
-
-
-//// [index.d.ts]
-/// <reference types="dep" />
-declare class Src implements NS.Dep {
-}
diff --git a/tests/baselines/reference/declarationEmitPathMappingMonorepo.errors.txt b/tests/baselines/reference/declarationEmitPathMappingMonorepo.errors.txt
new file mode 100644
index 0000000000000..f9ea7d532a85c
--- /dev/null
+++ b/tests/baselines/reference/declarationEmitPathMappingMonorepo.errors.txt
@@ -0,0 +1,32 @@
+packages/b/src/index.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"@ts-bug/a"'
+
+
+==== packages/b/tsconfig.json (0 errors) ====
+    {
+        "compilerOptions": {
+            "outDir": "dist",
+            "declaration": true,
+            "baseUrl": ".",
+            "paths": {
+                "@ts-bug/a": ["../a"]
+            }
+        }
+    }
+    
+    
+==== packages/b/src/index.ts (1 errors) ====
+    import { a } from "@ts-bug/a";
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"@ts-bug/a"'
+    
+    export function b(text: string) {
+      return a(text);
+    }
+==== packages/a/index.d.ts (0 errors) ====
+    declare module "@ts-bug/a" {
+        export type AText = {
+          value: string;
+        };
+        export function a(text: string): AText;
+      }
+      
\ No newline at end of file
diff --git a/tests/baselines/reference/declarationEmitPathMappingMonorepo.js b/tests/baselines/reference/declarationEmitPathMappingMonorepo.js
index dbc3ac66c6d21..fa09a99ef2863 100644
--- a/tests/baselines/reference/declarationEmitPathMappingMonorepo.js
+++ b/tests/baselines/reference/declarationEmitPathMappingMonorepo.js
@@ -24,8 +24,3 @@ function b(text) {
     return (0, a_1.a)(text);
 }
 exports.b = b;
-
-
-//// [index.d.ts]
-/// <reference types="@ts-bug/a" />
-export declare function b(text: string): import("@ts-bug/a").AText;
diff --git a/tests/baselines/reference/declarationEmitTripleSlashReferenceAmbientModule.errors.txt b/tests/baselines/reference/declarationEmitTripleSlashReferenceAmbientModule.errors.txt
new file mode 100644
index 0000000000000..d1b95fce9f1eb
--- /dev/null
+++ b/tests/baselines/reference/declarationEmitTripleSlashReferenceAmbientModule.errors.txt
@@ -0,0 +1,28 @@
+/usage1.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"node"'
+/usage2.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"node"'
+/usage3.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"node"'
+
+
+==== /node_modules/@types/node/index.d.ts (0 errors) ====
+    declare module "url" {
+      export class Url {}
+      export function parse(): Url; 
+    }
+    
+==== /usage1.ts (1 errors) ====
+    export { parse } from "url";
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"node"'
+    
+==== /usage2.ts (1 errors) ====
+    import { parse } from "url";
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"node"'
+    export const thing: import("url").Url = parse(); 
+    
+==== /usage3.ts (1 errors) ====
+    import { parse } from "url";
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"node"'
+    export const thing = parse();
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/declarationEmitTripleSlashReferenceAmbientModule.js b/tests/baselines/reference/declarationEmitTripleSlashReferenceAmbientModule.js
deleted file mode 100644
index b283b08edcd9e..0000000000000
--- a/tests/baselines/reference/declarationEmitTripleSlashReferenceAmbientModule.js
+++ /dev/null
@@ -1,31 +0,0 @@
-//// [tests/cases/compiler/declarationEmitTripleSlashReferenceAmbientModule.ts] ////
-
-//// [index.d.ts]
-declare module "url" {
-  export class Url {}
-  export function parse(): Url; 
-}
-
-//// [usage1.ts]
-export { parse } from "url";
-
-//// [usage2.ts]
-import { parse } from "url";
-export const thing: import("url").Url = parse(); 
-
-//// [usage3.ts]
-import { parse } from "url";
-export const thing = parse();
-
-
-
-
-//// [usage1.d.ts]
-/// <reference types="node" />
-export { parse } from "url";
-//// [usage2.d.ts]
-/// <reference types="node" />
-export declare const thing: import("url").Url;
-//// [usage3.d.ts]
-/// <reference types="node" />
-export declare const thing: import("url").Url;
diff --git a/tests/baselines/reference/declarationFilesWithTypeReferences2.errors.txt b/tests/baselines/reference/declarationFilesWithTypeReferences2.errors.txt
new file mode 100644
index 0000000000000..c5b37a9848814
--- /dev/null
+++ b/tests/baselines/reference/declarationFilesWithTypeReferences2.errors.txt
@@ -0,0 +1,14 @@
+/app.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"node"'
+
+
+==== /node_modules/@types/node/index.d.ts (0 errors) ====
+    interface Error2 {
+        stack2: string;
+    }
+    
+==== /app.ts (1 errors) ====
+    function foo(): Error2 {
+    ~~~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"node"'
+        return undefined;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/declarationFilesWithTypeReferences2.js b/tests/baselines/reference/declarationFilesWithTypeReferences2.js
index 6852d90d594b6..10bae488a7321 100644
--- a/tests/baselines/reference/declarationFilesWithTypeReferences2.js
+++ b/tests/baselines/reference/declarationFilesWithTypeReferences2.js
@@ -14,8 +14,3 @@ function foo(): Error2 {
 function foo() {
     return undefined;
 }
-
-
-//// [app.d.ts]
-/// <reference types="node" />
-declare function foo(): Error2;
diff --git a/tests/baselines/reference/importAliasFromNamespace.errors.txt b/tests/baselines/reference/importAliasFromNamespace.errors.txt
new file mode 100644
index 0000000000000..b9d667d79246f
--- /dev/null
+++ b/tests/baselines/reference/importAliasFromNamespace.errors.txt
@@ -0,0 +1,25 @@
+usage.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"internal.d.ts"'
+
+
+==== usage.ts (1 errors) ====
+    /// <reference path="./internal.ts" />
+    namespace SomeOther.Thing {
+    ~~~~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"internal.d.ts"'
+        import Internal = My.Internal;
+        export class Foo {
+            private _which: Internal.WhichThing;
+            constructor() {
+                Internal.getThing();
+                Internal.WhichThing.A ? "foo" : "bar";
+            }
+        }
+    }
+==== internal.ts (0 errors) ====
+    namespace My.Internal {
+        export function getThing(): void {}
+        export const enum WhichThing {
+            A, B, C
+        }
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/importAliasFromNamespace.js b/tests/baselines/reference/importAliasFromNamespace.js
index 0b24d2c091c79..f1bccc2bba728 100644
--- a/tests/baselines/reference/importAliasFromNamespace.js
+++ b/tests/baselines/reference/importAliasFromNamespace.js
@@ -58,11 +58,3 @@ declare namespace My.Internal {
         C = 2
     }
 }
-//// [usage.d.ts]
-/// <reference path="internal.d.ts" />
-declare namespace SomeOther.Thing {
-    class Foo {
-        private _which;
-        constructor();
-    }
-}
diff --git a/tests/baselines/reference/importDecl.errors.txt b/tests/baselines/reference/importDecl.errors.txt
new file mode 100644
index 0000000000000..15ae1313e4513
--- /dev/null
+++ b/tests/baselines/reference/importDecl.errors.txt
@@ -0,0 +1,85 @@
+importDecl_1.ts(6,1): error TS18056: Declaration file contains synthesized file reference directives: '"importDecl_require3.d.ts", "importDecl_require4.d.ts"'
+
+
+==== importDecl_1.ts (1 errors) ====
+    ///<reference path='importDecl_require.ts'/>
+    ///<reference path='importDecl_require1.ts'/>
+    ///<reference path='importDecl_require2.ts'/>
+    ///<reference path='importDecl_require3.ts'/>
+    ///<reference path='importDecl_require4.ts'/>
+    import m4 = require("./importDecl_require"); // Emit used
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"importDecl_require3.d.ts", "importDecl_require4.d.ts"'
+    export var x4 = m4.x;
+    export var d4 = m4.d;
+    export var f4 = m4.foo();
+    
+    export module m1 {
+        export var x2 = m4.x;
+        export var d2 = m4.d;
+        export var f2 = m4.foo();
+    
+        var x3 = m4.x;
+        var d3 = m4.d;
+        var f3 = m4.foo();
+    }
+    
+    //Emit global only usage
+    import glo_m4 = require("./importDecl_require1");
+    export var useGlo_m4_d4 = glo_m4.d;
+    export var useGlo_m4_f4 = glo_m4.foo();
+    
+    //Emit even when used just in function type
+    import fncOnly_m4 = require("./importDecl_require2");
+    export var useFncOnly_m4_f4 = fncOnly_m4.foo();
+    
+    // only used privately no need to emit
+    import private_m4 = require("./importDecl_require3");
+    export module usePrivate_m4_m1 {
+        var x3 = private_m4.x;
+        var d3 = private_m4.d;
+        var f3 = private_m4.foo();
+    }
+    
+    // Do not emit unused import
+    import m5 = require("./importDecl_require4");
+    export var d = m5.foo2();
+    
+    // Do not emit multiple used import statements
+    import multiImport_m4 = require("./importDecl_require"); // Emit used
+    export var useMultiImport_m4_x4 = multiImport_m4.x;
+    export var useMultiImport_m4_d4 = multiImport_m4.d;
+    export var useMultiImport_m4_f4 = multiImport_m4.foo();
+    
+==== importDecl_require.ts (0 errors) ====
+    export class d {
+        foo: string;
+    }
+    export var x: d;
+    export function foo(): d { return null; }
+    
+==== importDecl_require1.ts (0 errors) ====
+    export class d {
+        bar: string;
+    }
+    var x: d;
+    export function foo(): d { return null; }
+    
+==== importDecl_require2.ts (0 errors) ====
+    export class d {
+        baz: string;
+    }
+    export var x: d;
+    export function foo(): d { return null; }
+    
+==== importDecl_require3.ts (0 errors) ====
+    export class d {
+        bing: string;
+    }
+    export var x: d;
+    export function foo(): d { return null; }
+    
+==== importDecl_require4.ts (0 errors) ====
+    import m4 = require("./importDecl_require");
+    export function foo2(): m4.d { return null; }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/importDecl.js b/tests/baselines/reference/importDecl.js
index 7ac30532e4564..842200203accd 100644
--- a/tests/baselines/reference/importDecl.js
+++ b/tests/baselines/reference/importDecl.js
@@ -209,26 +209,3 @@ export declare function foo(): d;
 //// [importDecl_require4.d.ts]
 import m4 = require("./importDecl_require");
 export declare function foo2(): m4.d;
-//// [importDecl_1.d.ts]
-/// <reference path="importDecl_require3.d.ts" />
-/// <reference path="importDecl_require4.d.ts" />
-import m4 = require("./importDecl_require");
-export declare var x4: m4.d;
-export declare var d4: typeof m4.d;
-export declare var f4: m4.d;
-export declare namespace m1 {
-    var x2: m4.d;
-    var d2: typeof m4.d;
-    var f2: m4.d;
-}
-import glo_m4 = require("./importDecl_require1");
-export declare var useGlo_m4_d4: typeof glo_m4.d;
-export declare var useGlo_m4_f4: glo_m4.d;
-import fncOnly_m4 = require("./importDecl_require2");
-export declare var useFncOnly_m4_f4: fncOnly_m4.d;
-export declare namespace usePrivate_m4_m1 {
-}
-export declare var d: m4.d;
-export declare var useMultiImport_m4_x4: m4.d;
-export declare var useMultiImport_m4_d4: typeof m4.d;
-export declare var useMultiImport_m4_f4: m4.d;
diff --git a/tests/baselines/reference/importTypeGenericArrowTypeParenthesized.errors.txt b/tests/baselines/reference/importTypeGenericArrowTypeParenthesized.errors.txt
new file mode 100644
index 0000000000000..14e4756e6485f
--- /dev/null
+++ b/tests/baselines/reference/importTypeGenericArrowTypeParenthesized.errors.txt
@@ -0,0 +1,23 @@
+index.ts(1,1): error TS18056: Declaration file contains synthesized file reference directives: '"module.d.ts"'
+
+
+==== module.d.ts (0 errors) ====
+    declare module "module" {
+        export interface Modifier<T> { }
+    
+        export function fn<T>(x: T): Modifier<T>;
+    }
+==== index.ts (1 errors) ====
+    import { fn } from "module";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"module.d.ts"'
+    
+    export const fail1 = fn(<T>(x: T): T => x);
+    export const fail2 = fn(function<T>(x: T): T {
+      return x;
+    });
+    
+    export const works1 = fn((x: number) => x);
+    type MakeItWork = <T>(x: T) => T;
+    export const works2 = fn<MakeItWork>(x => x);
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/importTypeGenericArrowTypeParenthesized.js b/tests/baselines/reference/importTypeGenericArrowTypeParenthesized.js
index adb6657cb2a34..4bc5728013dd8 100644
--- a/tests/baselines/reference/importTypeGenericArrowTypeParenthesized.js
+++ b/tests/baselines/reference/importTypeGenericArrowTypeParenthesized.js
@@ -30,13 +30,3 @@ exports.fail2 = (0, module_1.fn)(function (x) {
 });
 exports.works1 = (0, module_1.fn)(function (x) { return x; });
 exports.works2 = (0, module_1.fn)(function (x) { return x; });
-
-
-//// [index.d.ts]
-/// <reference path="module.d.ts" />
-export declare const fail1: import("module").Modifier<(<T>(x: T) => T)>;
-export declare const fail2: import("module").Modifier<(<T>(x: T) => T)>;
-export declare const works1: import("module").Modifier<(x: number) => number>;
-type MakeItWork = <T>(x: T) => T;
-export declare const works2: import("module").Modifier<MakeItWork>;
-export {};
diff --git a/tests/baselines/reference/jsDeclarationsReactComponents.errors.txt b/tests/baselines/reference/jsDeclarationsReactComponents.errors.txt
new file mode 100644
index 0000000000000..362de3dad0080
--- /dev/null
+++ b/tests/baselines/reference/jsDeclarationsReactComponents.errors.txt
@@ -0,0 +1,102 @@
+jsDeclarationsReactComponents2.jsx(1,1): error TS18056: Declaration file contains synthesized file reference directives: '"../..react16.d.ts"'
+jsDeclarationsReactComponents5.jsx(1,1): error TS18056: Declaration file contains synthesized file reference directives: '"../..react16.d.ts"'
+
+
+==== jsDeclarationsReactComponents1.jsx (0 errors) ====
+    /// <reference path="/.lib/react16.d.ts" />
+    import React from "react";
+    import PropTypes from "prop-types"
+    
+    const TabbedShowLayout = ({
+    }) => {
+        return (
+            <div />
+        );
+    };
+    
+    TabbedShowLayout.propTypes = {
+        version: PropTypes.number,
+    
+    };
+    
+    TabbedShowLayout.defaultProps = {
+        tabs: undefined
+    };
+    
+    export default TabbedShowLayout;
+    
+==== jsDeclarationsReactComponents2.jsx (1 errors) ====
+    import React from "react";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../..react16.d.ts"'
+    /**
+     * @type {React.SFC}
+     */
+    const TabbedShowLayout = () => {
+        return (
+            <div className="" key="">
+                ok
+            </div>
+        );
+    };
+    
+    TabbedShowLayout.defaultProps = {
+        tabs: "default value"
+    };
+    
+    export default TabbedShowLayout;
+    
+==== jsDeclarationsReactComponents3.jsx (0 errors) ====
+    import React from "react";
+    /**
+     * @type {{defaultProps: {tabs: string}} & ((props?: {elem: string}) => JSX.Element)}
+     */
+    const TabbedShowLayout = () => {
+        return (
+            <div className="" key="">
+                ok
+            </div>
+        );
+    };
+    
+    TabbedShowLayout.defaultProps = {
+        tabs: "default value"
+    };
+    
+    export default TabbedShowLayout;
+    
+==== jsDeclarationsReactComponents4.jsx (0 errors) ====
+    import React from "react";
+    const TabbedShowLayout = (/** @type {{className: string}}*/prop) => {
+        return (
+            <div className={prop.className} key="">
+                ok
+            </div>
+        );
+    };
+    
+    TabbedShowLayout.defaultProps = {
+        tabs: "default value"
+    };
+    
+    export default TabbedShowLayout;
+==== jsDeclarationsReactComponents5.jsx (1 errors) ====
+    import React from 'react';
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../..react16.d.ts"'
+    import PropTypes from 'prop-types';
+    
+    function Tree({ allowDropOnRoot }) {
+      return <div />
+    }
+    
+    Tree.propTypes = {
+        classes: PropTypes.object,
+    };
+    
+    Tree.defaultProps = {
+        classes: {},
+        parentSource: 'parent_id',
+    };
+    
+    export default Tree;
\ No newline at end of file
diff --git a/tests/baselines/reference/jsDeclarationsReactComponents.js b/tests/baselines/reference/jsDeclarationsReactComponents.js
index d0c4a2415283a..29115447fc05e 100644
--- a/tests/baselines/reference/jsDeclarationsReactComponents.js
+++ b/tests/baselines/reference/jsDeclarationsReactComponents.js
@@ -197,14 +197,6 @@ declare namespace TabbedShowLayout {
     }
 }
 import PropTypes from "prop-types";
-//// [jsDeclarationsReactComponents2.d.ts]
-/// <reference path="../..react16.d.ts" />
-export default TabbedShowLayout;
-/**
- * @type {React.SFC}
- */
-declare const TabbedShowLayout: React.SFC;
-import React from "react";
 //// [jsDeclarationsReactComponents3.d.ts]
 export default TabbedShowLayout;
 /**
@@ -227,20 +219,3 @@ declare namespace TabbedShowLayout {
         let tabs: string;
     }
 }
-//// [jsDeclarationsReactComponents5.d.ts]
-/// <reference path="../..react16.d.ts" />
-export default Tree;
-declare function Tree({ allowDropOnRoot }: {
-    allowDropOnRoot: any;
-}): JSX.Element;
-declare namespace Tree {
-    namespace propTypes {
-        let classes: PropTypes.Requireable<object>;
-    }
-    namespace defaultProps {
-        let classes_1: {};
-        export { classes_1 as classes };
-        export let parentSource: string;
-    }
-}
-import PropTypes from 'prop-types';
diff --git a/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithNoOut.errors.txt b/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithNoOut.errors.txt
index 73149c42bd31d..01a6fbc46d37d 100644
--- a/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithNoOut.errors.txt
+++ b/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithNoOut.errors.txt
@@ -1,5 +1,6 @@
 error TS5055: Cannot write file 'c.js' because it would overwrite input file.
   Adding a tsconfig.json file will help organize projects that contain both TypeScript and JavaScript files. Learn more at https://aka.ms/tsconfig.
+b.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"c.d.ts"'
 
 
 !!! error TS5055: Cannot write file 'c.js' because it would overwrite input file.
@@ -8,10 +9,12 @@ error TS5055: Cannot write file 'c.js' because it would overwrite input file.
     class c {
     }
     
-==== b.ts (0 errors) ====
+==== b.ts (1 errors) ====
     /// <reference path="c.js"/>
     // b.d.ts should have c.d.ts as the reference path
     function foo() {
+    ~~~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"c.d.ts"'
     }
     
 ==== c.js (0 errors) ====
diff --git a/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithNoOut.js b/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithNoOut.js
index 7a0942b5ac718..69895fac21868 100644
--- a/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithNoOut.js
+++ b/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithNoOut.js
@@ -32,6 +32,3 @@ declare class c {
 }
 //// [c.d.ts]
 declare function bar(): void;
-//// [b.d.ts]
-/// <reference path="c.d.ts" />
-declare function foo(): void;
diff --git a/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithOut.errors.txt b/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithOut.errors.txt
index 7589b9a054900..ca7f67eb0028d 100644
--- a/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithOut.errors.txt
+++ b/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithOut.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+b.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"c.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -8,9 +9,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     class c {
     }
     
-==== b.ts (0 errors) ====
+==== b.ts (1 errors) ====
     /// <reference path="c.js"/>
     function foo() {
+    ~~~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"c.d.ts"'
     }
     
 ==== c.js (0 errors) ====
diff --git a/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithOutDir.errors.txt b/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithOutDir.errors.txt
new file mode 100644
index 0000000000000..a3a8a7863beb4
--- /dev/null
+++ b/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithOutDir.errors.txt
@@ -0,0 +1,17 @@
+b.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"c.d.ts"'
+
+
+==== a.ts (0 errors) ====
+    class c {
+    }
+    
+==== b.ts (1 errors) ====
+    /// <reference path="c.js"/>
+    function foo() {
+    ~~~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"c.d.ts"'
+    }
+    
+==== c.js (0 errors) ====
+    function bar() {
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithOutDir.js b/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithOutDir.js
index fe570fb330791..7ce2daa7aafde 100644
--- a/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithOutDir.js
+++ b/tests/baselines/reference/jsFileCompilationErrorOnDeclarationsWithJsFileReferenceWithOutDir.js
@@ -33,6 +33,3 @@ declare class c {
 }
 //// [c.d.ts]
 declare function bar(): void;
-//// [b.d.ts]
-/// <reference path="c.d.ts" />
-declare function foo(): void;
diff --git a/tests/baselines/reference/missingImportAfterModuleImport.errors.txt b/tests/baselines/reference/missingImportAfterModuleImport.errors.txt
new file mode 100644
index 0000000000000..bc9e9b40613ca
--- /dev/null
+++ b/tests/baselines/reference/missingImportAfterModuleImport.errors.txt
@@ -0,0 +1,26 @@
+missingImportAfterModuleImport_1.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"missingImportAfterModuleImport_0.d.ts"'
+
+
+==== missingImportAfterModuleImport_1.ts (1 errors) ====
+    ///<reference path='missingImportAfterModuleImport_0.ts'/>
+    import SubModule = require('SubModule');
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"missingImportAfterModuleImport_0.d.ts"'
+    class MainModule {
+        // public static SubModule: SubModule;
+        public SubModule: SubModule;
+        constructor() { }
+    }
+    export = MainModule;
+    
+    
+==== missingImportAfterModuleImport_0.ts (0 errors) ====
+    declare module "SubModule" {
+        class SubModule {
+            public static StaticVar: number;
+            public InstanceVar: number;
+            constructor();
+        }
+        export = SubModule;
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/missingImportAfterModuleImport.js b/tests/baselines/reference/missingImportAfterModuleImport.js
index a66e96932a3fc..7488b3bbeacee 100644
--- a/tests/baselines/reference/missingImportAfterModuleImport.js
+++ b/tests/baselines/reference/missingImportAfterModuleImport.js
@@ -42,11 +42,3 @@ declare module "SubModule" {
     }
     export = SubModule;
 }
-//// [missingImportAfterModuleImport_1.d.ts]
-/// <reference path="missingImportAfterModuleImport_0.d.ts" />
-import SubModule = require('SubModule');
-declare class MainModule {
-    SubModule: SubModule;
-    constructor();
-}
-export = MainModule;
diff --git a/tests/baselines/reference/moduleAugmentationsImports2.errors.txt b/tests/baselines/reference/moduleAugmentationsImports2.errors.txt
index 088ff6656864c..e920ca5ff6f27 100644
--- a/tests/baselines/reference/moduleAugmentationsImports2.errors.txt
+++ b/tests/baselines/reference/moduleAugmentationsImports2.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+e.ts(1,1): error TS18056: Declaration file contains synthesized file reference directives: '"c.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -29,8 +30,10 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
         }
     }
     
-==== e.ts (0 errors) ====
+==== e.ts (1 errors) ====
     import {A} from "./a";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"c.d.ts"'
     import {Cls} from "C";
     
     A.prototype.getCls = function () { return undefined; }
diff --git a/tests/baselines/reference/moduleSymbolMerging.errors.txt b/tests/baselines/reference/moduleSymbolMerging.errors.txt
new file mode 100644
index 0000000000000..9f34ada04b174
--- /dev/null
+++ b/tests/baselines/reference/moduleSymbolMerging.errors.txt
@@ -0,0 +1,16 @@
+B.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"A.d.ts"'
+
+
+==== B.ts (1 errors) ====
+    ///<reference path="A.ts" />
+    module A { ; }
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"A.d.ts"'
+    module B {
+    	export function f(): A.I { return null; }
+    }
+    
+    
+==== A.ts (0 errors) ====
+    module A { export interface I {} }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/moduleSymbolMerging.js b/tests/baselines/reference/moduleSymbolMerging.js
index db701f2092949..4984c702f01b1 100644
--- a/tests/baselines/reference/moduleSymbolMerging.js
+++ b/tests/baselines/reference/moduleSymbolMerging.js
@@ -31,9 +31,3 @@ declare namespace A {
     interface I {
     }
 }
-//// [B.d.ts]
-/// <reference path="A.d.ts" />
-declare namespace A { }
-declare namespace B {
-    function f(): A.I;
-}
diff --git a/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=node16).errors.txt b/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=node16).errors.txt
index 476c47f703e37..89b3cefc0001d 100644
--- a/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=node16).errors.txt
+++ b/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=node16).errors.txt
@@ -1,32 +1,41 @@
+file.js(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
 file.js(4,1): error TS8002: 'import ... =' can only be used in TypeScript files.
 file.js(6,1): error TS8002: 'import ... =' can only be used in TypeScript files.
+index.js(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
 index.js(2,1): error TS8002: 'import ... =' can only be used in TypeScript files.
 index.js(4,1): error TS8002: 'import ... =' can only be used in TypeScript files.
+subfolder/index.js(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../types.d.ts"'
 subfolder/index.js(2,1): error TS8002: 'import ... =' can only be used in TypeScript files.
 subfolder/index.js(4,1): error TS8002: 'import ... =' can only be used in TypeScript files.
 
 
-==== subfolder/index.js (2 errors) ====
+==== subfolder/index.js (3 errors) ====
     // cjs format file
     import fs = require("fs");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../types.d.ts"'
     ~~~~~~~~~~~~~~~~~~~~~~~~~~
 !!! error TS8002: 'import ... =' can only be used in TypeScript files.
     fs.readFile;
     export import fs2 = require("fs");
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 !!! error TS8002: 'import ... =' can only be used in TypeScript files.
-==== index.js (2 errors) ====
+==== index.js (3 errors) ====
     // esm format file
     import fs = require("fs");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
     ~~~~~~~~~~~~~~~~~~~~~~~~~~
 !!! error TS8002: 'import ... =' can only be used in TypeScript files.
     fs.readFile;
     export import fs2 = require("fs");
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 !!! error TS8002: 'import ... =' can only be used in TypeScript files.
-==== file.js (2 errors) ====
+==== file.js (3 errors) ====
     // esm format file
     const __require = null;
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
     const _createRequire = null;
     import fs = require("fs");
     ~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=node16).js b/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=node16).js
index d5c78197b0f13..3274d6ea65b93 100644
--- a/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=node16).js
+++ b/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=node16).js
@@ -55,14 +55,3 @@ const fs = __require_1("fs");
 fs.readFile;
 const fs2 = __require_1("fs");
 export { fs2 };
-
-
-//// [index.d.ts]
-/// <reference path="../../types.d.ts" />
-import fs2 = require("fs");
-//// [index.d.ts]
-/// <reference path="../types.d.ts" />
-import fs2 = require("fs");
-//// [file.d.ts]
-/// <reference path="../types.d.ts" />
-import fs2 = require("fs");
diff --git a/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=nodenext).errors.txt b/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=nodenext).errors.txt
index 476c47f703e37..89b3cefc0001d 100644
--- a/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=nodenext).errors.txt
+++ b/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=nodenext).errors.txt
@@ -1,32 +1,41 @@
+file.js(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
 file.js(4,1): error TS8002: 'import ... =' can only be used in TypeScript files.
 file.js(6,1): error TS8002: 'import ... =' can only be used in TypeScript files.
+index.js(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
 index.js(2,1): error TS8002: 'import ... =' can only be used in TypeScript files.
 index.js(4,1): error TS8002: 'import ... =' can only be used in TypeScript files.
+subfolder/index.js(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../types.d.ts"'
 subfolder/index.js(2,1): error TS8002: 'import ... =' can only be used in TypeScript files.
 subfolder/index.js(4,1): error TS8002: 'import ... =' can only be used in TypeScript files.
 
 
-==== subfolder/index.js (2 errors) ====
+==== subfolder/index.js (3 errors) ====
     // cjs format file
     import fs = require("fs");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../types.d.ts"'
     ~~~~~~~~~~~~~~~~~~~~~~~~~~
 !!! error TS8002: 'import ... =' can only be used in TypeScript files.
     fs.readFile;
     export import fs2 = require("fs");
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 !!! error TS8002: 'import ... =' can only be used in TypeScript files.
-==== index.js (2 errors) ====
+==== index.js (3 errors) ====
     // esm format file
     import fs = require("fs");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
     ~~~~~~~~~~~~~~~~~~~~~~~~~~
 !!! error TS8002: 'import ... =' can only be used in TypeScript files.
     fs.readFile;
     export import fs2 = require("fs");
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 !!! error TS8002: 'import ... =' can only be used in TypeScript files.
-==== file.js (2 errors) ====
+==== file.js (3 errors) ====
     // esm format file
     const __require = null;
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
     const _createRequire = null;
     import fs = require("fs");
     ~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=nodenext).js b/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=nodenext).js
index d5c78197b0f13..3274d6ea65b93 100644
--- a/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=nodenext).js
+++ b/tests/baselines/reference/nodeModulesAllowJsImportAssignment(module=nodenext).js
@@ -55,14 +55,3 @@ const fs = __require_1("fs");
 fs.readFile;
 const fs2 = __require_1("fs");
 export { fs2 };
-
-
-//// [index.d.ts]
-/// <reference path="../../types.d.ts" />
-import fs2 = require("fs");
-//// [index.d.ts]
-/// <reference path="../types.d.ts" />
-import fs2 = require("fs");
-//// [file.d.ts]
-/// <reference path="../types.d.ts" />
-import fs2 = require("fs");
diff --git a/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=node16).errors.txt b/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=node16).errors.txt
index 78bd927d81fe8..b25015d1bbae2 100644
--- a/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=node16).errors.txt
+++ b/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=node16).errors.txt
@@ -1,18 +1,24 @@
+index.js(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
+subfolder/index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../types.d.ts"'
 subfolder/index.ts(2,1): error TS2343: This syntax requires an imported helper named '__exportStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
 subfolder/index.ts(3,1): error TS2343: This syntax requires an imported helper named '__importStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
 
 
-==== subfolder/index.ts (2 errors) ====
+==== subfolder/index.ts (3 errors) ====
     // cjs format file
     export * from "fs";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../types.d.ts"'
     ~~~~~~~~~~~~~~~~~~~
 !!! error TS2343: This syntax requires an imported helper named '__exportStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
     export * as fs from "fs";
     ~~~~~~~~~~~~~~~~~~~~~~~~~
 !!! error TS2343: This syntax requires an imported helper named '__importStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
-==== index.js (0 errors) ====
+==== index.js (1 errors) ====
     // esm format file
     export * from "fs";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
     export * as fs from "fs";
 ==== package.json (0 errors) ====
     {
diff --git a/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=node16).js b/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=node16).js
index ea0c63e15ff91..33d2d6965dc07 100644
--- a/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=node16).js
+++ b/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=node16).js
@@ -37,13 +37,3 @@ exports.fs = tslib_1.__importStar(require("fs"));
 // esm format file
 export * from "fs";
 export * as fs from "fs";
-
-
-//// [index.d.ts]
-/// <reference path="../../types.d.ts" />
-export * from "fs";
-export * as fs from "fs";
-//// [index.d.ts]
-/// <reference path="../types.d.ts" />
-export * from "fs";
-export * as fs from "fs";
diff --git a/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=nodenext).errors.txt b/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=nodenext).errors.txt
index 78bd927d81fe8..b25015d1bbae2 100644
--- a/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=nodenext).errors.txt
+++ b/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=nodenext).errors.txt
@@ -1,18 +1,24 @@
+index.js(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
+subfolder/index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../types.d.ts"'
 subfolder/index.ts(2,1): error TS2343: This syntax requires an imported helper named '__exportStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
 subfolder/index.ts(3,1): error TS2343: This syntax requires an imported helper named '__importStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
 
 
-==== subfolder/index.ts (2 errors) ====
+==== subfolder/index.ts (3 errors) ====
     // cjs format file
     export * from "fs";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../types.d.ts"'
     ~~~~~~~~~~~~~~~~~~~
 !!! error TS2343: This syntax requires an imported helper named '__exportStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
     export * as fs from "fs";
     ~~~~~~~~~~~~~~~~~~~~~~~~~
 !!! error TS2343: This syntax requires an imported helper named '__importStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
-==== index.js (0 errors) ====
+==== index.js (1 errors) ====
     // esm format file
     export * from "fs";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
     export * as fs from "fs";
 ==== package.json (0 errors) ====
     {
diff --git a/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=nodenext).js b/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=nodenext).js
index ea0c63e15ff91..33d2d6965dc07 100644
--- a/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=nodenext).js
+++ b/tests/baselines/reference/nodeModulesAllowJsImportHelpersCollisions2(module=nodenext).js
@@ -37,13 +37,3 @@ exports.fs = tslib_1.__importStar(require("fs"));
 // esm format file
 export * from "fs";
 export * as fs from "fs";
-
-
-//// [index.d.ts]
-/// <reference path="../../types.d.ts" />
-export * from "fs";
-export * as fs from "fs";
-//// [index.d.ts]
-/// <reference path="../types.d.ts" />
-export * from "fs";
-export * as fs from "fs";
diff --git a/tests/baselines/reference/nodeModulesImportAssignments(module=node16).errors.txt b/tests/baselines/reference/nodeModulesImportAssignments(module=node16).errors.txt
new file mode 100644
index 0000000000000..d9ebc86f3e797
--- /dev/null
+++ b/tests/baselines/reference/nodeModulesImportAssignments(module=node16).errors.txt
@@ -0,0 +1,40 @@
+file.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
+index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
+subfolder/index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
+
+
+==== subfolder/index.ts (1 errors) ====
+    // cjs format file
+    import fs = require("fs");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
+    fs.readFile;
+    export import fs2 = require("fs");
+==== index.ts (1 errors) ====
+    // esm format file
+    import fs = require("fs");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
+    fs.readFile;
+    export import fs2 = require("fs");
+==== file.ts (1 errors) ====
+    // esm format file
+    const __require = null;
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
+    const _createRequire = null;
+    import fs = require("fs");
+    fs.readFile;
+    export import fs2 = require("fs");
+==== package.json (0 errors) ====
+    {
+        "name": "package",
+        "private": true,
+        "type": "module"
+    }
+==== subfolder/package.json (0 errors) ====
+    {
+        "type": "commonjs"
+    }
+==== types.d.ts (0 errors) ====
+    declare module "fs";
\ No newline at end of file
diff --git a/tests/baselines/reference/nodeModulesImportAssignments(module=node16).js b/tests/baselines/reference/nodeModulesImportAssignments(module=node16).js
index 580b35366e07d..509c046355ebe 100644
--- a/tests/baselines/reference/nodeModulesImportAssignments(module=node16).js
+++ b/tests/baselines/reference/nodeModulesImportAssignments(module=node16).js
@@ -55,14 +55,3 @@ const fs = __require_1("fs");
 fs.readFile;
 const fs2 = __require_1("fs");
 export { fs2 };
-
-
-//// [index.d.ts]
-/// <reference path="../types.d.ts" />
-export import fs2 = require("fs");
-//// [index.d.ts]
-/// <reference path="types.d.ts" />
-export import fs2 = require("fs");
-//// [file.d.ts]
-/// <reference path="types.d.ts" />
-export import fs2 = require("fs");
diff --git a/tests/baselines/reference/nodeModulesImportAssignments(module=nodenext).errors.txt b/tests/baselines/reference/nodeModulesImportAssignments(module=nodenext).errors.txt
new file mode 100644
index 0000000000000..d9ebc86f3e797
--- /dev/null
+++ b/tests/baselines/reference/nodeModulesImportAssignments(module=nodenext).errors.txt
@@ -0,0 +1,40 @@
+file.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
+index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
+subfolder/index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
+
+
+==== subfolder/index.ts (1 errors) ====
+    // cjs format file
+    import fs = require("fs");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
+    fs.readFile;
+    export import fs2 = require("fs");
+==== index.ts (1 errors) ====
+    // esm format file
+    import fs = require("fs");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
+    fs.readFile;
+    export import fs2 = require("fs");
+==== file.ts (1 errors) ====
+    // esm format file
+    const __require = null;
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
+    const _createRequire = null;
+    import fs = require("fs");
+    fs.readFile;
+    export import fs2 = require("fs");
+==== package.json (0 errors) ====
+    {
+        "name": "package",
+        "private": true,
+        "type": "module"
+    }
+==== subfolder/package.json (0 errors) ====
+    {
+        "type": "commonjs"
+    }
+==== types.d.ts (0 errors) ====
+    declare module "fs";
\ No newline at end of file
diff --git a/tests/baselines/reference/nodeModulesImportAssignments(module=nodenext).js b/tests/baselines/reference/nodeModulesImportAssignments(module=nodenext).js
index 580b35366e07d..509c046355ebe 100644
--- a/tests/baselines/reference/nodeModulesImportAssignments(module=nodenext).js
+++ b/tests/baselines/reference/nodeModulesImportAssignments(module=nodenext).js
@@ -55,14 +55,3 @@ const fs = __require_1("fs");
 fs.readFile;
 const fs2 = __require_1("fs");
 export { fs2 };
-
-
-//// [index.d.ts]
-/// <reference path="../types.d.ts" />
-export import fs2 = require("fs");
-//// [index.d.ts]
-/// <reference path="types.d.ts" />
-export import fs2 = require("fs");
-//// [file.d.ts]
-/// <reference path="types.d.ts" />
-export import fs2 = require("fs");
diff --git a/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=node16).errors.txt b/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=node16).errors.txt
index 176b3d13fe10e..16bb961fe91c0 100644
--- a/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=node16).errors.txt
+++ b/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=node16).errors.txt
@@ -1,18 +1,24 @@
+index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
+subfolder/index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
 subfolder/index.ts(2,1): error TS2343: This syntax requires an imported helper named '__exportStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
 subfolder/index.ts(3,1): error TS2343: This syntax requires an imported helper named '__importStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
 
 
-==== subfolder/index.ts (2 errors) ====
+==== subfolder/index.ts (3 errors) ====
     // cjs format file
     export * from "fs";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
     ~~~~~~~~~~~~~~~~~~~
 !!! error TS2343: This syntax requires an imported helper named '__exportStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
     export * as fs from "fs";
     ~~~~~~~~~~~~~~~~~~~~~~~~~
 !!! error TS2343: This syntax requires an imported helper named '__importStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
-==== index.ts (0 errors) ====
+==== index.ts (1 errors) ====
     // esm format file
     export * from "fs";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
     export * as fs from "fs";
 ==== package.json (0 errors) ====
     {
diff --git a/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=node16).js b/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=node16).js
index 722b9c9ff61e0..ab4cb1492b745 100644
--- a/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=node16).js
+++ b/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=node16).js
@@ -37,13 +37,3 @@ exports.fs = tslib_1.__importStar(require("fs"));
 // esm format file
 export * from "fs";
 export * as fs from "fs";
-
-
-//// [index.d.ts]
-/// <reference path="../types.d.ts" />
-export * from "fs";
-export * as fs from "fs";
-//// [index.d.ts]
-/// <reference path="types.d.ts" />
-export * from "fs";
-export * as fs from "fs";
diff --git a/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=nodenext).errors.txt b/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=nodenext).errors.txt
index 176b3d13fe10e..16bb961fe91c0 100644
--- a/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=nodenext).errors.txt
+++ b/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=nodenext).errors.txt
@@ -1,18 +1,24 @@
+index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
+subfolder/index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
 subfolder/index.ts(2,1): error TS2343: This syntax requires an imported helper named '__exportStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
 subfolder/index.ts(3,1): error TS2343: This syntax requires an imported helper named '__importStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
 
 
-==== subfolder/index.ts (2 errors) ====
+==== subfolder/index.ts (3 errors) ====
     // cjs format file
     export * from "fs";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
     ~~~~~~~~~~~~~~~~~~~
 !!! error TS2343: This syntax requires an imported helper named '__exportStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
     export * as fs from "fs";
     ~~~~~~~~~~~~~~~~~~~~~~~~~
 !!! error TS2343: This syntax requires an imported helper named '__importStar' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
-==== index.ts (0 errors) ====
+==== index.ts (1 errors) ====
     // esm format file
     export * from "fs";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
     export * as fs from "fs";
 ==== package.json (0 errors) ====
     {
diff --git a/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=nodenext).js b/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=nodenext).js
index 722b9c9ff61e0..ab4cb1492b745 100644
--- a/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=nodenext).js
+++ b/tests/baselines/reference/nodeModulesImportHelpersCollisions2(module=nodenext).js
@@ -37,13 +37,3 @@ exports.fs = tslib_1.__importStar(require("fs"));
 // esm format file
 export * from "fs";
 export * as fs from "fs";
-
-
-//// [index.d.ts]
-/// <reference path="../types.d.ts" />
-export * from "fs";
-export * as fs from "fs";
-//// [index.d.ts]
-/// <reference path="types.d.ts" />
-export * from "fs";
-export * as fs from "fs";
diff --git a/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=node16).errors.txt b/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=node16).errors.txt
index a5f7cf4be1399..9aa9ac97ff81a 100644
--- a/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=node16).errors.txt
+++ b/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=node16).errors.txt
@@ -1,14 +1,20 @@
+index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
+subfolder/index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
 subfolder/index.ts(2,9): error TS2343: This syntax requires an imported helper named '__importDefault' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
 
 
-==== subfolder/index.ts (1 errors) ====
+==== subfolder/index.ts (2 errors) ====
     // cjs format file
     export {default} from "fs";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
             ~~~~~~~
 !!! error TS2343: This syntax requires an imported helper named '__importDefault' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
-==== index.ts (0 errors) ====
+==== index.ts (1 errors) ====
     // esm format file
     export {default} from "fs";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
 ==== package.json (0 errors) ====
     {
         "name": "package",
diff --git a/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=node16).js b/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=node16).js
index 5f98164aaaa84..b541d7253fb3d 100644
--- a/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=node16).js
+++ b/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=node16).js
@@ -36,11 +36,3 @@ Object.defineProperty(exports, "default", { enumerable: true, get: function () {
 //// [index.js]
 // esm format file
 export { default } from "fs";
-
-
-//// [index.d.ts]
-/// <reference path="../types.d.ts" />
-export { default } from "fs";
-//// [index.d.ts]
-/// <reference path="types.d.ts" />
-export { default } from "fs";
diff --git a/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=nodenext).errors.txt b/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=nodenext).errors.txt
index a5f7cf4be1399..9aa9ac97ff81a 100644
--- a/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=nodenext).errors.txt
+++ b/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=nodenext).errors.txt
@@ -1,14 +1,20 @@
+index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
+subfolder/index.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
 subfolder/index.ts(2,9): error TS2343: This syntax requires an imported helper named '__importDefault' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
 
 
-==== subfolder/index.ts (1 errors) ====
+==== subfolder/index.ts (2 errors) ====
     // cjs format file
     export {default} from "fs";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../types.d.ts"'
             ~~~~~~~
 !!! error TS2343: This syntax requires an imported helper named '__importDefault' which does not exist in 'tslib'. Consider upgrading your version of 'tslib'.
-==== index.ts (0 errors) ====
+==== index.ts (1 errors) ====
     // esm format file
     export {default} from "fs";
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"types.d.ts"'
 ==== package.json (0 errors) ====
     {
         "name": "package",
diff --git a/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=nodenext).js b/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=nodenext).js
index 5f98164aaaa84..b541d7253fb3d 100644
--- a/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=nodenext).js
+++ b/tests/baselines/reference/nodeModulesImportHelpersCollisions3(module=nodenext).js
@@ -36,11 +36,3 @@ Object.defineProperty(exports, "default", { enumerable: true, get: function () {
 //// [index.js]
 // esm format file
 export { default } from "fs";
-
-
-//// [index.d.ts]
-/// <reference path="../types.d.ts" />
-export { default } from "fs";
-//// [index.d.ts]
-/// <reference path="types.d.ts" />
-export { default } from "fs";
diff --git a/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=node16).errors.txt b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=node16).errors.txt
new file mode 100644
index 0000000000000..3db48df489d67
--- /dev/null
+++ b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=node16).errors.txt
@@ -0,0 +1,32 @@
+/index.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"pkg"'
+
+
+==== /index.ts (1 errors) ====
+    import obj from "./uses.js"
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"pkg"'
+    export default (obj as typeof obj);
+==== /node_modules/pkg/package.json (0 errors) ====
+    {
+        "name": "pkg",
+        "version": "0.0.1",
+        "exports": {
+            "import": "./import.js",
+            "require": "./require.js"
+        }
+    }
+==== /node_modules/pkg/import.d.ts (0 errors) ====
+    export {};
+    declare global {
+        interface ImportInterface {}
+        function getInterI(): ImportInterface;
+    }
+==== /node_modules/pkg/require.d.ts (0 errors) ====
+    export {};
+    declare global {
+        interface RequireInterface {}
+        function getInterR(): RequireInterface;
+    }
+==== /uses.ts (0 errors) ====
+    /// <reference types="pkg" />
+    export default getInterR();
\ No newline at end of file
diff --git a/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=node16).js b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=node16).js
index 34117c328c5e1..4938b64a5e11c 100644
--- a/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=node16).js
+++ b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=node16).js
@@ -47,7 +47,3 @@ exports.default = uses_js_1.default;
 /// <reference types="pkg" />
 declare const _default: RequireInterface;
 export default _default;
-//// [index.d.ts]
-/// <reference types="pkg" />
-declare const _default: RequireInterface;
-export default _default;
diff --git a/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=nodenext).errors.txt b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=nodenext).errors.txt
new file mode 100644
index 0000000000000..3db48df489d67
--- /dev/null
+++ b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=nodenext).errors.txt
@@ -0,0 +1,32 @@
+/index.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"pkg"'
+
+
+==== /index.ts (1 errors) ====
+    import obj from "./uses.js"
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"pkg"'
+    export default (obj as typeof obj);
+==== /node_modules/pkg/package.json (0 errors) ====
+    {
+        "name": "pkg",
+        "version": "0.0.1",
+        "exports": {
+            "import": "./import.js",
+            "require": "./require.js"
+        }
+    }
+==== /node_modules/pkg/import.d.ts (0 errors) ====
+    export {};
+    declare global {
+        interface ImportInterface {}
+        function getInterI(): ImportInterface;
+    }
+==== /node_modules/pkg/require.d.ts (0 errors) ====
+    export {};
+    declare global {
+        interface RequireInterface {}
+        function getInterR(): RequireInterface;
+    }
+==== /uses.ts (0 errors) ====
+    /// <reference types="pkg" />
+    export default getInterR();
\ No newline at end of file
diff --git a/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=nodenext).js b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=nodenext).js
index 34117c328c5e1..4938b64a5e11c 100644
--- a/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=nodenext).js
+++ b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit6(module=nodenext).js
@@ -47,7 +47,3 @@ exports.default = uses_js_1.default;
 /// <reference types="pkg" />
 declare const _default: RequireInterface;
 export default _default;
-//// [index.d.ts]
-/// <reference types="pkg" />
-declare const _default: RequireInterface;
-export default _default;
diff --git a/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=node16).errors.txt b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=node16).errors.txt
new file mode 100644
index 0000000000000..9aa922d600d1b
--- /dev/null
+++ b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=node16).errors.txt
@@ -0,0 +1,52 @@
+/index.ts(2,1): error TS18055: Declaration file contains synthesized type reference directives: '"pkg", "pkg"'
+
+
+==== /index.ts (1 errors) ====
+    // only an esm file can `import` both kinds of files
+    import obj1 from "./sub1/uses.js"
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"pkg", "pkg"'
+    import obj2 from "./sub2/uses.js"
+    export default [obj1, obj2.default] as const;
+==== /node_modules/pkg/package.json (0 errors) ====
+    {
+        "name": "pkg",
+        "version": "0.0.1",
+        "exports": {
+            "import": "./import.js",
+            "require": "./require.js"
+        }
+    }
+==== /node_modules/pkg/import.d.ts (0 errors) ====
+    export {};
+    declare global {
+        interface ImportInterface { _i: any; }
+        function getInterI(): ImportInterface;
+    }
+==== /node_modules/pkg/require.d.ts (0 errors) ====
+    export {};
+    declare global {
+        interface RequireInterface { _r: any; }
+        function getInterR(): RequireInterface;
+    }
+==== /sub1/uses.ts (0 errors) ====
+    /// <reference types="pkg" />
+    export default getInterI();
+==== /sub1/package.json (0 errors) ====
+    {
+        "private": true,
+        "type": "module"
+    }
+==== /sub2/uses.ts (0 errors) ====
+    /// <reference types="pkg" />
+    export default getInterR();
+==== /sub2/package.json (0 errors) ====
+    {
+        "private": true,
+        "type": "commonjs"
+    }
+==== /package.json (0 errors) ====
+    {
+        "private": true,
+        "type": "module"
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=node16).js b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=node16).js
index 2426cb28b2597..474dfd718d3da 100644
--- a/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=node16).js
+++ b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=node16).js
@@ -71,8 +71,3 @@ export default _default;
 /// <reference types="pkg" />
 declare const _default: RequireInterface;
 export default _default;
-//// [index.d.ts]
-/// <reference types="pkg" />
-/// <reference types="pkg" resolution-mode="require"/>
-declare const _default: readonly [ImportInterface, RequireInterface];
-export default _default;
diff --git a/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=nodenext).errors.txt b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=nodenext).errors.txt
new file mode 100644
index 0000000000000..9aa922d600d1b
--- /dev/null
+++ b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=nodenext).errors.txt
@@ -0,0 +1,52 @@
+/index.ts(2,1): error TS18055: Declaration file contains synthesized type reference directives: '"pkg", "pkg"'
+
+
+==== /index.ts (1 errors) ====
+    // only an esm file can `import` both kinds of files
+    import obj1 from "./sub1/uses.js"
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"pkg", "pkg"'
+    import obj2 from "./sub2/uses.js"
+    export default [obj1, obj2.default] as const;
+==== /node_modules/pkg/package.json (0 errors) ====
+    {
+        "name": "pkg",
+        "version": "0.0.1",
+        "exports": {
+            "import": "./import.js",
+            "require": "./require.js"
+        }
+    }
+==== /node_modules/pkg/import.d.ts (0 errors) ====
+    export {};
+    declare global {
+        interface ImportInterface { _i: any; }
+        function getInterI(): ImportInterface;
+    }
+==== /node_modules/pkg/require.d.ts (0 errors) ====
+    export {};
+    declare global {
+        interface RequireInterface { _r: any; }
+        function getInterR(): RequireInterface;
+    }
+==== /sub1/uses.ts (0 errors) ====
+    /// <reference types="pkg" />
+    export default getInterI();
+==== /sub1/package.json (0 errors) ====
+    {
+        "private": true,
+        "type": "module"
+    }
+==== /sub2/uses.ts (0 errors) ====
+    /// <reference types="pkg" />
+    export default getInterR();
+==== /sub2/package.json (0 errors) ====
+    {
+        "private": true,
+        "type": "commonjs"
+    }
+==== /package.json (0 errors) ====
+    {
+        "private": true,
+        "type": "module"
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=nodenext).js b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=nodenext).js
index 2426cb28b2597..474dfd718d3da 100644
--- a/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=nodenext).js
+++ b/tests/baselines/reference/nodeModulesTripleSlashReferenceModeDeclarationEmit7(module=nodenext).js
@@ -71,8 +71,3 @@ export default _default;
 /// <reference types="pkg" />
 declare const _default: RequireInterface;
 export default _default;
-//// [index.d.ts]
-/// <reference types="pkg" />
-/// <reference types="pkg" resolution-mode="require"/>
-declare const _default: readonly [ImportInterface, RequireInterface];
-export default _default;
diff --git a/tests/baselines/reference/outModuleTripleSlashRefs.errors.txt b/tests/baselines/reference/outModuleTripleSlashRefs.errors.txt
new file mode 100644
index 0000000000000..9e4b48355eab1
--- /dev/null
+++ b/tests/baselines/reference/outModuleTripleSlashRefs.errors.txt
@@ -0,0 +1,33 @@
+ref/a.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"b.d.ts"'
+
+
+==== ref/a.ts (1 errors) ====
+    /// <reference path="./b.ts" />
+    export class A {
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"b.d.ts"'
+    	member: typeof GlobalFoo;
+    }
+    
+==== ref/b.ts (0 errors) ====
+    /// <reference path="./c.d.ts" />
+    class Foo {
+    	member: Bar;
+    }
+    declare var GlobalFoo: Foo;
+    
+==== ref/c.d.ts (0 errors) ====
+    /// <reference path="./d.d.ts" />
+    declare class Bar {
+    	member: Baz;
+    }
+    
+==== ref/d.d.ts (0 errors) ====
+    declare class Baz {
+    	member: number;
+    }
+    
+==== b.ts (0 errors) ====
+    import {A} from "./ref/a";
+    export class B extends A { }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/privacyCannotNameAccessorDeclFile.errors.txt b/tests/baselines/reference/privacyCannotNameAccessorDeclFile.errors.txt
new file mode 100644
index 0000000000000..6e83d2250a1ee
--- /dev/null
+++ b/tests/baselines/reference/privacyCannotNameAccessorDeclFile.errors.txt
@@ -0,0 +1,142 @@
+privacyCannotNameAccessorDeclFile_consumer.ts(1,1): error TS18056: Declaration file contains synthesized file reference directives: '"privacyCannotNameAccessorDeclFile_GlobalWidgets.d.ts"'
+privacyCannotNameAccessorDeclFile_exporter.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"privacyCannotNameAccessorDeclFile_GlobalWidgets.d.ts"'
+
+
+==== privacyCannotNameAccessorDeclFile_consumer.ts (1 errors) ====
+    import exporter = require("./privacyCannotNameAccessorDeclFile_exporter");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"privacyCannotNameAccessorDeclFile_GlobalWidgets.d.ts"'
+    export class publicClassWithWithPrivateGetAccessorTypes {
+        static get myPublicStaticMethod() { // Error
+            return exporter.createExportedWidget1();
+        }
+        private static get myPrivateStaticMethod() {
+            return exporter.createExportedWidget1();
+        }
+        get myPublicMethod() { // Error
+            return exporter.createExportedWidget1();
+        }
+        private get myPrivateMethod() {
+            return exporter.createExportedWidget1();
+        }
+        static get myPublicStaticMethod1() { // Error
+            return exporter.createExportedWidget3();
+        }
+        private static get myPrivateStaticMethod1() {
+            return exporter.createExportedWidget3();
+        }
+        get myPublicMethod1() { // Error
+            return exporter.createExportedWidget3();
+        }
+        private get myPrivateMethod1() {
+            return exporter.createExportedWidget3();
+        }
+    }
+    
+    class privateClassWithWithPrivateGetAccessorTypes {
+        static get myPublicStaticMethod() { 
+            return exporter.createExportedWidget1();
+        }
+        private static get myPrivateStaticMethod() {
+            return exporter.createExportedWidget1();
+        }
+        get myPublicMethod() { 
+            return exporter.createExportedWidget1();
+        }
+        private get myPrivateMethod() {
+            return exporter.createExportedWidget1();
+        }
+        static get myPublicStaticMethod1() { 
+            return exporter.createExportedWidget3();
+        }
+        private static get myPrivateStaticMethod1() {
+            return exporter.createExportedWidget3();
+        }
+        get myPublicMethod1() { 
+            return exporter.createExportedWidget3();
+        }
+        private get myPrivateMethod1() {
+            return exporter.createExportedWidget3();
+        }
+    }
+    
+    export class publicClassWithPrivateModuleGetAccessorTypes {
+        static get myPublicStaticMethod() { // Error
+            return exporter.createExportedWidget2();
+        }
+        get myPublicMethod() { // Error
+            return exporter.createExportedWidget2();
+        }
+        static get myPublicStaticMethod1() { // Error
+            return exporter.createExportedWidget4();
+        }
+        get myPublicMethod1() { // Error
+            return exporter.createExportedWidget4();
+        }
+    }
+    
+    class privateClassWithPrivateModuleGetAccessorTypes {
+        static get myPublicStaticMethod() { 
+            return exporter.createExportedWidget2();
+        }
+        get myPublicMethod() { 
+            return exporter.createExportedWidget2();
+        }
+        static get myPublicStaticMethod1() { 
+            return exporter.createExportedWidget4();
+        }
+        get myPublicMethod1() { 
+            return exporter.createExportedWidget4();
+        }
+    }
+==== privacyCannotNameAccessorDeclFile_GlobalWidgets.ts (0 errors) ====
+    declare module "GlobalWidgets" {
+        export class Widget3 {
+            name: string;
+        }
+        export function createWidget3(): Widget3;
+    
+        export module SpecializedGlobalWidget {
+            export class Widget4 {
+                name: string;
+            }
+            function createWidget4(): Widget4;
+        }
+    }
+    
+==== privacyCannotNameAccessorDeclFile_Widgets.ts (0 errors) ====
+    export class Widget1 {
+        name = 'one';
+    }
+    export function createWidget1() {
+        return new Widget1();
+    }
+    
+    export module SpecializedWidget {
+        export class Widget2 {
+            name = 'one';
+        }
+        export function createWidget2() {
+            return new Widget2();
+        }
+    }
+    
+==== privacyCannotNameAccessorDeclFile_exporter.ts (1 errors) ====
+    ///<reference path='privacyCannotNameAccessorDeclFile_GlobalWidgets.ts'/>
+    import Widgets = require("./privacyCannotNameAccessorDeclFile_Widgets");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"privacyCannotNameAccessorDeclFile_GlobalWidgets.d.ts"'
+    import Widgets1 = require("GlobalWidgets");
+    export function createExportedWidget1() {
+        return Widgets.createWidget1();
+    }
+    export function createExportedWidget2() {
+        return Widgets.SpecializedWidget.createWidget2();
+    }
+    export function createExportedWidget3() {
+        return Widgets1.createWidget3();
+    }
+    export function createExportedWidget4() {
+        return Widgets1.SpecializedGlobalWidget.createWidget4();
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/privacyCannotNameAccessorDeclFile.js b/tests/baselines/reference/privacyCannotNameAccessorDeclFile.js
index 310d337fa478a..2133d362120e9 100644
--- a/tests/baselines/reference/privacyCannotNameAccessorDeclFile.js
+++ b/tests/baselines/reference/privacyCannotNameAccessorDeclFile.js
@@ -409,29 +409,3 @@ export declare namespace SpecializedWidget {
     }
     function createWidget2(): Widget2;
 }
-//// [privacyCannotNameAccessorDeclFile_exporter.d.ts]
-/// <reference path="privacyCannotNameAccessorDeclFile_GlobalWidgets.d.ts" />
-import Widgets = require("./privacyCannotNameAccessorDeclFile_Widgets");
-import Widgets1 = require("GlobalWidgets");
-export declare function createExportedWidget1(): Widgets.Widget1;
-export declare function createExportedWidget2(): Widgets.SpecializedWidget.Widget2;
-export declare function createExportedWidget3(): Widgets1.Widget3;
-export declare function createExportedWidget4(): Widgets1.SpecializedGlobalWidget.Widget4;
-//// [privacyCannotNameAccessorDeclFile_consumer.d.ts]
-/// <reference path="privacyCannotNameAccessorDeclFile_GlobalWidgets.d.ts" />
-export declare class publicClassWithWithPrivateGetAccessorTypes {
-    static get myPublicStaticMethod(): import("./privacyCannotNameAccessorDeclFile_Widgets").Widget1;
-    private static get myPrivateStaticMethod();
-    get myPublicMethod(): import("./privacyCannotNameAccessorDeclFile_Widgets").Widget1;
-    private get myPrivateMethod();
-    static get myPublicStaticMethod1(): import("GlobalWidgets").Widget3;
-    private static get myPrivateStaticMethod1();
-    get myPublicMethod1(): import("GlobalWidgets").Widget3;
-    private get myPrivateMethod1();
-}
-export declare class publicClassWithPrivateModuleGetAccessorTypes {
-    static get myPublicStaticMethod(): import("./privacyCannotNameAccessorDeclFile_Widgets").SpecializedWidget.Widget2;
-    get myPublicMethod(): import("./privacyCannotNameAccessorDeclFile_Widgets").SpecializedWidget.Widget2;
-    static get myPublicStaticMethod1(): import("GlobalWidgets").SpecializedGlobalWidget.Widget4;
-    get myPublicMethod1(): import("GlobalWidgets").SpecializedGlobalWidget.Widget4;
-}
diff --git a/tests/baselines/reference/privacyCannotNameVarTypeDeclFile.errors.txt b/tests/baselines/reference/privacyCannotNameVarTypeDeclFile.errors.txt
new file mode 100644
index 0000000000000..52feb74181149
--- /dev/null
+++ b/tests/baselines/reference/privacyCannotNameVarTypeDeclFile.errors.txt
@@ -0,0 +1,105 @@
+privacyCannotNameVarTypeDeclFile_consumer.ts(1,1): error TS18056: Declaration file contains synthesized file reference directives: '"privacyCannotNameVarTypeDeclFile_GlobalWidgets.d.ts"'
+privacyCannotNameVarTypeDeclFile_exporter.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"privacyCannotNameVarTypeDeclFile_GlobalWidgets.d.ts"'
+
+
+==== privacyCannotNameVarTypeDeclFile_consumer.ts (1 errors) ====
+    import exporter = require("./privacyCannotNameVarTypeDeclFile_exporter");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"privacyCannotNameVarTypeDeclFile_GlobalWidgets.d.ts"'
+    export class publicClassWithWithPrivatePropertyTypes {
+        static myPublicStaticProperty = exporter.createExportedWidget1(); // Error
+        private static myPrivateStaticProperty = exporter.createExportedWidget1();
+        myPublicProperty = exporter.createExportedWidget1(); // Error
+        private myPrivateProperty = exporter.createExportedWidget1();
+    
+        static myPublicStaticProperty1 = exporter.createExportedWidget3(); // Error
+        private static myPrivateStaticProperty1 = exporter.createExportedWidget3();
+        myPublicProperty1 = exporter.createExportedWidget3(); // Error
+        private myPrivateProperty1 = exporter.createExportedWidget3();
+    }
+    
+    class privateClassWithWithPrivatePropertyTypes {
+        static myPublicStaticProperty = exporter.createExportedWidget1(); 
+        private static myPrivateStaticProperty = exporter.createExportedWidget1();
+        myPublicProperty = exporter.createExportedWidget1(); 
+        private myPrivateProperty = exporter.createExportedWidget1();
+    
+        static myPublicStaticProperty1 = exporter.createExportedWidget3(); 
+        private static myPrivateStaticProperty1 = exporter.createExportedWidget3();
+        myPublicProperty1 = exporter.createExportedWidget3(); 
+        private myPrivateProperty1 = exporter.createExportedWidget3();
+    }
+    
+    export var publicVarWithPrivatePropertyTypes= exporter.createExportedWidget1(); // Error
+    var privateVarWithPrivatePropertyTypes= exporter.createExportedWidget1();
+    export var publicVarWithPrivatePropertyTypes1 = exporter.createExportedWidget3(); // Error
+    var privateVarWithPrivatePropertyTypes1 = exporter.createExportedWidget3();
+    
+    export class publicClassWithPrivateModulePropertyTypes {
+        static myPublicStaticProperty= exporter.createExportedWidget2(); // Error
+        myPublicProperty = exporter.createExportedWidget2(); // Error
+        static myPublicStaticProperty1 = exporter.createExportedWidget4(); // Error
+        myPublicProperty1 = exporter.createExportedWidget4(); // Error
+    }
+    export var publicVarWithPrivateModulePropertyTypes= exporter.createExportedWidget2(); // Error
+    export var publicVarWithPrivateModulePropertyTypes1 = exporter.createExportedWidget4(); // Error
+    
+    class privateClassWithPrivateModulePropertyTypes {
+        static myPublicStaticProperty= exporter.createExportedWidget2();
+        myPublicProperty= exporter.createExportedWidget2();
+        static myPublicStaticProperty1 = exporter.createExportedWidget4();
+        myPublicProperty1 = exporter.createExportedWidget4();
+    }
+    var privateVarWithPrivateModulePropertyTypes= exporter.createExportedWidget2();
+    var privateVarWithPrivateModulePropertyTypes1 = exporter.createExportedWidget4();
+==== privacyCannotNameVarTypeDeclFile_GlobalWidgets.ts (0 errors) ====
+    declare module "GlobalWidgets" {
+        export class Widget3 {
+            name: string;
+        }
+        export function createWidget3(): Widget3;
+    
+        export module SpecializedGlobalWidget {
+            export class Widget4 {
+                name: string;
+            }
+            function createWidget4(): Widget4;
+        }
+    }
+    
+==== privacyCannotNameVarTypeDeclFile_Widgets.ts (0 errors) ====
+    export class Widget1 {
+        name = 'one';
+    }
+    export function createWidget1() {
+        return new Widget1();
+    }
+    
+    export module SpecializedWidget {
+        export class Widget2 {
+            name = 'one';
+        }
+        export function createWidget2() {
+            return new Widget2();
+        }
+    }
+    
+==== privacyCannotNameVarTypeDeclFile_exporter.ts (1 errors) ====
+    ///<reference path='privacyCannotNameVarTypeDeclFile_GlobalWidgets.ts'/>
+    import Widgets = require("./privacyCannotNameVarTypeDeclFile_Widgets");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"privacyCannotNameVarTypeDeclFile_GlobalWidgets.d.ts"'
+    import Widgets1 = require("GlobalWidgets");
+    export function createExportedWidget1() {
+        return Widgets.createWidget1();
+    }
+    export function createExportedWidget2() {
+        return Widgets.SpecializedWidget.createWidget2();
+    }
+    export function createExportedWidget3() {
+        return Widgets1.createWidget3();
+    }
+    export function createExportedWidget4() {
+        return Widgets1.SpecializedGlobalWidget.createWidget4();
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/privacyCannotNameVarTypeDeclFile.js b/tests/baselines/reference/privacyCannotNameVarTypeDeclFile.js
index a7f9b6a94d7c3..1a13eb5d19eeb 100644
--- a/tests/baselines/reference/privacyCannotNameVarTypeDeclFile.js
+++ b/tests/baselines/reference/privacyCannotNameVarTypeDeclFile.js
@@ -236,33 +236,3 @@ export declare namespace SpecializedWidget {
     }
     function createWidget2(): Widget2;
 }
-//// [privacyCannotNameVarTypeDeclFile_exporter.d.ts]
-/// <reference path="privacyCannotNameVarTypeDeclFile_GlobalWidgets.d.ts" />
-import Widgets = require("./privacyCannotNameVarTypeDeclFile_Widgets");
-import Widgets1 = require("GlobalWidgets");
-export declare function createExportedWidget1(): Widgets.Widget1;
-export declare function createExportedWidget2(): Widgets.SpecializedWidget.Widget2;
-export declare function createExportedWidget3(): Widgets1.Widget3;
-export declare function createExportedWidget4(): Widgets1.SpecializedGlobalWidget.Widget4;
-//// [privacyCannotNameVarTypeDeclFile_consumer.d.ts]
-/// <reference path="privacyCannotNameVarTypeDeclFile_GlobalWidgets.d.ts" />
-export declare class publicClassWithWithPrivatePropertyTypes {
-    static myPublicStaticProperty: import("./privacyCannotNameVarTypeDeclFile_Widgets").Widget1;
-    private static myPrivateStaticProperty;
-    myPublicProperty: import("./privacyCannotNameVarTypeDeclFile_Widgets").Widget1;
-    private myPrivateProperty;
-    static myPublicStaticProperty1: import("GlobalWidgets").Widget3;
-    private static myPrivateStaticProperty1;
-    myPublicProperty1: import("GlobalWidgets").Widget3;
-    private myPrivateProperty1;
-}
-export declare var publicVarWithPrivatePropertyTypes: import("./privacyCannotNameVarTypeDeclFile_Widgets").Widget1;
-export declare var publicVarWithPrivatePropertyTypes1: import("GlobalWidgets").Widget3;
-export declare class publicClassWithPrivateModulePropertyTypes {
-    static myPublicStaticProperty: import("./privacyCannotNameVarTypeDeclFile_Widgets").SpecializedWidget.Widget2;
-    myPublicProperty: import("./privacyCannotNameVarTypeDeclFile_Widgets").SpecializedWidget.Widget2;
-    static myPublicStaticProperty1: import("GlobalWidgets").SpecializedGlobalWidget.Widget4;
-    myPublicProperty1: import("GlobalWidgets").SpecializedGlobalWidget.Widget4;
-}
-export declare var publicVarWithPrivateModulePropertyTypes: import("./privacyCannotNameVarTypeDeclFile_Widgets").SpecializedWidget.Widget2;
-export declare var publicVarWithPrivateModulePropertyTypes1: import("GlobalWidgets").SpecializedGlobalWidget.Widget4;
diff --git a/tests/baselines/reference/privacyFunctionCannotNameParameterTypeDeclFile.errors.txt b/tests/baselines/reference/privacyFunctionCannotNameParameterTypeDeclFile.errors.txt
new file mode 100644
index 0000000000000..800a15b80d7c1
--- /dev/null
+++ b/tests/baselines/reference/privacyFunctionCannotNameParameterTypeDeclFile.errors.txt
@@ -0,0 +1,161 @@
+privacyFunctionCannotNameParameterTypeDeclFile_consumer.ts(1,1): error TS18056: Declaration file contains synthesized file reference directives: '"privacyFunctionCannotNameParameterTypeDeclFile_GlobalWidgets.d.ts"'
+privacyFunctionCannotNameParameterTypeDeclFile_exporter.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"privacyFunctionCannotNameParameterTypeDeclFile_GlobalWidgets.d.ts"'
+
+
+==== privacyFunctionCannotNameParameterTypeDeclFile_consumer.ts (1 errors) ====
+    import exporter = require("./privacyFunctionCannotNameParameterTypeDeclFile_exporter");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"privacyFunctionCannotNameParameterTypeDeclFile_GlobalWidgets.d.ts"'
+    export class publicClassWithWithPrivateParmeterTypes {
+        static myPublicStaticMethod(param = exporter.createExportedWidget1()) { // Error
+        }
+        private static myPrivateStaticMethod(param = exporter.createExportedWidget1()) {
+        }
+        myPublicMethod(param  = exporter.createExportedWidget1()) { // Error
+        }
+        private myPrivateMethod(param = exporter.createExportedWidget1()) {
+        }
+        constructor(param = exporter.createExportedWidget1(), private param1 = exporter.createExportedWidget1(), public param2 = exporter.createExportedWidget1()) { // Error
+        }
+    }
+    export class publicClassWithWithPrivateParmeterTypes1 {
+        static myPublicStaticMethod(param = exporter.createExportedWidget3()) { // Error
+        }
+        private static myPrivateStaticMethod(param = exporter.createExportedWidget3()) {
+        }
+        myPublicMethod(param  = exporter.createExportedWidget3()) { // Error
+        }
+        private myPrivateMethod(param = exporter.createExportedWidget3()) {
+        }
+        constructor(param = exporter.createExportedWidget3(), private param1 = exporter.createExportedWidget3(), public param2 = exporter.createExportedWidget3()) { // Error
+        }
+    }
+    
+    class privateClassWithWithPrivateParmeterTypes {
+        static myPublicStaticMethod(param = exporter.createExportedWidget1()) {
+        }
+        private static myPrivateStaticMethod(param = exporter.createExportedWidget1()) {
+        }
+        myPublicMethod(param  = exporter.createExportedWidget1()) {
+        }
+        private myPrivateMethod(param = exporter.createExportedWidget1()) {
+        }
+        constructor(param = exporter.createExportedWidget1(), private param1 = exporter.createExportedWidget1(), public param2 = exporter.createExportedWidget1()) {
+        }
+    }
+    class privateClassWithWithPrivateParmeterTypes2 {
+        static myPublicStaticMethod(param = exporter.createExportedWidget3()) {
+        }
+        private static myPrivateStaticMethod(param = exporter.createExportedWidget3()) {
+        }
+        myPublicMethod(param  = exporter.createExportedWidget3()) {
+        }
+        private myPrivateMethod(param = exporter.createExportedWidget3()) {
+        }
+        constructor(param = exporter.createExportedWidget3(), private param1 = exporter.createExportedWidget3(), public param2 = exporter.createExportedWidget3()) {
+        }
+    }
+    
+    export function publicFunctionWithPrivateParmeterTypes(param = exporter.createExportedWidget1()) { // Error
+    }
+    function privateFunctionWithPrivateParmeterTypes(param = exporter.createExportedWidget1()) {
+    }
+    export function publicFunctionWithPrivateParmeterTypes1(param = exporter.createExportedWidget3()) { // Error
+    }
+    function privateFunctionWithPrivateParmeterTypes1(param = exporter.createExportedWidget3()) {
+    }
+    
+    
+    export class publicClassWithPrivateModuleParameterTypes {
+        static myPublicStaticMethod(param= exporter.createExportedWidget2()) { // Error
+        }
+        myPublicMethod(param= exporter.createExportedWidget2()) { // Error
+        }
+        constructor(param= exporter.createExportedWidget2(), private param1= exporter.createExportedWidget2(), public param2= exporter.createExportedWidget2()) { // Error
+        }
+    }
+    export class publicClassWithPrivateModuleParameterTypes2 {
+        static myPublicStaticMethod(param= exporter.createExportedWidget4()) { // Error
+        }
+        myPublicMethod(param= exporter.createExportedWidget4()) { // Error
+        }
+        constructor(param= exporter.createExportedWidget4(), private param1= exporter.createExportedWidget4(), public param2= exporter.createExportedWidget4()) { // Error
+        }
+    }
+    export function publicFunctionWithPrivateModuleParameterTypes(param= exporter.createExportedWidget2()) { // Error
+    }
+    export function publicFunctionWithPrivateModuleParameterTypes1(param= exporter.createExportedWidget4()) { // Error
+    }
+    
+    
+    class privateClassWithPrivateModuleParameterTypes {
+        static myPublicStaticMethod(param= exporter.createExportedWidget2()) {
+        }
+        myPublicMethod(param= exporter.createExportedWidget2()) {
+        }
+        constructor(param= exporter.createExportedWidget2(), private param1= exporter.createExportedWidget2(), public param2= exporter.createExportedWidget2()) {
+        }
+    }
+    class privateClassWithPrivateModuleParameterTypes1 {
+        static myPublicStaticMethod(param= exporter.createExportedWidget4()) {
+        }
+        myPublicMethod(param= exporter.createExportedWidget4()) {
+        }
+        constructor(param= exporter.createExportedWidget4(), private param1= exporter.createExportedWidget4(), public param2= exporter.createExportedWidget4()) {
+        }
+    }
+    function privateFunctionWithPrivateModuleParameterTypes(param= exporter.createExportedWidget2()) {
+    }
+    function privateFunctionWithPrivateModuleParameterTypes1(param= exporter.createExportedWidget4()) {
+    }
+==== privacyFunctionCannotNameParameterTypeDeclFile_GlobalWidgets.ts (0 errors) ====
+    declare module "GlobalWidgets" {
+        export class Widget3 {
+            name: string;
+        }
+        export function createWidget3(): Widget3;
+    
+        export module SpecializedGlobalWidget {
+            export class Widget4 {
+                name: string;
+            }
+            function createWidget4(): Widget4;
+        }
+    }
+    
+==== privacyFunctionCannotNameParameterTypeDeclFile_Widgets.ts (0 errors) ====
+    export class Widget1 {
+        name = 'one';
+    }
+    export function createWidget1() {
+        return new Widget1();
+    }
+    
+    export module SpecializedWidget {
+        export class Widget2 {
+            name = 'one';
+        }
+        export function createWidget2() {
+            return new Widget2();
+        }
+    }
+    
+==== privacyFunctionCannotNameParameterTypeDeclFile_exporter.ts (1 errors) ====
+    ///<reference path='privacyFunctionCannotNameParameterTypeDeclFile_GlobalWidgets.ts'/>
+    import Widgets = require("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"privacyFunctionCannotNameParameterTypeDeclFile_GlobalWidgets.d.ts"'
+    import Widgets1 = require("GlobalWidgets");
+    export function createExportedWidget1() {
+        return Widgets.createWidget1();
+    }
+    export function createExportedWidget2() {
+        return Widgets.SpecializedWidget.createWidget2();
+    }
+    export function createExportedWidget3() {
+        return Widgets1.createWidget3();
+    }
+    export function createExportedWidget4() {
+        return Widgets1.SpecializedGlobalWidget.createWidget4();
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/privacyFunctionCannotNameParameterTypeDeclFile.js b/tests/baselines/reference/privacyFunctionCannotNameParameterTypeDeclFile.js
index d4c321577beeb..9ab47941294c5 100644
--- a/tests/baselines/reference/privacyFunctionCannotNameParameterTypeDeclFile.js
+++ b/tests/baselines/reference/privacyFunctionCannotNameParameterTypeDeclFile.js
@@ -422,49 +422,3 @@ export declare namespace SpecializedWidget {
     }
     function createWidget2(): Widget2;
 }
-//// [privacyFunctionCannotNameParameterTypeDeclFile_exporter.d.ts]
-/// <reference path="privacyFunctionCannotNameParameterTypeDeclFile_GlobalWidgets.d.ts" />
-import Widgets = require("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets");
-import Widgets1 = require("GlobalWidgets");
-export declare function createExportedWidget1(): Widgets.Widget1;
-export declare function createExportedWidget2(): Widgets.SpecializedWidget.Widget2;
-export declare function createExportedWidget3(): Widgets1.Widget3;
-export declare function createExportedWidget4(): Widgets1.SpecializedGlobalWidget.Widget4;
-//// [privacyFunctionCannotNameParameterTypeDeclFile_consumer.d.ts]
-/// <reference path="privacyFunctionCannotNameParameterTypeDeclFile_GlobalWidgets.d.ts" />
-export declare class publicClassWithWithPrivateParmeterTypes {
-    private param1;
-    param2: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").Widget1;
-    static myPublicStaticMethod(param?: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").Widget1): void;
-    private static myPrivateStaticMethod;
-    myPublicMethod(param?: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").Widget1): void;
-    private myPrivateMethod;
-    constructor(param?: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").Widget1, param1?: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").Widget1, param2?: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").Widget1);
-}
-export declare class publicClassWithWithPrivateParmeterTypes1 {
-    private param1;
-    param2: import("GlobalWidgets").Widget3;
-    static myPublicStaticMethod(param?: import("GlobalWidgets").Widget3): void;
-    private static myPrivateStaticMethod;
-    myPublicMethod(param?: import("GlobalWidgets").Widget3): void;
-    private myPrivateMethod;
-    constructor(param?: import("GlobalWidgets").Widget3, param1?: import("GlobalWidgets").Widget3, param2?: import("GlobalWidgets").Widget3);
-}
-export declare function publicFunctionWithPrivateParmeterTypes(param?: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").Widget1): void;
-export declare function publicFunctionWithPrivateParmeterTypes1(param?: import("GlobalWidgets").Widget3): void;
-export declare class publicClassWithPrivateModuleParameterTypes {
-    private param1;
-    param2: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").SpecializedWidget.Widget2;
-    static myPublicStaticMethod(param?: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").SpecializedWidget.Widget2): void;
-    myPublicMethod(param?: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").SpecializedWidget.Widget2): void;
-    constructor(param?: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").SpecializedWidget.Widget2, param1?: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").SpecializedWidget.Widget2, param2?: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").SpecializedWidget.Widget2);
-}
-export declare class publicClassWithPrivateModuleParameterTypes2 {
-    private param1;
-    param2: import("GlobalWidgets").SpecializedGlobalWidget.Widget4;
-    static myPublicStaticMethod(param?: import("GlobalWidgets").SpecializedGlobalWidget.Widget4): void;
-    myPublicMethod(param?: import("GlobalWidgets").SpecializedGlobalWidget.Widget4): void;
-    constructor(param?: import("GlobalWidgets").SpecializedGlobalWidget.Widget4, param1?: import("GlobalWidgets").SpecializedGlobalWidget.Widget4, param2?: import("GlobalWidgets").SpecializedGlobalWidget.Widget4);
-}
-export declare function publicFunctionWithPrivateModuleParameterTypes(param?: import("./privacyFunctionCannotNameParameterTypeDeclFile_Widgets").SpecializedWidget.Widget2): void;
-export declare function publicFunctionWithPrivateModuleParameterTypes1(param?: import("GlobalWidgets").SpecializedGlobalWidget.Widget4): void;
diff --git a/tests/baselines/reference/privacyFunctionCannotNameReturnTypeDeclFile.errors.txt b/tests/baselines/reference/privacyFunctionCannotNameReturnTypeDeclFile.errors.txt
new file mode 100644
index 0000000000000..ba6ca8950c5cf
--- /dev/null
+++ b/tests/baselines/reference/privacyFunctionCannotNameReturnTypeDeclFile.errors.txt
@@ -0,0 +1,168 @@
+privacyFunctionReturnTypeDeclFile_consumer.ts(1,1): error TS18056: Declaration file contains synthesized file reference directives: '"privacyFunctionReturnTypeDeclFile_GlobalWidgets.d.ts"'
+privacyFunctionReturnTypeDeclFile_exporter.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"privacyFunctionReturnTypeDeclFile_GlobalWidgets.d.ts"'
+
+
+==== privacyFunctionReturnTypeDeclFile_consumer.ts (1 errors) ====
+    import exporter = require("./privacyFunctionReturnTypeDeclFile_exporter");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"privacyFunctionReturnTypeDeclFile_GlobalWidgets.d.ts"'
+    export class publicClassWithWithPrivateParmeterTypes {
+        static myPublicStaticMethod() { // Error
+            return exporter.createExportedWidget1();
+        }
+        private static myPrivateStaticMethod() {
+            return exporter.createExportedWidget1();;
+        }
+        myPublicMethod() { // Error
+            return exporter.createExportedWidget1();;
+        }
+        private myPrivateMethod() {
+            return exporter.createExportedWidget1();;
+        }
+        static myPublicStaticMethod1() { // Error
+            return exporter.createExportedWidget3();
+        }
+        private static myPrivateStaticMethod1() {
+            return exporter.createExportedWidget3();;
+        }
+        myPublicMethod1() { // Error
+            return exporter.createExportedWidget3();;
+        }
+        private myPrivateMethod1() {
+            return exporter.createExportedWidget3();;
+        }
+    }
+    
+    class privateClassWithWithPrivateParmeterTypes {
+        static myPublicStaticMethod() { 
+            return exporter.createExportedWidget1();
+        }
+        private static myPrivateStaticMethod() {
+            return exporter.createExportedWidget1();;
+        }
+        myPublicMethod() { 
+            return exporter.createExportedWidget1();;
+        }
+        private myPrivateMethod() {
+            return exporter.createExportedWidget1();;
+        }
+        static myPublicStaticMethod1() { 
+            return exporter.createExportedWidget3();
+        }
+        private static myPrivateStaticMethod1() {
+            return exporter.createExportedWidget3();;
+        }
+        myPublicMethod1() { 
+            return exporter.createExportedWidget3();;
+        }
+        private myPrivateMethod1() {
+            return exporter.createExportedWidget3();;
+        }
+    }
+    
+    export function publicFunctionWithPrivateParmeterTypes() { // Error
+        return exporter.createExportedWidget1();
+    }
+    function privateFunctionWithPrivateParmeterTypes()   {
+        return exporter.createExportedWidget1();
+    }
+    export function publicFunctionWithPrivateParmeterTypes1() { // Error
+        return exporter.createExportedWidget3();
+    }
+    function privateFunctionWithPrivateParmeterTypes1() {
+        return exporter.createExportedWidget3();
+    }
+    
+    export class publicClassWithPrivateModuleReturnTypes {
+        static myPublicStaticMethod() { // Error
+            return exporter.createExportedWidget2();
+        }
+        myPublicMethod() { // Error
+            return exporter.createExportedWidget2();
+        }
+        static myPublicStaticMethod1() { // Error
+            return exporter.createExportedWidget4();
+        }
+        myPublicMethod1() { // Error
+            return exporter.createExportedWidget4();
+        }
+    }
+    export function publicFunctionWithPrivateModuleReturnTypes() { // Error
+        return exporter.createExportedWidget2();
+    }
+    export function publicFunctionWithPrivateModuleReturnTypes1() { // Error
+        return exporter.createExportedWidget4();
+    }
+    
+    class privateClassWithPrivateModuleReturnTypes {
+        static myPublicStaticMethod() { 
+            return exporter.createExportedWidget2();
+        }
+        myPublicMethod() { 
+            return exporter.createExportedWidget2();
+        }
+        static myPublicStaticMethod1() { // Error
+            return exporter.createExportedWidget4();
+        }
+        myPublicMethod1() { // Error
+            return exporter.createExportedWidget4();
+        }
+    }
+    function privateFunctionWithPrivateModuleReturnTypes() { 
+        return exporter.createExportedWidget2();
+    }
+    function privateFunctionWithPrivateModuleReturnTypes1() {
+        return exporter.createExportedWidget4();
+    }
+    
+==== privacyFunctionReturnTypeDeclFile_GlobalWidgets.ts (0 errors) ====
+    declare module "GlobalWidgets" {
+        export class Widget3 {
+            name: string;
+        }
+        export function createWidget3(): Widget3;
+    
+        export module SpecializedGlobalWidget {
+            export class Widget4 {
+                name: string;
+            }
+            function createWidget4(): Widget4;
+        }
+    }
+    
+==== privacyFunctionReturnTypeDeclFile_Widgets.ts (0 errors) ====
+    export class Widget1 {
+        name = 'one';
+    }
+    export function createWidget1() {
+        return new Widget1();
+    }
+    
+    export module SpecializedWidget {
+        export class Widget2 {
+            name = 'one';
+        }
+        export function createWidget2() {
+            return new Widget2();
+        }
+    }
+    
+==== privacyFunctionReturnTypeDeclFile_exporter.ts (1 errors) ====
+    ///<reference path='privacyFunctionReturnTypeDeclFile_GlobalWidgets.ts'/>
+    import Widgets = require("./privacyFunctionReturnTypeDeclFile_Widgets");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"privacyFunctionReturnTypeDeclFile_GlobalWidgets.d.ts"'
+    import Widgets1 = require("GlobalWidgets");
+    export function createExportedWidget1() {
+        return Widgets.createWidget1();
+    }
+    export function createExportedWidget2() {
+        return Widgets.SpecializedWidget.createWidget2();
+    }
+    export function createExportedWidget3() {
+        return Widgets1.createWidget3();
+    }
+    export function createExportedWidget4() {
+        return Widgets1.SpecializedGlobalWidget.createWidget4();
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/privacyFunctionCannotNameReturnTypeDeclFile.js b/tests/baselines/reference/privacyFunctionCannotNameReturnTypeDeclFile.js
index 87a0b6b32b808..e98eaf3846cfc 100644
--- a/tests/baselines/reference/privacyFunctionCannotNameReturnTypeDeclFile.js
+++ b/tests/baselines/reference/privacyFunctionCannotNameReturnTypeDeclFile.js
@@ -379,33 +379,3 @@ export declare namespace SpecializedWidget {
     }
     function createWidget2(): Widget2;
 }
-//// [privacyFunctionReturnTypeDeclFile_exporter.d.ts]
-/// <reference path="privacyFunctionReturnTypeDeclFile_GlobalWidgets.d.ts" />
-import Widgets = require("./privacyFunctionReturnTypeDeclFile_Widgets");
-import Widgets1 = require("GlobalWidgets");
-export declare function createExportedWidget1(): Widgets.Widget1;
-export declare function createExportedWidget2(): Widgets.SpecializedWidget.Widget2;
-export declare function createExportedWidget3(): Widgets1.Widget3;
-export declare function createExportedWidget4(): Widgets1.SpecializedGlobalWidget.Widget4;
-//// [privacyFunctionReturnTypeDeclFile_consumer.d.ts]
-/// <reference path="privacyFunctionReturnTypeDeclFile_GlobalWidgets.d.ts" />
-export declare class publicClassWithWithPrivateParmeterTypes {
-    static myPublicStaticMethod(): import("./privacyFunctionReturnTypeDeclFile_Widgets").Widget1;
-    private static myPrivateStaticMethod;
-    myPublicMethod(): import("./privacyFunctionReturnTypeDeclFile_Widgets").Widget1;
-    private myPrivateMethod;
-    static myPublicStaticMethod1(): import("GlobalWidgets").Widget3;
-    private static myPrivateStaticMethod1;
-    myPublicMethod1(): import("GlobalWidgets").Widget3;
-    private myPrivateMethod1;
-}
-export declare function publicFunctionWithPrivateParmeterTypes(): import("./privacyFunctionReturnTypeDeclFile_Widgets").Widget1;
-export declare function publicFunctionWithPrivateParmeterTypes1(): import("GlobalWidgets").Widget3;
-export declare class publicClassWithPrivateModuleReturnTypes {
-    static myPublicStaticMethod(): import("./privacyFunctionReturnTypeDeclFile_Widgets").SpecializedWidget.Widget2;
-    myPublicMethod(): import("./privacyFunctionReturnTypeDeclFile_Widgets").SpecializedWidget.Widget2;
-    static myPublicStaticMethod1(): import("GlobalWidgets").SpecializedGlobalWidget.Widget4;
-    myPublicMethod1(): import("GlobalWidgets").SpecializedGlobalWidget.Widget4;
-}
-export declare function publicFunctionWithPrivateModuleReturnTypes(): import("./privacyFunctionReturnTypeDeclFile_Widgets").SpecializedWidget.Widget2;
-export declare function publicFunctionWithPrivateModuleReturnTypes1(): import("GlobalWidgets").SpecializedGlobalWidget.Widget4;
diff --git a/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithExport.errors.txt b/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithExport.errors.txt
index 87a5dd9508f92..101236868027b 100644
--- a/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithExport.errors.txt
+++ b/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithExport.errors.txt
@@ -1,12 +1,15 @@
+privacyTopLevelAmbientExternalModuleImportWithExport_core.ts(4,1): error TS18056: Declaration file contains synthesized file reference directives: '"privacyTopLevelAmbientExternalModuleImportWithExport_require2.d.ts", "privacyTopLevelAmbientExternalModuleImportWithExport_require3.d.ts"'
 privacyTopLevelAmbientExternalModuleImportWithExport_core.ts(15,12): error TS2323: Cannot redeclare exported variable 'publicUse_im_public_mi_public'.
 privacyTopLevelAmbientExternalModuleImportWithExport_core.ts(17,12): error TS2323: Cannot redeclare exported variable 'publicUse_im_public_mi_public'.
 
 
-==== privacyTopLevelAmbientExternalModuleImportWithExport_core.ts (2 errors) ====
+==== privacyTopLevelAmbientExternalModuleImportWithExport_core.ts (3 errors) ====
     ///<reference path='privacyTopLevelAmbientExternalModuleImportWithExport_require2.ts'/>
     ///<reference path='privacyTopLevelAmbientExternalModuleImportWithExport_require3.ts'/>
     // Privacy errors - importing private elements
     export import im_public_mi_private = require("./privacyTopLevelAmbientExternalModuleImportWithExport_require");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"privacyTopLevelAmbientExternalModuleImportWithExport_require2.d.ts", "privacyTopLevelAmbientExternalModuleImportWithExport_require3.d.ts"'
     export import im_public_mu_private = require("./privacyTopLevelAmbientExternalModuleImportWithExport_require1");
     export import im_public_mi_public = require("m");
     export import im_public_mu_public = require("m2");
diff --git a/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithExport.js b/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithExport.js
index eb5ea0ffad1b2..12219be59c180 100644
--- a/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithExport.js
+++ b/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithExport.js
@@ -113,14 +113,3 @@ export declare class c_public {
 export declare class c_public {
     bar: string;
 }
-//// [privacyTopLevelAmbientExternalModuleImportWithExport_core.d.ts]
-/// <reference path="privacyTopLevelAmbientExternalModuleImportWithExport_require2.d.ts" />
-/// <reference path="privacyTopLevelAmbientExternalModuleImportWithExport_require3.d.ts" />
-export import im_public_mi_private = require("./privacyTopLevelAmbientExternalModuleImportWithExport_require");
-export import im_public_mu_private = require("./privacyTopLevelAmbientExternalModuleImportWithExport_require1");
-export import im_public_mi_public = require("m");
-export import im_public_mu_public = require("m2");
-export declare var publicUse_im_public_mi_private: im_public_mi_private.c_public;
-export declare var publicUse_im_public_mu_private: im_public_mu_private.c_public;
-export declare var publicUse_im_public_mi_public: im_public_mi_public.c_private;
-export declare var publicUse_im_public_mi_public: im_public_mi_public.c_private;
diff --git a/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithoutExport.errors.txt b/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithoutExport.errors.txt
index 1ecaca60d6aa6..8ae7650e0c97a 100644
--- a/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithoutExport.errors.txt
+++ b/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithoutExport.errors.txt
@@ -1,12 +1,15 @@
+privacyTopLevelAmbientExternalModuleImportWithoutExport_core.ts(4,1): error TS18056: Declaration file contains synthesized file reference directives: '"privacyTopLevelAmbientExternalModuleImportWithoutExport_require2.d.ts", "privacyTopLevelAmbientExternalModuleImportWithoutExport_require3.d.ts"'
 privacyTopLevelAmbientExternalModuleImportWithoutExport_core.ts(15,12): error TS2323: Cannot redeclare exported variable 'publicUse_im_private_mi_public'.
 privacyTopLevelAmbientExternalModuleImportWithoutExport_core.ts(17,12): error TS2323: Cannot redeclare exported variable 'publicUse_im_private_mi_public'.
 
 
-==== privacyTopLevelAmbientExternalModuleImportWithoutExport_core.ts (2 errors) ====
+==== privacyTopLevelAmbientExternalModuleImportWithoutExport_core.ts (3 errors) ====
     ///<reference path='privacyTopLevelAmbientExternalModuleImportWithoutExport_require2.ts'/>
     ///<reference path='privacyTopLevelAmbientExternalModuleImportWithoutExport_require3.ts'/>
     // Privacy errors - importing private elements
     import im_private_mi_private = require("m");
+    ~~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"privacyTopLevelAmbientExternalModuleImportWithoutExport_require2.d.ts", "privacyTopLevelAmbientExternalModuleImportWithoutExport_require3.d.ts"'
     import im_private_mu_private = require("m2");
     import im_private_mi_public = require("privacyTopLevelAmbientExternalModuleImportWithoutExport_require");
     import im_private_mu_public = require("privacyTopLevelAmbientExternalModuleImportWithoutExport_require1");
diff --git a/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithoutExport.js b/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithoutExport.js
index eec9fa4a74fee..a9ba122889147 100644
--- a/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithoutExport.js
+++ b/tests/baselines/reference/privacyTopLevelAmbientExternalModuleImportWithoutExport.js
@@ -111,13 +111,3 @@ export declare class c_public {
 export declare class c_public {
     bar: string;
 }
-//// [privacyTopLevelAmbientExternalModuleImportWithoutExport_core.d.ts]
-/// <reference path="privacyTopLevelAmbientExternalModuleImportWithoutExport_require2.d.ts" />
-/// <reference path="privacyTopLevelAmbientExternalModuleImportWithoutExport_require3.d.ts" />
-import im_private_mi_private = require("m");
-import im_private_mu_private = require("m2");
-import im_private_mi_public = require("privacyTopLevelAmbientExternalModuleImportWithoutExport_require");
-export declare var publicUse_im_private_mi_private: im_private_mi_private.c_private;
-export declare var publicUse_im_private_mu_private: im_private_mu_private.c_private;
-export declare var publicUse_im_private_mi_public: im_private_mi_public.c_public;
-export declare var publicUse_im_private_mi_public: im_private_mi_public.c_public;
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/amd/mapRootAbsolutePathMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/amd/mapRootAbsolutePathMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/amd/mapRootAbsolutePathMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/amd/mapRootAbsolutePathMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/amd/mapRootAbsolutePathMixedSubfolderNoOutdir.json
index 1ab0b95ea404d..00204ef628a1d 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/amd/mapRootAbsolutePathMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/amd/mapRootAbsolutePathMixedSubfolderNoOutdir.json
@@ -25,7 +25,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/node/mapRootAbsolutePathMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/node/mapRootAbsolutePathMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/node/mapRootAbsolutePathMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/node/mapRootAbsolutePathMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/node/mapRootAbsolutePathMixedSubfolderNoOutdir.json
index 1ab0b95ea404d..00204ef628a1d 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/node/mapRootAbsolutePathMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderNoOutdir/node/mapRootAbsolutePathMixedSubfolderNoOutdir.json
@@ -25,7 +25,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json
index f2a9aeb56aa97..2fa89ce2f0a70 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json
@@ -26,7 +26,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json
index f2a9aeb56aa97..2fa89ce2f0a70 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json
@@ -26,7 +26,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/amd/mapRootAbsolutePathMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/amd/mapRootAbsolutePathMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/amd/mapRootAbsolutePathMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/amd/mapRootAbsolutePathMultifolderNoOutdir.json b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/amd/mapRootAbsolutePathMultifolderNoOutdir.json
index 1b941103759fb..2319d80db9602 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/amd/mapRootAbsolutePathMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/amd/mapRootAbsolutePathMultifolderNoOutdir.json
@@ -25,7 +25,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/node/mapRootAbsolutePathMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/node/mapRootAbsolutePathMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/node/mapRootAbsolutePathMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/node/mapRootAbsolutePathMultifolderNoOutdir.json b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/node/mapRootAbsolutePathMultifolderNoOutdir.json
index 1b941103759fb..2319d80db9602 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/node/mapRootAbsolutePathMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderNoOutdir/node/mapRootAbsolutePathMultifolderNoOutdir.json
@@ -25,7 +25,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.json
index 027ddf5273957..91735a9477bda 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.json
@@ -26,7 +26,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/node/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/node/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/node/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/node/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/node/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.json
index 027ddf5273957..91735a9477bda 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/node/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputDirectory/node/mapRootAbsolutePathMultifolderSpecifyOutputDirectory.json
@@ -26,7 +26,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputFile/amd/mapRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputFile/amd/mapRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
index a644c1c6d296d..d87bb0a33d8b0 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputFile/amd/mapRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputFile/amd/mapRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputFile/node/mapRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputFile/node/mapRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
index ec74fc9a4ee8d..dde665c17c0b4 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputFile/node/mapRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathMultifolderSpecifyOutputFile/node/mapRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/amd/mapRootAbsolutePathSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/amd/mapRootAbsolutePathSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/amd/mapRootAbsolutePathSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/amd/mapRootAbsolutePathSimpleNoOutdir.json b/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/amd/mapRootAbsolutePathSimpleNoOutdir.json
index 0de76b2a8a462..3420411131c50 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/amd/mapRootAbsolutePathSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/amd/mapRootAbsolutePathSimpleNoOutdir.json
@@ -21,7 +21,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/node/mapRootAbsolutePathSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/node/mapRootAbsolutePathSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/node/mapRootAbsolutePathSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/node/mapRootAbsolutePathSimpleNoOutdir.json b/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/node/mapRootAbsolutePathSimpleNoOutdir.json
index 0de76b2a8a462..3420411131c50 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/node/mapRootAbsolutePathSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSimpleNoOutdir/node/mapRootAbsolutePathSimpleNoOutdir.json
@@ -21,7 +21,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/amd/mapRootAbsolutePathSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/amd/mapRootAbsolutePathSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/amd/mapRootAbsolutePathSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/amd/mapRootAbsolutePathSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/amd/mapRootAbsolutePathSimpleSpecifyOutputDirectory.json
index 29953e63de0f7..a5a6ed8edcb48 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/amd/mapRootAbsolutePathSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/amd/mapRootAbsolutePathSimpleSpecifyOutputDirectory.json
@@ -22,7 +22,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/node/mapRootAbsolutePathSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/node/mapRootAbsolutePathSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/node/mapRootAbsolutePathSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/node/mapRootAbsolutePathSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/node/mapRootAbsolutePathSimpleSpecifyOutputDirectory.json
index 29953e63de0f7..a5a6ed8edcb48 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/node/mapRootAbsolutePathSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputDirectory/node/mapRootAbsolutePathSimpleSpecifyOutputDirectory.json
@@ -22,7 +22,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputFile/amd/mapRootAbsolutePathSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputFile/amd/mapRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
index 44fdc1b33985f..68a8fe34d4d59 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputFile/amd/mapRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputFile/amd/mapRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputFile/node/mapRootAbsolutePathSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputFile/node/mapRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
index a9a9b2cc4a371..694e41d780fed 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputFile/node/mapRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSimpleSpecifyOutputFile/node/mapRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/amd/mapRootAbsolutePathSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/amd/mapRootAbsolutePathSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/amd/mapRootAbsolutePathSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/amd/mapRootAbsolutePathSubfolderNoOutdir.json b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/amd/mapRootAbsolutePathSubfolderNoOutdir.json
index 148b2606c16d5..1de627430dd43 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/amd/mapRootAbsolutePathSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/amd/mapRootAbsolutePathSubfolderNoOutdir.json
@@ -21,7 +21,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/node/mapRootAbsolutePathSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/node/mapRootAbsolutePathSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/node/mapRootAbsolutePathSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/node/mapRootAbsolutePathSubfolderNoOutdir.json b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/node/mapRootAbsolutePathSubfolderNoOutdir.json
index 148b2606c16d5..1de627430dd43 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/node/mapRootAbsolutePathSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderNoOutdir/node/mapRootAbsolutePathSubfolderNoOutdir.json
@@ -21,7 +21,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.json
index 299c72fa3c9ee..db2ba9d746f6e 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.json
@@ -22,7 +22,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.json
index 299c72fa3c9ee..db2ba9d746f6e 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputDirectory/node/mapRootAbsolutePathSubfolderSpecifyOutputDirectory.json
@@ -22,7 +22,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
index 9d44caf58785e..f2efcd555ce88 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputFile/amd/mapRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputFile/node/mapRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputFile/node/mapRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
index 5b48bc2c2c178..938e038fd9114 100644
--- a/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputFile/node/mapRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootAbsolutePathSubfolderSpecifyOutputFile/node/mapRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/amd/mapRootRelativePathMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/amd/mapRootRelativePathMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/amd/mapRootRelativePathMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/amd/mapRootRelativePathMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/amd/mapRootRelativePathMixedSubfolderNoOutdir.json
index 5ed8625f1874e..2d141037cef7a 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/amd/mapRootRelativePathMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/amd/mapRootRelativePathMixedSubfolderNoOutdir.json
@@ -24,7 +24,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/node/mapRootRelativePathMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/node/mapRootRelativePathMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/node/mapRootRelativePathMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/node/mapRootRelativePathMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/node/mapRootRelativePathMixedSubfolderNoOutdir.json
index 5ed8625f1874e..2d141037cef7a 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/node/mapRootRelativePathMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderNoOutdir/node/mapRootRelativePathMixedSubfolderNoOutdir.json
@@ -24,7 +24,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.json
index 2936add88e5d8..133908cc395e7 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.json
index 2936add88e5d8..133908cc395e7 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFile/node/mapRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/mapRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/amd/mapRootRelativePathMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/amd/mapRootRelativePathMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/amd/mapRootRelativePathMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/amd/mapRootRelativePathMultifolderNoOutdir.json b/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/amd/mapRootRelativePathMultifolderNoOutdir.json
index fcff52e05e85a..d10185ec8acb6 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/amd/mapRootRelativePathMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/amd/mapRootRelativePathMultifolderNoOutdir.json
@@ -24,7 +24,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/node/mapRootRelativePathMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/node/mapRootRelativePathMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/node/mapRootRelativePathMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/node/mapRootRelativePathMultifolderNoOutdir.json b/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/node/mapRootRelativePathMultifolderNoOutdir.json
index fcff52e05e85a..d10185ec8acb6 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/node/mapRootRelativePathMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderNoOutdir/node/mapRootRelativePathMultifolderNoOutdir.json
@@ -24,7 +24,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/amd/mapRootRelativePathMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/amd/mapRootRelativePathMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/amd/mapRootRelativePathMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/amd/mapRootRelativePathMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/amd/mapRootRelativePathMultifolderSpecifyOutputDirectory.json
index 49302ac140810..d3986cc3d7c98 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/amd/mapRootRelativePathMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/amd/mapRootRelativePathMultifolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/node/mapRootRelativePathMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/node/mapRootRelativePathMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/node/mapRootRelativePathMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/node/mapRootRelativePathMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/node/mapRootRelativePathMultifolderSpecifyOutputDirectory.json
index 49302ac140810..d3986cc3d7c98 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/node/mapRootRelativePathMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputDirectory/node/mapRootRelativePathMultifolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/mapRootRelativePathMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/mapRootRelativePathMultifolderSpecifyOutputFile.errors.txt
index a644c1c6d296d..d87bb0a33d8b0 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/mapRootRelativePathMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/amd/mapRootRelativePathMultifolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/mapRootRelativePathMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/mapRootRelativePathMultifolderSpecifyOutputFile.errors.txt
index ec74fc9a4ee8d..dde665c17c0b4 100644
--- a/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/mapRootRelativePathMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathMultifolderSpecifyOutputFile/node/mapRootRelativePathMultifolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/amd/mapRootRelativePathSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/amd/mapRootRelativePathSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/amd/mapRootRelativePathSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/amd/mapRootRelativePathSimpleNoOutdir.json b/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/amd/mapRootRelativePathSimpleNoOutdir.json
index 778f5091ba142..d2931ce1c896b 100644
--- a/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/amd/mapRootRelativePathSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/amd/mapRootRelativePathSimpleNoOutdir.json
@@ -20,7 +20,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/node/mapRootRelativePathSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/node/mapRootRelativePathSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/node/mapRootRelativePathSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/node/mapRootRelativePathSimpleNoOutdir.json b/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/node/mapRootRelativePathSimpleNoOutdir.json
index 778f5091ba142..d2931ce1c896b 100644
--- a/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/node/mapRootRelativePathSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootRelativePathSimpleNoOutdir/node/mapRootRelativePathSimpleNoOutdir.json
@@ -20,7 +20,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/amd/mapRootRelativePathSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/amd/mapRootRelativePathSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/amd/mapRootRelativePathSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/amd/mapRootRelativePathSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/amd/mapRootRelativePathSimpleSpecifyOutputDirectory.json
index ffe4d88702961..02541a5232d2c 100644
--- a/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/amd/mapRootRelativePathSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/amd/mapRootRelativePathSimpleSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/node/mapRootRelativePathSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/node/mapRootRelativePathSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/node/mapRootRelativePathSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/node/mapRootRelativePathSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/node/mapRootRelativePathSimpleSpecifyOutputDirectory.json
index ffe4d88702961..02541a5232d2c 100644
--- a/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/node/mapRootRelativePathSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputDirectory/node/mapRootRelativePathSimpleSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputFile/amd/mapRootRelativePathSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputFile/amd/mapRootRelativePathSimpleSpecifyOutputFile.errors.txt
index 44fdc1b33985f..68a8fe34d4d59 100644
--- a/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputFile/amd/mapRootRelativePathSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputFile/amd/mapRootRelativePathSimpleSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputFile/node/mapRootRelativePathSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputFile/node/mapRootRelativePathSimpleSpecifyOutputFile.errors.txt
index a9a9b2cc4a371..694e41d780fed 100644
--- a/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputFile/node/mapRootRelativePathSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathSimpleSpecifyOutputFile/node/mapRootRelativePathSimpleSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/amd/mapRootRelativePathSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/amd/mapRootRelativePathSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/amd/mapRootRelativePathSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/amd/mapRootRelativePathSubfolderNoOutdir.json b/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/amd/mapRootRelativePathSubfolderNoOutdir.json
index e046c89c6fd7e..e2667a8055d75 100644
--- a/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/amd/mapRootRelativePathSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/amd/mapRootRelativePathSubfolderNoOutdir.json
@@ -20,7 +20,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/node/mapRootRelativePathSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/node/mapRootRelativePathSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/node/mapRootRelativePathSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/node/mapRootRelativePathSubfolderNoOutdir.json b/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/node/mapRootRelativePathSubfolderNoOutdir.json
index e046c89c6fd7e..e2667a8055d75 100644
--- a/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/node/mapRootRelativePathSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/mapRootRelativePathSubfolderNoOutdir/node/mapRootRelativePathSubfolderNoOutdir.json
@@ -20,7 +20,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathSubfolderSpecifyOutputDirectory.json
index 7a760aeed6e42..53762bdd4b095 100644
--- a/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/amd/mapRootRelativePathSubfolderSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/node/mapRootRelativePathSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/node/mapRootRelativePathSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/node/mapRootRelativePathSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/node/mapRootRelativePathSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/node/mapRootRelativePathSubfolderSpecifyOutputDirectory.json
index 7a760aeed6e42..53762bdd4b095 100644
--- a/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/node/mapRootRelativePathSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputDirectory/node/mapRootRelativePathSubfolderSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputFile/amd/mapRootRelativePathSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputFile/amd/mapRootRelativePathSubfolderSpecifyOutputFile.errors.txt
index 9d44caf58785e..f2efcd555ce88 100644
--- a/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputFile/amd/mapRootRelativePathSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputFile/amd/mapRootRelativePathSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputFile/node/mapRootRelativePathSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputFile/node/mapRootRelativePathSubfolderSpecifyOutputFile.errors.txt
index 5b48bc2c2c178..938e038fd9114 100644
--- a/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputFile/node/mapRootRelativePathSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/mapRootRelativePathSubfolderSpecifyOutputFile/node/mapRootRelativePathSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/amd/maprootUrlMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/amd/maprootUrlMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/amd/maprootUrlMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/amd/maprootUrlMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/amd/maprootUrlMixedSubfolderNoOutdir.json
index 28d5d8a562868..c1297c7aa10d0 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/amd/maprootUrlMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/amd/maprootUrlMixedSubfolderNoOutdir.json
@@ -24,7 +24,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/node/maprootUrlMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/node/maprootUrlMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/node/maprootUrlMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/node/maprootUrlMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/node/maprootUrlMixedSubfolderNoOutdir.json
index 28d5d8a562868..c1297c7aa10d0 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/node/maprootUrlMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderNoOutdir/node/maprootUrlMixedSubfolderNoOutdir.json
@@ -24,7 +24,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputDirectory.json
index ff578111c3dc9..e8f0e4ce45079 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputDirectory.json
index ff578111c3dc9..e8f0e4ce45079 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlMixedSubfolderSpecifyOutputFile.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/amd/maprootUrlMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/amd/maprootUrlMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/amd/maprootUrlMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/amd/maprootUrlMultifolderNoOutdir.json b/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/amd/maprootUrlMultifolderNoOutdir.json
index 37ab432cedcd3..4be71f404d37f 100644
--- a/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/amd/maprootUrlMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/amd/maprootUrlMultifolderNoOutdir.json
@@ -24,7 +24,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/node/maprootUrlMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/node/maprootUrlMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/node/maprootUrlMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/node/maprootUrlMultifolderNoOutdir.json b/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/node/maprootUrlMultifolderNoOutdir.json
index 37ab432cedcd3..4be71f404d37f 100644
--- a/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/node/maprootUrlMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlMultifolderNoOutdir/node/maprootUrlMultifolderNoOutdir.json
@@ -24,7 +24,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlMultifolderSpecifyOutputDirectory.json
index 0f75f10c07243..4080b891f4cb6 100644
--- a/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlMultifolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlMultifolderSpecifyOutputDirectory.json
index 0f75f10c07243..4080b891f4cb6 100644
--- a/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlMultifolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputFile/amd/maprootUrlMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputFile/amd/maprootUrlMultifolderSpecifyOutputFile.errors.txt
index a644c1c6d296d..d87bb0a33d8b0 100644
--- a/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputFile/amd/maprootUrlMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputFile/amd/maprootUrlMultifolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputFile/node/maprootUrlMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputFile/node/maprootUrlMultifolderSpecifyOutputFile.errors.txt
index ec74fc9a4ee8d..dde665c17c0b4 100644
--- a/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputFile/node/maprootUrlMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlMultifolderSpecifyOutputFile/node/maprootUrlMultifolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/amd/maprootUrlSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/amd/maprootUrlSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/amd/maprootUrlSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/amd/maprootUrlSimpleNoOutdir.json b/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/amd/maprootUrlSimpleNoOutdir.json
index da40b52a456f5..29e76410a041d 100644
--- a/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/amd/maprootUrlSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/amd/maprootUrlSimpleNoOutdir.json
@@ -20,7 +20,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/node/maprootUrlSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/node/maprootUrlSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/node/maprootUrlSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/node/maprootUrlSimpleNoOutdir.json b/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/node/maprootUrlSimpleNoOutdir.json
index da40b52a456f5..29e76410a041d 100644
--- a/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/node/maprootUrlSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlSimpleNoOutdir/node/maprootUrlSimpleNoOutdir.json
@@ -20,7 +20,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlSimpleSpecifyOutputDirectory.json
index f49e46054f146..eecb99565fc00 100644
--- a/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlSimpleSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/node/maprootUrlSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/node/maprootUrlSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/node/maprootUrlSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/node/maprootUrlSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/node/maprootUrlSimpleSpecifyOutputDirectory.json
index f49e46054f146..eecb99565fc00 100644
--- a/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/node/maprootUrlSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputDirectory/node/maprootUrlSimpleSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputFile/amd/maprootUrlSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputFile/amd/maprootUrlSimpleSpecifyOutputFile.errors.txt
index 44fdc1b33985f..68a8fe34d4d59 100644
--- a/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputFile/amd/maprootUrlSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputFile/amd/maprootUrlSimpleSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputFile/node/maprootUrlSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputFile/node/maprootUrlSimpleSpecifyOutputFile.errors.txt
index a9a9b2cc4a371..694e41d780fed 100644
--- a/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputFile/node/maprootUrlSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlSimpleSpecifyOutputFile/node/maprootUrlSimpleSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/amd/maprootUrlSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/amd/maprootUrlSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/amd/maprootUrlSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/amd/maprootUrlSubfolderNoOutdir.json b/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/amd/maprootUrlSubfolderNoOutdir.json
index 7e13b1db80f40..1154b899f4f71 100644
--- a/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/amd/maprootUrlSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/amd/maprootUrlSubfolderNoOutdir.json
@@ -20,7 +20,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/node/maprootUrlSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/node/maprootUrlSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/node/maprootUrlSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/node/maprootUrlSubfolderNoOutdir.json b/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/node/maprootUrlSubfolderNoOutdir.json
index 7e13b1db80f40..1154b899f4f71 100644
--- a/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/node/maprootUrlSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlSubfolderNoOutdir/node/maprootUrlSubfolderNoOutdir.json
@@ -20,7 +20,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlSubfolderSpecifyOutputDirectory.json
index f00776700f7f0..1c7cc4f38ebb7 100644
--- a/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlSubfolderSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlSubfolderSpecifyOutputDirectory.json
index f00776700f7f0..1c7cc4f38ebb7 100644
--- a/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlSubfolderSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputFile/amd/maprootUrlSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputFile/amd/maprootUrlSubfolderSpecifyOutputFile.errors.txt
index 9d44caf58785e..f2efcd555ce88 100644
--- a/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputFile/amd/maprootUrlSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputFile/amd/maprootUrlSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputFile/node/maprootUrlSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputFile/node/maprootUrlSubfolderSpecifyOutputFile.errors.txt
index 5b48bc2c2c178..938e038fd9114 100644
--- a/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputFile/node/maprootUrlSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlSubfolderSpecifyOutputFile/node/maprootUrlSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/amd/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/amd/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/amd/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/amd/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/amd/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.json
index e1c0360c2a4ad..a162048521c3e 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/amd/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/amd/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.json
@@ -25,7 +25,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/node/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/node/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/node/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/node/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/node/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.json
index e1c0360c2a4ad..a162048521c3e 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/node/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderNoOutdir/node/maprootUrlsourcerootUrlMixedSubfolderNoOutdir.json
@@ -25,7 +25,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.json
index 90a87d8a5064b..7e73bc72a2996 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.json
@@ -26,7 +26,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.json
index 90a87d8a5064b..7e73bc72a2996 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputDirectory.json
@@ -26,7 +26,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/maprootUrlsourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/amd/maprootUrlsourcerootUrlMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/amd/maprootUrlsourcerootUrlMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/amd/maprootUrlsourcerootUrlMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/amd/maprootUrlsourcerootUrlMultifolderNoOutdir.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/amd/maprootUrlsourcerootUrlMultifolderNoOutdir.json
index efc6778bfc8bd..8504f5397b51d 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/amd/maprootUrlsourcerootUrlMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/amd/maprootUrlsourcerootUrlMultifolderNoOutdir.json
@@ -25,7 +25,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/node/maprootUrlsourcerootUrlMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/node/maprootUrlsourcerootUrlMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/node/maprootUrlsourcerootUrlMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/node/maprootUrlsourcerootUrlMultifolderNoOutdir.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/node/maprootUrlsourcerootUrlMultifolderNoOutdir.json
index efc6778bfc8bd..8504f5397b51d 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/node/maprootUrlsourcerootUrlMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderNoOutdir/node/maprootUrlsourcerootUrlMultifolderNoOutdir.json
@@ -25,7 +25,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.json
index 8c703fa5ccc6d..d6b40778cc999 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.json
@@ -26,7 +26,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.json
index 8c703fa5ccc6d..d6b40778cc999 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputDirectory.json
@@ -26,7 +26,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile.errors.txt
index a644c1c6d296d..d87bb0a33d8b0 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile.errors.txt
index ec74fc9a4ee8d..dde665c17c0b4 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile/node/maprootUrlsourcerootUrlMultifolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/amd/maprootUrlsourcerootUrlSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/amd/maprootUrlsourcerootUrlSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/amd/maprootUrlsourcerootUrlSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/amd/maprootUrlsourcerootUrlSimpleNoOutdir.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/amd/maprootUrlsourcerootUrlSimpleNoOutdir.json
index 458e16811a45f..e06df12d686eb 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/amd/maprootUrlsourcerootUrlSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/amd/maprootUrlsourcerootUrlSimpleNoOutdir.json
@@ -21,7 +21,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/node/maprootUrlsourcerootUrlSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/node/maprootUrlsourcerootUrlSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/node/maprootUrlsourcerootUrlSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/node/maprootUrlsourcerootUrlSimpleNoOutdir.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/node/maprootUrlsourcerootUrlSimpleNoOutdir.json
index 458e16811a45f..e06df12d686eb 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/node/maprootUrlsourcerootUrlSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleNoOutdir/node/maprootUrlsourcerootUrlSimpleNoOutdir.json
@@ -21,7 +21,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.json
index d4302e162b5d7..f4ff1d2bad03f 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.json
@@ -22,7 +22,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.json
index d4302e162b5d7..f4ff1d2bad03f 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSimpleSpecifyOutputDirectory.json
@@ -22,7 +22,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputFile/amd/maprootUrlsourcerootUrlSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputFile/amd/maprootUrlsourcerootUrlSimpleSpecifyOutputFile.errors.txt
index 44fdc1b33985f..68a8fe34d4d59 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputFile/amd/maprootUrlsourcerootUrlSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputFile/amd/maprootUrlsourcerootUrlSimpleSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlSimpleSpecifyOutputFile.errors.txt
index a9a9b2cc4a371..694e41d780fed 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSimpleSpecifyOutputFile/node/maprootUrlsourcerootUrlSimpleSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/amd/maprootUrlsourcerootUrlSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/amd/maprootUrlsourcerootUrlSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/amd/maprootUrlsourcerootUrlSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/amd/maprootUrlsourcerootUrlSubfolderNoOutdir.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/amd/maprootUrlsourcerootUrlSubfolderNoOutdir.json
index d0db93b829613..b5cc654e24579 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/amd/maprootUrlsourcerootUrlSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/amd/maprootUrlsourcerootUrlSubfolderNoOutdir.json
@@ -21,7 +21,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/node/maprootUrlsourcerootUrlSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/node/maprootUrlsourcerootUrlSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/node/maprootUrlsourcerootUrlSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/node/maprootUrlsourcerootUrlSubfolderNoOutdir.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/node/maprootUrlsourcerootUrlSubfolderNoOutdir.json
index d0db93b829613..b5cc654e24579 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/node/maprootUrlsourcerootUrlSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderNoOutdir/node/maprootUrlsourcerootUrlSubfolderNoOutdir.json
@@ -21,7 +21,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.json
index 0b4f7b711a761..651fc8f23614e 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/amd/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.json
@@ -22,7 +22,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.json
index 0b4f7b711a761..651fc8f23614e 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputDirectory.json
@@ -22,7 +22,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile.errors.txt
index 9d44caf58785e..f2efcd555ce88 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile/amd/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile.errors.txt
index 5b48bc2c2c178..938e038fd9114 100644
--- a/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile/node/maprootUrlsourcerootUrlSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/outMixedSubfolderNoOutdir/amd/outMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/outMixedSubfolderNoOutdir/amd/outMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/outMixedSubfolderNoOutdir/amd/outMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMixedSubfolderNoOutdir/amd/outMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/outMixedSubfolderNoOutdir/amd/outMixedSubfolderNoOutdir.json
index 8c7a98f959c01..3ff43142d269f 100644
--- a/tests/baselines/reference/project/outMixedSubfolderNoOutdir/amd/outMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/outMixedSubfolderNoOutdir/amd/outMixedSubfolderNoOutdir.json
@@ -19,7 +19,6 @@
         "ref/m1.d.ts",
         "ref/m2.js",
         "ref/m2.d.ts",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMixedSubfolderNoOutdir/node/outMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/outMixedSubfolderNoOutdir/node/outMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/outMixedSubfolderNoOutdir/node/outMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMixedSubfolderNoOutdir/node/outMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/outMixedSubfolderNoOutdir/node/outMixedSubfolderNoOutdir.json
index 8c7a98f959c01..3ff43142d269f 100644
--- a/tests/baselines/reference/project/outMixedSubfolderNoOutdir/node/outMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/outMixedSubfolderNoOutdir/node/outMixedSubfolderNoOutdir.json
@@ -19,7 +19,6 @@
         "ref/m1.d.ts",
         "ref/m2.js",
         "ref/m2.d.ts",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/amd/outMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/amd/outMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/amd/outMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/amd/outMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/amd/outMixedSubfolderSpecifyOutputDirectory.json
index 3852d0dd2148e..e9f28b425459e 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/amd/outMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/amd/outMixedSubfolderSpecifyOutputDirectory.json
@@ -20,7 +20,6 @@
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/node/outMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/node/outMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/node/outMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/node/outMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/node/outMixedSubfolderSpecifyOutputDirectory.json
index 3852d0dd2148e..e9f28b425459e 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/node/outMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputDirectory/node/outMixedSubfolderSpecifyOutputDirectory.json
@@ -20,7 +20,6 @@
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/outMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/outMixedSubfolderSpecifyOutputFile.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/outMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/amd/outMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/outMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/outMixedSubfolderSpecifyOutputFile.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/outMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFile/node/outMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/outMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/outMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/outMultifolderNoOutdir/amd/outMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/outMultifolderNoOutdir/amd/outMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/outMultifolderNoOutdir/amd/outMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMultifolderNoOutdir/amd/outMultifolderNoOutdir.json b/tests/baselines/reference/project/outMultifolderNoOutdir/amd/outMultifolderNoOutdir.json
index 60b2a61bf94d9..b6b2d816fdca6 100644
--- a/tests/baselines/reference/project/outMultifolderNoOutdir/amd/outMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/outMultifolderNoOutdir/amd/outMultifolderNoOutdir.json
@@ -19,7 +19,6 @@
         "ref/m1.d.ts",
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMultifolderNoOutdir/node/outMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/outMultifolderNoOutdir/node/outMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/outMultifolderNoOutdir/node/outMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMultifolderNoOutdir/node/outMultifolderNoOutdir.json b/tests/baselines/reference/project/outMultifolderNoOutdir/node/outMultifolderNoOutdir.json
index 60b2a61bf94d9..b6b2d816fdca6 100644
--- a/tests/baselines/reference/project/outMultifolderNoOutdir/node/outMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/outMultifolderNoOutdir/node/outMultifolderNoOutdir.json
@@ -19,7 +19,6 @@
         "ref/m1.d.ts",
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/amd/outMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/amd/outMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/amd/outMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/amd/outMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/amd/outMultifolderSpecifyOutputDirectory.json
index 9eb7aecbcf907..b7a5b0de449e6 100644
--- a/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/amd/outMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/amd/outMultifolderSpecifyOutputDirectory.json
@@ -20,7 +20,6 @@
         "outdir/simple/outputdir_multifolder/ref/m1.d.ts",
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/node/outMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/node/outMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/node/outMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/node/outMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/node/outMultifolderSpecifyOutputDirectory.json
index 9eb7aecbcf907..b7a5b0de449e6 100644
--- a/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/node/outMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/outMultifolderSpecifyOutputDirectory/node/outMultifolderSpecifyOutputDirectory.json
@@ -20,7 +20,6 @@
         "outdir/simple/outputdir_multifolder/ref/m1.d.ts",
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outMultifolderSpecifyOutputFile/amd/outMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outMultifolderSpecifyOutputFile/amd/outMultifolderSpecifyOutputFile.errors.txt
index a644c1c6d296d..d87bb0a33d8b0 100644
--- a/tests/baselines/reference/project/outMultifolderSpecifyOutputFile/amd/outMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/outMultifolderSpecifyOutputFile/amd/outMultifolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/outMultifolderSpecifyOutputFile/node/outMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outMultifolderSpecifyOutputFile/node/outMultifolderSpecifyOutputFile.errors.txt
index ec74fc9a4ee8d..dde665c17c0b4 100644
--- a/tests/baselines/reference/project/outMultifolderSpecifyOutputFile/node/outMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/outMultifolderSpecifyOutputFile/node/outMultifolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/outSimpleNoOutdir/amd/outSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/outSimpleNoOutdir/amd/outSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/outSimpleNoOutdir/amd/outSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSimpleNoOutdir/amd/outSimpleNoOutdir.json b/tests/baselines/reference/project/outSimpleNoOutdir/amd/outSimpleNoOutdir.json
index 09b9c2f1b2c7f..47b5cc9015ce4 100644
--- a/tests/baselines/reference/project/outSimpleNoOutdir/amd/outSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/outSimpleNoOutdir/amd/outSimpleNoOutdir.json
@@ -16,7 +16,6 @@
     "emittedFiles": [
         "m1.js",
         "m1.d.ts",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSimpleNoOutdir/node/outSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/outSimpleNoOutdir/node/outSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/outSimpleNoOutdir/node/outSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSimpleNoOutdir/node/outSimpleNoOutdir.json b/tests/baselines/reference/project/outSimpleNoOutdir/node/outSimpleNoOutdir.json
index 09b9c2f1b2c7f..47b5cc9015ce4 100644
--- a/tests/baselines/reference/project/outSimpleNoOutdir/node/outSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/outSimpleNoOutdir/node/outSimpleNoOutdir.json
@@ -16,7 +16,6 @@
     "emittedFiles": [
         "m1.js",
         "m1.d.ts",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/amd/outSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/amd/outSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/amd/outSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/amd/outSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/amd/outSimpleSpecifyOutputDirectory.json
index a378c869c6997..60db9a934a146 100644
--- a/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/amd/outSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/amd/outSimpleSpecifyOutputDirectory.json
@@ -17,7 +17,6 @@
     "emittedFiles": [
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/node/outSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/node/outSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/node/outSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/node/outSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/node/outSimpleSpecifyOutputDirectory.json
index a378c869c6997..60db9a934a146 100644
--- a/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/node/outSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/outSimpleSpecifyOutputDirectory/node/outSimpleSpecifyOutputDirectory.json
@@ -17,7 +17,6 @@
     "emittedFiles": [
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSimpleSpecifyOutputFile/amd/outSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outSimpleSpecifyOutputFile/amd/outSimpleSpecifyOutputFile.errors.txt
index 44fdc1b33985f..68a8fe34d4d59 100644
--- a/tests/baselines/reference/project/outSimpleSpecifyOutputFile/amd/outSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/outSimpleSpecifyOutputFile/amd/outSimpleSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/outSimpleSpecifyOutputFile/node/outSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outSimpleSpecifyOutputFile/node/outSimpleSpecifyOutputFile.errors.txt
index a9a9b2cc4a371..694e41d780fed 100644
--- a/tests/baselines/reference/project/outSimpleSpecifyOutputFile/node/outSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/outSimpleSpecifyOutputFile/node/outSimpleSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/outSubfolderNoOutdir/amd/outSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/outSubfolderNoOutdir/amd/outSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/outSubfolderNoOutdir/amd/outSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSubfolderNoOutdir/amd/outSubfolderNoOutdir.json b/tests/baselines/reference/project/outSubfolderNoOutdir/amd/outSubfolderNoOutdir.json
index 5b54aaad20c5e..48c63551640c3 100644
--- a/tests/baselines/reference/project/outSubfolderNoOutdir/amd/outSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/outSubfolderNoOutdir/amd/outSubfolderNoOutdir.json
@@ -16,7 +16,6 @@
     "emittedFiles": [
         "ref/m1.js",
         "ref/m1.d.ts",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSubfolderNoOutdir/node/outSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/outSubfolderNoOutdir/node/outSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/outSubfolderNoOutdir/node/outSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSubfolderNoOutdir/node/outSubfolderNoOutdir.json b/tests/baselines/reference/project/outSubfolderNoOutdir/node/outSubfolderNoOutdir.json
index 5b54aaad20c5e..48c63551640c3 100644
--- a/tests/baselines/reference/project/outSubfolderNoOutdir/node/outSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/outSubfolderNoOutdir/node/outSubfolderNoOutdir.json
@@ -16,7 +16,6 @@
     "emittedFiles": [
         "ref/m1.js",
         "ref/m1.d.ts",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/amd/outSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/amd/outSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/amd/outSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/amd/outSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/amd/outSubfolderSpecifyOutputDirectory.json
index 61a8efaf3f303..6dc4e605567f8 100644
--- a/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/amd/outSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/amd/outSubfolderSpecifyOutputDirectory.json
@@ -17,7 +17,6 @@
     "emittedFiles": [
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/node/outSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/node/outSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/node/outSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/node/outSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/node/outSubfolderSpecifyOutputDirectory.json
index 61a8efaf3f303..6dc4e605567f8 100644
--- a/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/node/outSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/outSubfolderSpecifyOutputDirectory/node/outSubfolderSpecifyOutputDirectory.json
@@ -17,7 +17,6 @@
     "emittedFiles": [
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/outSubfolderSpecifyOutputFile/amd/outSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outSubfolderSpecifyOutputFile/amd/outSubfolderSpecifyOutputFile.errors.txt
index 9d44caf58785e..f2efcd555ce88 100644
--- a/tests/baselines/reference/project/outSubfolderSpecifyOutputFile/amd/outSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/outSubfolderSpecifyOutputFile/amd/outSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/outSubfolderSpecifyOutputFile/node/outSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/outSubfolderSpecifyOutputFile/node/outSubfolderSpecifyOutputFile.errors.txt
index 5b48bc2c2c178..938e038fd9114 100644
--- a/tests/baselines/reference/project/outSubfolderSpecifyOutputFile/node/outSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/outSubfolderSpecifyOutputFile/node/outSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/quotesInFileAndDirectoryNames/amd/quotesInFileAndDirectoryNames.errors.txt b/tests/baselines/reference/project/quotesInFileAndDirectoryNames/amd/quotesInFileAndDirectoryNames.errors.txt
new file mode 100644
index 0000000000000..947babca48155
--- /dev/null
+++ b/tests/baselines/reference/project/quotesInFileAndDirectoryNames/amd/quotesInFileAndDirectoryNames.errors.txt
@@ -0,0 +1,20 @@
+m'ain.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"li'b/class'A.d.ts"'
+m'ain.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"li'b/class'A.d.ts"'
+
+
+==== li'b/class'A.ts (0 errors) ====
+    module test {
+        export class ClassA
+        {
+            public method() { }
+        }
+    }
+==== m'ain.ts (2 errors) ====
+    /// <reference path="li'b/class'A.ts" />
+    
+    class ClassC extends test.ClassA {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"li'b/class'A.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"li'b/class'A.d.ts"'
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/quotesInFileAndDirectoryNames/amd/quotesInFileAndDirectoryNames.json b/tests/baselines/reference/project/quotesInFileAndDirectoryNames/amd/quotesInFileAndDirectoryNames.json
index 94f1eb4843501..c2a08f9811f11 100644
--- a/tests/baselines/reference/project/quotesInFileAndDirectoryNames/amd/quotesInFileAndDirectoryNames.json
+++ b/tests/baselines/reference/project/quotesInFileAndDirectoryNames/amd/quotesInFileAndDirectoryNames.json
@@ -16,7 +16,6 @@
     "emittedFiles": [
         "li'b/class'A.js",
         "li'b/class'A.d.ts",
-        "m'ain.js",
-        "m'ain.d.ts"
+        "m'ain.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/quotesInFileAndDirectoryNames/node/quotesInFileAndDirectoryNames.errors.txt b/tests/baselines/reference/project/quotesInFileAndDirectoryNames/node/quotesInFileAndDirectoryNames.errors.txt
new file mode 100644
index 0000000000000..947babca48155
--- /dev/null
+++ b/tests/baselines/reference/project/quotesInFileAndDirectoryNames/node/quotesInFileAndDirectoryNames.errors.txt
@@ -0,0 +1,20 @@
+m'ain.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"li'b/class'A.d.ts"'
+m'ain.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"li'b/class'A.d.ts"'
+
+
+==== li'b/class'A.ts (0 errors) ====
+    module test {
+        export class ClassA
+        {
+            public method() { }
+        }
+    }
+==== m'ain.ts (2 errors) ====
+    /// <reference path="li'b/class'A.ts" />
+    
+    class ClassC extends test.ClassA {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"li'b/class'A.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"li'b/class'A.d.ts"'
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/quotesInFileAndDirectoryNames/node/quotesInFileAndDirectoryNames.json b/tests/baselines/reference/project/quotesInFileAndDirectoryNames/node/quotesInFileAndDirectoryNames.json
index 94f1eb4843501..c2a08f9811f11 100644
--- a/tests/baselines/reference/project/quotesInFileAndDirectoryNames/node/quotesInFileAndDirectoryNames.json
+++ b/tests/baselines/reference/project/quotesInFileAndDirectoryNames/node/quotesInFileAndDirectoryNames.json
@@ -16,7 +16,6 @@
     "emittedFiles": [
         "li'b/class'A.js",
         "li'b/class'A.d.ts",
-        "m'ain.js",
-        "m'ain.d.ts"
+        "m'ain.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/referenceResolutionRelativePaths/amd/referenceResolutionRelativePaths.errors.txt b/tests/baselines/reference/project/referenceResolutionRelativePaths/amd/referenceResolutionRelativePaths.errors.txt
new file mode 100644
index 0000000000000..c8736af93b15b
--- /dev/null
+++ b/tests/baselines/reference/project/referenceResolutionRelativePaths/amd/referenceResolutionRelativePaths.errors.txt
@@ -0,0 +1,24 @@
+../../../bar/bar.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+../../../bar/bar.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+foo.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+foo.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+
+
+==== ../../../bar/bar.ts (2 errors) ====
+    /// <reference path="../src/ts/foo/foo.ts" />
+    // This is bar.ts
+    class bar {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+    }
+==== foo.ts (2 errors) ====
+    /// <reference path="../../../bar/bar.ts" />
+    
+    class foo {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/referenceResolutionRelativePaths/amd/referenceResolutionRelativePaths.json b/tests/baselines/reference/project/referenceResolutionRelativePaths/amd/referenceResolutionRelativePaths.json
index 129ce13db40ea..25e9d74822fcc 100644
--- a/tests/baselines/reference/project/referenceResolutionRelativePaths/amd/referenceResolutionRelativePaths.json
+++ b/tests/baselines/reference/project/referenceResolutionRelativePaths/amd/referenceResolutionRelativePaths.json
@@ -15,8 +15,6 @@
     ],
     "emittedFiles": [
         "../../../bar/bar.js",
-        "../../../bar/bar.d.ts",
-        "foo.js",
-        "foo.d.ts"
+        "foo.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/referenceResolutionRelativePaths/node/referenceResolutionRelativePaths.errors.txt b/tests/baselines/reference/project/referenceResolutionRelativePaths/node/referenceResolutionRelativePaths.errors.txt
new file mode 100644
index 0000000000000..c8736af93b15b
--- /dev/null
+++ b/tests/baselines/reference/project/referenceResolutionRelativePaths/node/referenceResolutionRelativePaths.errors.txt
@@ -0,0 +1,24 @@
+../../../bar/bar.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+../../../bar/bar.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+foo.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+foo.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+
+
+==== ../../../bar/bar.ts (2 errors) ====
+    /// <reference path="../src/ts/foo/foo.ts" />
+    // This is bar.ts
+    class bar {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+    }
+==== foo.ts (2 errors) ====
+    /// <reference path="../../../bar/bar.ts" />
+    
+    class foo {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/referenceResolutionRelativePaths/node/referenceResolutionRelativePaths.json b/tests/baselines/reference/project/referenceResolutionRelativePaths/node/referenceResolutionRelativePaths.json
index 129ce13db40ea..25e9d74822fcc 100644
--- a/tests/baselines/reference/project/referenceResolutionRelativePaths/node/referenceResolutionRelativePaths.json
+++ b/tests/baselines/reference/project/referenceResolutionRelativePaths/node/referenceResolutionRelativePaths.json
@@ -15,8 +15,6 @@
     ],
     "emittedFiles": [
         "../../../bar/bar.js",
-        "../../../bar/bar.d.ts",
-        "foo.js",
-        "foo.d.ts"
+        "foo.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/amd/referenceResolutionRelativePathsFromRootDirectory.errors.txt b/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/amd/referenceResolutionRelativePathsFromRootDirectory.errors.txt
new file mode 100644
index 0000000000000..d4ef192844ad0
--- /dev/null
+++ b/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/amd/referenceResolutionRelativePathsFromRootDirectory.errors.txt
@@ -0,0 +1,24 @@
+bar/bar.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+bar/bar.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+src/ts/foo/foo.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+src/ts/foo/foo.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+
+
+==== bar/bar.ts (2 errors) ====
+    /// <reference path="../src/ts/foo/foo.ts" />
+    // This is bar.ts
+    class bar {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+    }
+==== src/ts/foo/foo.ts (2 errors) ====
+    /// <reference path="../../../bar/bar.ts" />
+    
+    class foo {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/amd/referenceResolutionRelativePathsFromRootDirectory.json b/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/amd/referenceResolutionRelativePathsFromRootDirectory.json
index c443a64e1df3f..3885b75e2e5ce 100644
--- a/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/amd/referenceResolutionRelativePathsFromRootDirectory.json
+++ b/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/amd/referenceResolutionRelativePathsFromRootDirectory.json
@@ -15,8 +15,6 @@
     ],
     "emittedFiles": [
         "bar/bar.js",
-        "bar/bar.d.ts",
-        "src/ts/foo/foo.js",
-        "src/ts/foo/foo.d.ts"
+        "src/ts/foo/foo.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/node/referenceResolutionRelativePathsFromRootDirectory.errors.txt b/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/node/referenceResolutionRelativePathsFromRootDirectory.errors.txt
new file mode 100644
index 0000000000000..d4ef192844ad0
--- /dev/null
+++ b/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/node/referenceResolutionRelativePathsFromRootDirectory.errors.txt
@@ -0,0 +1,24 @@
+bar/bar.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+bar/bar.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+src/ts/foo/foo.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+src/ts/foo/foo.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+
+
+==== bar/bar.ts (2 errors) ====
+    /// <reference path="../src/ts/foo/foo.ts" />
+    // This is bar.ts
+    class bar {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+    }
+==== src/ts/foo/foo.ts (2 errors) ====
+    /// <reference path="../../../bar/bar.ts" />
+    
+    class foo {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/node/referenceResolutionRelativePathsFromRootDirectory.json b/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/node/referenceResolutionRelativePathsFromRootDirectory.json
index c443a64e1df3f..3885b75e2e5ce 100644
--- a/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/node/referenceResolutionRelativePathsFromRootDirectory.json
+++ b/tests/baselines/reference/project/referenceResolutionRelativePathsFromRootDirectory/node/referenceResolutionRelativePathsFromRootDirectory.json
@@ -15,8 +15,6 @@
     ],
     "emittedFiles": [
         "bar/bar.js",
-        "bar/bar.d.ts",
-        "src/ts/foo/foo.js",
-        "src/ts/foo/foo.d.ts"
+        "src/ts/foo/foo.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/amd/referenceResolutionRelativePathsRelativeToRootDirectory.errors.txt b/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/amd/referenceResolutionRelativePathsRelativeToRootDirectory.errors.txt
new file mode 100644
index 0000000000000..3afbf39d21b3a
--- /dev/null
+++ b/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/amd/referenceResolutionRelativePathsRelativeToRootDirectory.errors.txt
@@ -0,0 +1,24 @@
+../../../bar/bar.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+../../../bar/bar.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+../../../src/ts/foo/foo.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+../../../src/ts/foo/foo.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+
+
+==== ../../../bar/bar.ts (2 errors) ====
+    /// <reference path="../src/ts/foo/foo.ts" />
+    // This is bar.ts
+    class bar {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+    }
+==== ../../../src/ts/foo/foo.ts (2 errors) ====
+    /// <reference path="../../../bar/bar.ts" />
+    
+    class foo {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/amd/referenceResolutionRelativePathsRelativeToRootDirectory.json b/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/amd/referenceResolutionRelativePathsRelativeToRootDirectory.json
index 1cefdbe7921bf..4f5f8d0fe675e 100644
--- a/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/amd/referenceResolutionRelativePathsRelativeToRootDirectory.json
+++ b/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/amd/referenceResolutionRelativePathsRelativeToRootDirectory.json
@@ -15,8 +15,6 @@
     ],
     "emittedFiles": [
         "../../../bar/bar.js",
-        "../../../bar/bar.d.ts",
-        "../../../src/ts/foo/foo.js",
-        "../../../src/ts/foo/foo.d.ts"
+        "../../../src/ts/foo/foo.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/node/referenceResolutionRelativePathsRelativeToRootDirectory.errors.txt b/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/node/referenceResolutionRelativePathsRelativeToRootDirectory.errors.txt
new file mode 100644
index 0000000000000..3afbf39d21b3a
--- /dev/null
+++ b/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/node/referenceResolutionRelativePathsRelativeToRootDirectory.errors.txt
@@ -0,0 +1,24 @@
+../../../bar/bar.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+../../../bar/bar.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+../../../src/ts/foo/foo.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+../../../src/ts/foo/foo.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+
+
+==== ../../../bar/bar.ts (2 errors) ====
+    /// <reference path="../src/ts/foo/foo.ts" />
+    // This is bar.ts
+    class bar {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../src/ts/foo/foo.d.ts"'
+    }
+==== ../../../src/ts/foo/foo.ts (2 errors) ====
+    /// <reference path="../../../bar/bar.ts" />
+    
+    class foo {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../../bar/bar.d.ts"'
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/node/referenceResolutionRelativePathsRelativeToRootDirectory.json b/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/node/referenceResolutionRelativePathsRelativeToRootDirectory.json
index 1cefdbe7921bf..4f5f8d0fe675e 100644
--- a/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/node/referenceResolutionRelativePathsRelativeToRootDirectory.json
+++ b/tests/baselines/reference/project/referenceResolutionRelativePathsRelativeToRootDirectory/node/referenceResolutionRelativePathsRelativeToRootDirectory.json
@@ -15,8 +15,6 @@
     ],
     "emittedFiles": [
         "../../../bar/bar.js",
-        "../../../bar/bar.d.ts",
-        "../../../src/ts/foo/foo.js",
-        "../../../src/ts/foo/foo.d.ts"
+        "../../../src/ts/foo/foo.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/amd/rootDirectory.errors.txt b/tests/baselines/reference/project/rootDirectory/amd/rootDirectory.errors.txt
new file mode 100644
index 0000000000000..dad0b95b8bbe6
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/amd/rootDirectory.errors.txt
@@ -0,0 +1,18 @@
+FolderA/FolderB/fileB.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"FolderC/fileC.d.ts"'
+FolderA/FolderB/fileB.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"FolderC/fileC.d.ts"'
+
+
+==== FolderA/FolderB/FolderC/fileC.ts (0 errors) ====
+    class C {
+    }
+    
+==== FolderA/FolderB/fileB.ts (2 errors) ====
+    /// <reference path='FolderC/fileC.ts'/>
+    class B {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"FolderC/fileC.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"FolderC/fileC.d.ts"'
+        public c: C;
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/amd/rootDirectory.json b/tests/baselines/reference/project/rootDirectory/amd/rootDirectory.json
index 96ae34f24c745..614487f073bb6 100644
--- a/tests/baselines/reference/project/rootDirectory/amd/rootDirectory.json
+++ b/tests/baselines/reference/project/rootDirectory/amd/rootDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/FolderB/FolderC/fileC.js",
         "outdir/simple/FolderB/FolderC/fileC.d.ts",
         "outdir/simple/FolderB/fileB.js.map",
-        "outdir/simple/FolderB/fileB.js",
-        "outdir/simple/FolderB/fileB.d.ts"
+        "outdir/simple/FolderB/fileB.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/node/rootDirectory.errors.txt b/tests/baselines/reference/project/rootDirectory/node/rootDirectory.errors.txt
new file mode 100644
index 0000000000000..dad0b95b8bbe6
--- /dev/null
+++ b/tests/baselines/reference/project/rootDirectory/node/rootDirectory.errors.txt
@@ -0,0 +1,18 @@
+FolderA/FolderB/fileB.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"FolderC/fileC.d.ts"'
+FolderA/FolderB/fileB.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"FolderC/fileC.d.ts"'
+
+
+==== FolderA/FolderB/FolderC/fileC.ts (0 errors) ====
+    class C {
+    }
+    
+==== FolderA/FolderB/fileB.ts (2 errors) ====
+    /// <reference path='FolderC/fileC.ts'/>
+    class B {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"FolderC/fileC.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"FolderC/fileC.d.ts"'
+        public c: C;
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectory/node/rootDirectory.json b/tests/baselines/reference/project/rootDirectory/node/rootDirectory.json
index 96ae34f24c745..614487f073bb6 100644
--- a/tests/baselines/reference/project/rootDirectory/node/rootDirectory.json
+++ b/tests/baselines/reference/project/rootDirectory/node/rootDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/FolderB/FolderC/fileC.js",
         "outdir/simple/FolderB/FolderC/fileC.d.ts",
         "outdir/simple/FolderB/fileB.js.map",
-        "outdir/simple/FolderB/fileB.js",
-        "outdir/simple/FolderB/fileB.d.ts"
+        "outdir/simple/FolderB/fileB.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.errors.txt b/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.errors.txt
index 4e3492c206fdb..5e3c427a9f26a 100644
--- a/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.errors.txt
+++ b/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.errors.txt
@@ -1,6 +1,8 @@
 error TS6059: File 'FolderA/FolderB/fileB.ts' is not under 'rootDir' 'FolderA/FolderB/FolderC'. 'rootDir' is expected to contain all source files.
   The file is in the program because:
     Root file specified for compilation
+FolderA/FolderB/fileB.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../outdir/simple/fileC.d.ts"'
+FolderA/FolderB/fileB.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../outdir/simple/fileC.d.ts"'
 
 
 !!! error TS6059: File 'FolderA/FolderB/fileB.ts' is not under 'rootDir' 'FolderA/FolderB/FolderC'. 'rootDir' is expected to contain all source files.
@@ -10,9 +12,13 @@ error TS6059: File 'FolderA/FolderB/fileB.ts' is not under 'rootDir' 'FolderA/Fo
     class C {
     }
     
-==== FolderA/FolderB/fileB.ts (0 errors) ====
+==== FolderA/FolderB/fileB.ts (2 errors) ====
     /// <reference path='FolderC/fileC.ts'/>
     class B {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../outdir/simple/fileC.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../outdir/simple/fileC.d.ts"'
         public c: C;
     }
     
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.json b/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.json
index 29426144daa0b..72f9b28fc5c45 100644
--- a/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.json
+++ b/tests/baselines/reference/project/rootDirectoryErrors/amd/rootDirectoryErrors.json
@@ -18,7 +18,6 @@
     "emittedFiles": [
         "outdir/simple/fileC.js",
         "outdir/simple/fileC.d.ts",
-        "FolderA/FolderB/fileB.js",
-        "FolderA/FolderB/fileB.d.ts"
+        "FolderA/FolderB/fileB.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.errors.txt b/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.errors.txt
index 4e3492c206fdb..5e3c427a9f26a 100644
--- a/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.errors.txt
+++ b/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.errors.txt
@@ -1,6 +1,8 @@
 error TS6059: File 'FolderA/FolderB/fileB.ts' is not under 'rootDir' 'FolderA/FolderB/FolderC'. 'rootDir' is expected to contain all source files.
   The file is in the program because:
     Root file specified for compilation
+FolderA/FolderB/fileB.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../outdir/simple/fileC.d.ts"'
+FolderA/FolderB/fileB.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"../../outdir/simple/fileC.d.ts"'
 
 
 !!! error TS6059: File 'FolderA/FolderB/fileB.ts' is not under 'rootDir' 'FolderA/FolderB/FolderC'. 'rootDir' is expected to contain all source files.
@@ -10,9 +12,13 @@ error TS6059: File 'FolderA/FolderB/fileB.ts' is not under 'rootDir' 'FolderA/Fo
     class C {
     }
     
-==== FolderA/FolderB/fileB.ts (0 errors) ====
+==== FolderA/FolderB/fileB.ts (2 errors) ====
     /// <reference path='FolderC/fileC.ts'/>
     class B {
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../outdir/simple/fileC.d.ts"'
+    ~~~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"../../outdir/simple/fileC.d.ts"'
         public c: C;
     }
     
\ No newline at end of file
diff --git a/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.json b/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.json
index 29426144daa0b..72f9b28fc5c45 100644
--- a/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.json
+++ b/tests/baselines/reference/project/rootDirectoryErrors/node/rootDirectoryErrors.json
@@ -18,7 +18,6 @@
     "emittedFiles": [
         "outdir/simple/fileC.js",
         "outdir/simple/fileC.d.ts",
-        "FolderA/FolderB/fileB.js",
-        "FolderA/FolderB/fileB.d.ts"
+        "FolderA/FolderB/fileB.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/amd/sourceRootAbsolutePathMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/amd/sourceRootAbsolutePathMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/amd/sourceRootAbsolutePathMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/amd/sourceRootAbsolutePathMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/amd/sourceRootAbsolutePathMixedSubfolderNoOutdir.json
index 54dc140e1dfa4..2ed7bd706e0d3 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/amd/sourceRootAbsolutePathMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/amd/sourceRootAbsolutePathMixedSubfolderNoOutdir.json
@@ -25,7 +25,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/node/sourceRootAbsolutePathMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/node/sourceRootAbsolutePathMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/node/sourceRootAbsolutePathMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/node/sourceRootAbsolutePathMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/node/sourceRootAbsolutePathMixedSubfolderNoOutdir.json
index 54dc140e1dfa4..2ed7bd706e0d3 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/node/sourceRootAbsolutePathMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderNoOutdir/node/sourceRootAbsolutePathMixedSubfolderNoOutdir.json
@@ -25,7 +25,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json
index 99a53de496918..54e2192856114 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json
@@ -26,7 +26,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json
index 99a53de496918..54e2192856114 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputDirectory.json
@@ -26,7 +26,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootAbsolutePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/amd/sourceRootAbsolutePathMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/amd/sourceRootAbsolutePathMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/amd/sourceRootAbsolutePathMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/amd/sourceRootAbsolutePathMultifolderNoOutdir.json b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/amd/sourceRootAbsolutePathMultifolderNoOutdir.json
index 74a242027c28e..7eba46ce9cb96 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/amd/sourceRootAbsolutePathMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/amd/sourceRootAbsolutePathMultifolderNoOutdir.json
@@ -25,7 +25,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/node/sourceRootAbsolutePathMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/node/sourceRootAbsolutePathMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/node/sourceRootAbsolutePathMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/node/sourceRootAbsolutePathMultifolderNoOutdir.json b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/node/sourceRootAbsolutePathMultifolderNoOutdir.json
index 74a242027c28e..7eba46ce9cb96 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/node/sourceRootAbsolutePathMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderNoOutdir/node/sourceRootAbsolutePathMultifolderNoOutdir.json
@@ -25,7 +25,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.json
index d9a269478d964..870a47db540ad 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.json
@@ -26,7 +26,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.json
index d9a269478d964..870a47db540ad 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory/node/sourceRootAbsolutePathMultifolderSpecifyOutputDirectory.json
@@ -26,7 +26,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputFile/amd/sourceRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputFile/amd/sourceRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
index a644c1c6d296d..d87bb0a33d8b0 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputFile/amd/sourceRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputFile/amd/sourceRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
index ec74fc9a4ee8d..dde665c17c0b4 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathMultifolderSpecifyOutputFile/node/sourceRootAbsolutePathMultifolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/amd/sourceRootAbsolutePathSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/amd/sourceRootAbsolutePathSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/amd/sourceRootAbsolutePathSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/amd/sourceRootAbsolutePathSimpleNoOutdir.json b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/amd/sourceRootAbsolutePathSimpleNoOutdir.json
index ff8d63233067a..91e4056a56b6f 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/amd/sourceRootAbsolutePathSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/amd/sourceRootAbsolutePathSimpleNoOutdir.json
@@ -21,7 +21,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/node/sourceRootAbsolutePathSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/node/sourceRootAbsolutePathSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/node/sourceRootAbsolutePathSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/node/sourceRootAbsolutePathSimpleNoOutdir.json b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/node/sourceRootAbsolutePathSimpleNoOutdir.json
index ff8d63233067a..91e4056a56b6f 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/node/sourceRootAbsolutePathSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleNoOutdir/node/sourceRootAbsolutePathSimpleNoOutdir.json
@@ -21,7 +21,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/amd/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/amd/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/amd/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/amd/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/amd/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.json
index bcc8bbe3da8ba..0450fed651f93 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/amd/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/amd/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.json
@@ -22,7 +22,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/node/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/node/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/node/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/node/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/node/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.json
index bcc8bbe3da8ba..0450fed651f93 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/node/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputDirectory/node/sourceRootAbsolutePathSimpleSpecifyOutputDirectory.json
@@ -22,7 +22,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputFile/amd/sourceRootAbsolutePathSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputFile/amd/sourceRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
index 44fdc1b33985f..68a8fe34d4d59 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputFile/amd/sourceRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputFile/amd/sourceRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputFile/node/sourceRootAbsolutePathSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputFile/node/sourceRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
index a9a9b2cc4a371..694e41d780fed 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputFile/node/sourceRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSimpleSpecifyOutputFile/node/sourceRootAbsolutePathSimpleSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/amd/sourceRootAbsolutePathSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/amd/sourceRootAbsolutePathSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/amd/sourceRootAbsolutePathSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/amd/sourceRootAbsolutePathSubfolderNoOutdir.json b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/amd/sourceRootAbsolutePathSubfolderNoOutdir.json
index f1567a8882a1f..0014dcea5219c 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/amd/sourceRootAbsolutePathSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/amd/sourceRootAbsolutePathSubfolderNoOutdir.json
@@ -21,7 +21,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/node/sourceRootAbsolutePathSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/node/sourceRootAbsolutePathSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/node/sourceRootAbsolutePathSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/node/sourceRootAbsolutePathSubfolderNoOutdir.json b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/node/sourceRootAbsolutePathSubfolderNoOutdir.json
index f1567a8882a1f..0014dcea5219c 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/node/sourceRootAbsolutePathSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderNoOutdir/node/sourceRootAbsolutePathSubfolderNoOutdir.json
@@ -21,7 +21,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.json
index 0cf86077a686c..e66bd968e0e98 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/amd/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.json
@@ -22,7 +22,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.json
index 0cf86077a686c..e66bd968e0e98 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory/node/sourceRootAbsolutePathSubfolderSpecifyOutputDirectory.json
@@ -22,7 +22,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
index 9d44caf58785e..f2efcd555ce88 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputFile/amd/sourceRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
index 5b48bc2c2c178..938e038fd9114 100644
--- a/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootAbsolutePathSubfolderSpecifyOutputFile/node/sourceRootAbsolutePathSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/amd/sourceRootRelativePathMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/amd/sourceRootRelativePathMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/amd/sourceRootRelativePathMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/amd/sourceRootRelativePathMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/amd/sourceRootRelativePathMixedSubfolderNoOutdir.json
index e88496235ff0a..713509e206876 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/amd/sourceRootRelativePathMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/amd/sourceRootRelativePathMixedSubfolderNoOutdir.json
@@ -24,7 +24,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/node/sourceRootRelativePathMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/node/sourceRootRelativePathMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/node/sourceRootRelativePathMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/node/sourceRootRelativePathMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/node/sourceRootRelativePathMixedSubfolderNoOutdir.json
index e88496235ff0a..713509e206876 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/node/sourceRootRelativePathMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderNoOutdir/node/sourceRootRelativePathMixedSubfolderNoOutdir.json
@@ -24,7 +24,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.json
index 215bf5be82ce7..e000b1cc14fc1 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.json
index 215bf5be82ce7..e000b1cc14fc1 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFile/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourceRootRelativePathMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/amd/sourceRootRelativePathMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/amd/sourceRootRelativePathMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/amd/sourceRootRelativePathMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/amd/sourceRootRelativePathMultifolderNoOutdir.json b/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/amd/sourceRootRelativePathMultifolderNoOutdir.json
index b606a4dda8f9f..8f802651e05ce 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/amd/sourceRootRelativePathMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/amd/sourceRootRelativePathMultifolderNoOutdir.json
@@ -24,7 +24,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/node/sourceRootRelativePathMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/node/sourceRootRelativePathMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/node/sourceRootRelativePathMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/node/sourceRootRelativePathMultifolderNoOutdir.json b/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/node/sourceRootRelativePathMultifolderNoOutdir.json
index b606a4dda8f9f..8f802651e05ce 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/node/sourceRootRelativePathMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathMultifolderNoOutdir/node/sourceRootRelativePathMultifolderNoOutdir.json
@@ -24,7 +24,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/amd/sourceRootRelativePathMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/amd/sourceRootRelativePathMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/amd/sourceRootRelativePathMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/amd/sourceRootRelativePathMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/amd/sourceRootRelativePathMultifolderSpecifyOutputDirectory.json
index b50d1c469f44c..ca7f4822fe09c 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/amd/sourceRootRelativePathMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/amd/sourceRootRelativePathMultifolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/node/sourceRootRelativePathMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/node/sourceRootRelativePathMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/node/sourceRootRelativePathMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/node/sourceRootRelativePathMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/node/sourceRootRelativePathMultifolderSpecifyOutputDirectory.json
index b50d1c469f44c..ca7f4822fe09c 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/node/sourceRootRelativePathMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputDirectory/node/sourceRootRelativePathMultifolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputFile/amd/sourceRootRelativePathMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputFile/amd/sourceRootRelativePathMultifolderSpecifyOutputFile.errors.txt
index a644c1c6d296d..d87bb0a33d8b0 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputFile/amd/sourceRootRelativePathMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputFile/amd/sourceRootRelativePathMultifolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputFile/node/sourceRootRelativePathMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputFile/node/sourceRootRelativePathMultifolderSpecifyOutputFile.errors.txt
index ec74fc9a4ee8d..dde665c17c0b4 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputFile/node/sourceRootRelativePathMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathMultifolderSpecifyOutputFile/node/sourceRootRelativePathMultifolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/amd/sourceRootRelativePathSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/amd/sourceRootRelativePathSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/amd/sourceRootRelativePathSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/amd/sourceRootRelativePathSimpleNoOutdir.json b/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/amd/sourceRootRelativePathSimpleNoOutdir.json
index 52b7b4e339932..dfc31e919811d 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/amd/sourceRootRelativePathSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/amd/sourceRootRelativePathSimpleNoOutdir.json
@@ -20,7 +20,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/node/sourceRootRelativePathSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/node/sourceRootRelativePathSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/node/sourceRootRelativePathSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/node/sourceRootRelativePathSimpleNoOutdir.json b/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/node/sourceRootRelativePathSimpleNoOutdir.json
index 52b7b4e339932..dfc31e919811d 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/node/sourceRootRelativePathSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathSimpleNoOutdir/node/sourceRootRelativePathSimpleNoOutdir.json
@@ -20,7 +20,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/amd/sourceRootRelativePathSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/amd/sourceRootRelativePathSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/amd/sourceRootRelativePathSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/amd/sourceRootRelativePathSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/amd/sourceRootRelativePathSimpleSpecifyOutputDirectory.json
index bed9b7a091da4..91b2a16f7fa0b 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/amd/sourceRootRelativePathSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/amd/sourceRootRelativePathSimpleSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/node/sourceRootRelativePathSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/node/sourceRootRelativePathSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/node/sourceRootRelativePathSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/node/sourceRootRelativePathSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/node/sourceRootRelativePathSimpleSpecifyOutputDirectory.json
index bed9b7a091da4..91b2a16f7fa0b 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/node/sourceRootRelativePathSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputDirectory/node/sourceRootRelativePathSimpleSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputFile/amd/sourceRootRelativePathSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputFile/amd/sourceRootRelativePathSimpleSpecifyOutputFile.errors.txt
index 44fdc1b33985f..68a8fe34d4d59 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputFile/amd/sourceRootRelativePathSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputFile/amd/sourceRootRelativePathSimpleSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputFile/node/sourceRootRelativePathSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputFile/node/sourceRootRelativePathSimpleSpecifyOutputFile.errors.txt
index a9a9b2cc4a371..694e41d780fed 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputFile/node/sourceRootRelativePathSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathSimpleSpecifyOutputFile/node/sourceRootRelativePathSimpleSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/amd/sourceRootRelativePathSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/amd/sourceRootRelativePathSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/amd/sourceRootRelativePathSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/amd/sourceRootRelativePathSubfolderNoOutdir.json b/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/amd/sourceRootRelativePathSubfolderNoOutdir.json
index 10a988c4c140d..bb38f6098d082 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/amd/sourceRootRelativePathSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/amd/sourceRootRelativePathSubfolderNoOutdir.json
@@ -20,7 +20,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/node/sourceRootRelativePathSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/node/sourceRootRelativePathSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/node/sourceRootRelativePathSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/node/sourceRootRelativePathSubfolderNoOutdir.json b/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/node/sourceRootRelativePathSubfolderNoOutdir.json
index 10a988c4c140d..bb38f6098d082 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/node/sourceRootRelativePathSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathSubfolderNoOutdir/node/sourceRootRelativePathSubfolderNoOutdir.json
@@ -20,7 +20,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathSubfolderSpecifyOutputDirectory.json
index 2d9abc19c8cba..ed5b333d88685 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/amd/sourceRootRelativePathSubfolderSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathSubfolderSpecifyOutputDirectory.json
index 2d9abc19c8cba..ed5b333d88685 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputDirectory/node/sourceRootRelativePathSubfolderSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputFile/amd/sourceRootRelativePathSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputFile/amd/sourceRootRelativePathSubfolderSpecifyOutputFile.errors.txt
index 9d44caf58785e..f2efcd555ce88 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputFile/amd/sourceRootRelativePathSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputFile/amd/sourceRootRelativePathSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputFile/node/sourceRootRelativePathSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputFile/node/sourceRootRelativePathSubfolderSpecifyOutputFile.errors.txt
index 5b48bc2c2c178..938e038fd9114 100644
--- a/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputFile/node/sourceRootRelativePathSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourceRootRelativePathSubfolderSpecifyOutputFile/node/sourceRootRelativePathSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/amd/sourcemapMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/amd/sourcemapMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/amd/sourcemapMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/amd/sourcemapMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/amd/sourcemapMixedSubfolderNoOutdir.json
index 57da4ec829679..2266d204c2a65 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/amd/sourcemapMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/amd/sourcemapMixedSubfolderNoOutdir.json
@@ -23,7 +23,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/node/sourcemapMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/node/sourcemapMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/node/sourcemapMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/node/sourcemapMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/node/sourcemapMixedSubfolderNoOutdir.json
index 57da4ec829679..2266d204c2a65 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/node/sourcemapMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderNoOutdir/node/sourcemapMixedSubfolderNoOutdir.json
@@ -23,7 +23,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputDirectory.json
index 75e5d91e3b6fb..cd3706b2cc43f 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputDirectory.json
@@ -24,7 +24,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputDirectory.json
index 75e5d91e3b6fb..cd3706b2cc43f 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputDirectory.json
@@ -24,7 +24,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/sourcemapMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/sourcemapMixedSubfolderSpecifyOutputFile.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/sourcemapMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/amd/sourcemapMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFile/node/sourcemapMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcemapMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/amd/sourcemapMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/amd/sourcemapMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/amd/sourcemapMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/amd/sourcemapMultifolderNoOutdir.json b/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/amd/sourcemapMultifolderNoOutdir.json
index df52282f135a8..3362fb07be052 100644
--- a/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/amd/sourcemapMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/amd/sourcemapMultifolderNoOutdir.json
@@ -23,7 +23,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/node/sourcemapMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/node/sourcemapMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/node/sourcemapMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/node/sourcemapMultifolderNoOutdir.json b/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/node/sourcemapMultifolderNoOutdir.json
index df52282f135a8..3362fb07be052 100644
--- a/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/node/sourcemapMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourcemapMultifolderNoOutdir/node/sourcemapMultifolderNoOutdir.json
@@ -23,7 +23,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/amd/sourcemapMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/amd/sourcemapMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/amd/sourcemapMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/amd/sourcemapMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/amd/sourcemapMultifolderSpecifyOutputDirectory.json
index a571424b3927d..8b2b760d0ecd3 100644
--- a/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/amd/sourcemapMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/amd/sourcemapMultifolderSpecifyOutputDirectory.json
@@ -24,7 +24,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/node/sourcemapMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/node/sourcemapMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/node/sourcemapMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/node/sourcemapMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/node/sourcemapMultifolderSpecifyOutputDirectory.json
index a571424b3927d..8b2b760d0ecd3 100644
--- a/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/node/sourcemapMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputDirectory/node/sourcemapMultifolderSpecifyOutputDirectory.json
@@ -24,7 +24,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputFile/amd/sourcemapMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputFile/amd/sourcemapMultifolderSpecifyOutputFile.errors.txt
index a644c1c6d296d..d87bb0a33d8b0 100644
--- a/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputFile/amd/sourcemapMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputFile/amd/sourcemapMultifolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputFile/node/sourcemapMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputFile/node/sourcemapMultifolderSpecifyOutputFile.errors.txt
index ec74fc9a4ee8d..dde665c17c0b4 100644
--- a/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputFile/node/sourcemapMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcemapMultifolderSpecifyOutputFile/node/sourcemapMultifolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcemapSimpleNoOutdir/amd/sourcemapSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/sourcemapSimpleNoOutdir/amd/sourcemapSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapSimpleNoOutdir/amd/sourcemapSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSimpleNoOutdir/amd/sourcemapSimpleNoOutdir.json b/tests/baselines/reference/project/sourcemapSimpleNoOutdir/amd/sourcemapSimpleNoOutdir.json
index dedc11ce3ed71..f59366816a82b 100644
--- a/tests/baselines/reference/project/sourcemapSimpleNoOutdir/amd/sourcemapSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/sourcemapSimpleNoOutdir/amd/sourcemapSimpleNoOutdir.json
@@ -19,7 +19,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSimpleNoOutdir/node/sourcemapSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/sourcemapSimpleNoOutdir/node/sourcemapSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapSimpleNoOutdir/node/sourcemapSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSimpleNoOutdir/node/sourcemapSimpleNoOutdir.json b/tests/baselines/reference/project/sourcemapSimpleNoOutdir/node/sourcemapSimpleNoOutdir.json
index dedc11ce3ed71..f59366816a82b 100644
--- a/tests/baselines/reference/project/sourcemapSimpleNoOutdir/node/sourcemapSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/sourcemapSimpleNoOutdir/node/sourcemapSimpleNoOutdir.json
@@ -19,7 +19,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/amd/sourcemapSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/amd/sourcemapSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/amd/sourcemapSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/amd/sourcemapSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/amd/sourcemapSimpleSpecifyOutputDirectory.json
index b5caaacbfc91a..183e7c791ab28 100644
--- a/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/amd/sourcemapSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/amd/sourcemapSimpleSpecifyOutputDirectory.json
@@ -20,7 +20,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/node/sourcemapSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/node/sourcemapSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/node/sourcemapSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/node/sourcemapSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/node/sourcemapSimpleSpecifyOutputDirectory.json
index b5caaacbfc91a..183e7c791ab28 100644
--- a/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/node/sourcemapSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputDirectory/node/sourcemapSimpleSpecifyOutputDirectory.json
@@ -20,7 +20,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputFile/amd/sourcemapSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputFile/amd/sourcemapSimpleSpecifyOutputFile.errors.txt
index 44fdc1b33985f..68a8fe34d4d59 100644
--- a/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputFile/amd/sourcemapSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputFile/amd/sourcemapSimpleSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputFile/node/sourcemapSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputFile/node/sourcemapSimpleSpecifyOutputFile.errors.txt
index a9a9b2cc4a371..694e41d780fed 100644
--- a/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputFile/node/sourcemapSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcemapSimpleSpecifyOutputFile/node/sourcemapSimpleSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/amd/sourcemapSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/amd/sourcemapSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/amd/sourcemapSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/amd/sourcemapSubfolderNoOutdir.json b/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/amd/sourcemapSubfolderNoOutdir.json
index 50a5c31f190b0..da5472bfd665a 100644
--- a/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/amd/sourcemapSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/amd/sourcemapSubfolderNoOutdir.json
@@ -19,7 +19,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/node/sourcemapSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/node/sourcemapSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/node/sourcemapSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/node/sourcemapSubfolderNoOutdir.json b/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/node/sourcemapSubfolderNoOutdir.json
index 50a5c31f190b0..da5472bfd665a 100644
--- a/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/node/sourcemapSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourcemapSubfolderNoOutdir/node/sourcemapSubfolderNoOutdir.json
@@ -19,7 +19,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/amd/sourcemapSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/amd/sourcemapSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/amd/sourcemapSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/amd/sourcemapSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/amd/sourcemapSubfolderSpecifyOutputDirectory.json
index 4ebbac59dda34..e6c9c7856d53e 100644
--- a/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/amd/sourcemapSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/amd/sourcemapSubfolderSpecifyOutputDirectory.json
@@ -20,7 +20,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/node/sourcemapSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/node/sourcemapSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/node/sourcemapSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/node/sourcemapSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/node/sourcemapSubfolderSpecifyOutputDirectory.json
index 4ebbac59dda34..e6c9c7856d53e 100644
--- a/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/node/sourcemapSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputDirectory/node/sourcemapSubfolderSpecifyOutputDirectory.json
@@ -20,7 +20,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputFile/amd/sourcemapSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputFile/amd/sourcemapSubfolderSpecifyOutputFile.errors.txt
index 9d44caf58785e..f2efcd555ce88 100644
--- a/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputFile/amd/sourcemapSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputFile/amd/sourcemapSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputFile/node/sourcemapSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputFile/node/sourcemapSubfolderSpecifyOutputFile.errors.txt
index 5b48bc2c2c178..938e038fd9114 100644
--- a/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputFile/node/sourcemapSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcemapSubfolderSpecifyOutputFile/node/sourcemapSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/amd/sourcerootUrlMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/amd/sourcerootUrlMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/amd/sourcerootUrlMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/amd/sourcerootUrlMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/amd/sourcerootUrlMixedSubfolderNoOutdir.json
index 8a7f79e478414..66ee4166eab1f 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/amd/sourcerootUrlMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/amd/sourcerootUrlMixedSubfolderNoOutdir.json
@@ -24,7 +24,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/node/sourcerootUrlMixedSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/node/sourcerootUrlMixedSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/node/sourcerootUrlMixedSubfolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/node/sourcerootUrlMixedSubfolderNoOutdir.json b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/node/sourcerootUrlMixedSubfolderNoOutdir.json
index 8a7f79e478414..66ee4166eab1f 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/node/sourcerootUrlMixedSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderNoOutdir/node/sourcerootUrlMixedSubfolderNoOutdir.json
@@ -24,7 +24,6 @@
         "ref/m2.js",
         "ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.json
index 2fed55ae75e25..a843aca176916 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..40515db90db53
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ref/m2.ts (0 errors) ====
+    export var m2_a1 = 10;
+    export class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    export var m2_instance1 = new m2_c1();
+    export function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.json
index 2fed55ae75e25..a843aca176916 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/ref/m2.js",
         "outdir/simple/ref/m2.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/sourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/sourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/sourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/amd/sourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFile/node/sourcerootUrlMixedSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 30fd9f0cf956d..89d6e593d83c1 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/amd/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
index 3658c2a02d5d9..5c96dc70b19ee 100644
--- a/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
+++ b/tests/baselines/reference/project/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory/node/sourcerootUrlMixedSubfolderSpecifyOutputFileAndOutputDirectory.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     export function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/amd/sourcerootUrlMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/amd/sourcerootUrlMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/amd/sourcerootUrlMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/amd/sourcerootUrlMultifolderNoOutdir.json b/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/amd/sourcerootUrlMultifolderNoOutdir.json
index ba83a6fcf4dde..67c2501ca4466 100644
--- a/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/amd/sourcerootUrlMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/amd/sourcerootUrlMultifolderNoOutdir.json
@@ -24,7 +24,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/node/sourcerootUrlMultifolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/node/sourcerootUrlMultifolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/node/sourcerootUrlMultifolderNoOutdir.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/node/sourcerootUrlMultifolderNoOutdir.json b/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/node/sourcerootUrlMultifolderNoOutdir.json
index ba83a6fcf4dde..67c2501ca4466 100644
--- a/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/node/sourcerootUrlMultifolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourcerootUrlMultifolderNoOutdir/node/sourcerootUrlMultifolderNoOutdir.json
@@ -24,7 +24,6 @@
         "../outputdir_multifolder_ref/m2.js",
         "../outputdir_multifolder_ref/m2.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/amd/sourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/amd/sourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/amd/sourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/amd/sourcerootUrlMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/amd/sourcerootUrlMultifolderSpecifyOutputDirectory.json
index e8ec5c9da4e73..c922bbf92c3df 100644
--- a/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/amd/sourcerootUrlMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/amd/sourcerootUrlMultifolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/node/sourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/node/sourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..6793727fb2c50
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/node/sourcerootUrlMultifolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,40 @@
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== ../outputdir_multifolder_ref/m2.ts (0 errors) ====
+    var m2_a1 = 10;
+    class m2_c1 {
+        public m2_c1_p1: number;
+    }
+    
+    var m2_instance1 = new m2_c1();
+    function m2_f1() {
+        return m2_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/node/sourcerootUrlMultifolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/node/sourcerootUrlMultifolderSpecifyOutputDirectory.json
index e8ec5c9da4e73..c922bbf92c3df 100644
--- a/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/node/sourcerootUrlMultifolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputDirectory/node/sourcerootUrlMultifolderSpecifyOutputDirectory.json
@@ -25,7 +25,6 @@
         "outdir/simple/outputdir_multifolder_ref/m2.js",
         "outdir/simple/outputdir_multifolder_ref/m2.d.ts",
         "outdir/simple/outputdir_multifolder/test.js.map",
-        "outdir/simple/outputdir_multifolder/test.js",
-        "outdir/simple/outputdir_multifolder/test.d.ts"
+        "outdir/simple/outputdir_multifolder/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputFile/amd/sourcerootUrlMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputFile/amd/sourcerootUrlMultifolderSpecifyOutputFile.errors.txt
index a644c1c6d296d..d87bb0a33d8b0 100644
--- a/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputFile/amd/sourcerootUrlMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputFile/amd/sourcerootUrlMultifolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -24,10 +25,12 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputFile/node/sourcerootUrlMultifolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputFile/node/sourcerootUrlMultifolderSpecifyOutputFile.errors.txt
index ec74fc9a4ee8d..dde665c17c0b4 100644
--- a/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputFile/node/sourcerootUrlMultifolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcerootUrlMultifolderSpecifyOutputFile/node/sourcerootUrlMultifolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(3,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -26,10 +27,12 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m2_f1() {
         return m2_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     /// <reference path='../outputdir_multifolder_ref/m2.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts", "../outputdir_multifolder_ref/m2.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/amd/sourcerootUrlSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/amd/sourcerootUrlSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/amd/sourcerootUrlSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/amd/sourcerootUrlSimpleNoOutdir.json b/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/amd/sourcerootUrlSimpleNoOutdir.json
index 0bb0b4fb96243..9f3ae33b86552 100644
--- a/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/amd/sourcerootUrlSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/amd/sourcerootUrlSimpleNoOutdir.json
@@ -20,7 +20,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/node/sourcerootUrlSimpleNoOutdir.errors.txt b/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/node/sourcerootUrlSimpleNoOutdir.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/node/sourcerootUrlSimpleNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/node/sourcerootUrlSimpleNoOutdir.json b/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/node/sourcerootUrlSimpleNoOutdir.json
index 0bb0b4fb96243..9f3ae33b86552 100644
--- a/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/node/sourcerootUrlSimpleNoOutdir.json
+++ b/tests/baselines/reference/project/sourcerootUrlSimpleNoOutdir/node/sourcerootUrlSimpleNoOutdir.json
@@ -20,7 +20,6 @@
         "m1.js",
         "m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/amd/sourcerootUrlSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/amd/sourcerootUrlSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/amd/sourcerootUrlSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/amd/sourcerootUrlSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/amd/sourcerootUrlSimpleSpecifyOutputDirectory.json
index 8d83bcbfa4a49..e3e58724c0bc3 100644
--- a/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/amd/sourcerootUrlSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/amd/sourcerootUrlSimpleSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/node/sourcerootUrlSimpleSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/node/sourcerootUrlSimpleSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..1ed558a9e81e7
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/node/sourcerootUrlSimpleSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+
+
+==== m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/node/sourcerootUrlSimpleSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/node/sourcerootUrlSimpleSpecifyOutputDirectory.json
index 8d83bcbfa4a49..e3e58724c0bc3 100644
--- a/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/node/sourcerootUrlSimpleSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputDirectory/node/sourcerootUrlSimpleSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/m1.js",
         "outdir/simple/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputFile/amd/sourcerootUrlSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputFile/amd/sourcerootUrlSimpleSpecifyOutputFile.errors.txt
index 44fdc1b33985f..68a8fe34d4d59 100644
--- a/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputFile/amd/sourcerootUrlSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputFile/amd/sourcerootUrlSimpleSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputFile/node/sourcerootUrlSimpleSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputFile/node/sourcerootUrlSimpleSpecifyOutputFile.errors.txt
index a9a9b2cc4a371..694e41d780fed 100644
--- a/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputFile/node/sourcerootUrlSimpleSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcerootUrlSimpleSpecifyOutputFile/node/sourcerootUrlSimpleSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/amd/sourcerootUrlSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/amd/sourcerootUrlSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/amd/sourcerootUrlSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/amd/sourcerootUrlSubfolderNoOutdir.json b/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/amd/sourcerootUrlSubfolderNoOutdir.json
index 4df27f46f032c..19567b8c353b3 100644
--- a/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/amd/sourcerootUrlSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/amd/sourcerootUrlSubfolderNoOutdir.json
@@ -20,7 +20,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/node/sourcerootUrlSubfolderNoOutdir.errors.txt b/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/node/sourcerootUrlSubfolderNoOutdir.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/node/sourcerootUrlSubfolderNoOutdir.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/node/sourcerootUrlSubfolderNoOutdir.json b/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/node/sourcerootUrlSubfolderNoOutdir.json
index 4df27f46f032c..19567b8c353b3 100644
--- a/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/node/sourcerootUrlSubfolderNoOutdir.json
+++ b/tests/baselines/reference/project/sourcerootUrlSubfolderNoOutdir/node/sourcerootUrlSubfolderNoOutdir.json
@@ -20,7 +20,6 @@
         "ref/m1.js",
         "ref/m1.d.ts",
         "test.js.map",
-        "test.js",
-        "test.d.ts"
+        "test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/amd/sourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/amd/sourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/amd/sourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/amd/sourcerootUrlSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/amd/sourcerootUrlSubfolderSpecifyOutputDirectory.json
index 1f41e0112914c..9535da39ea87f 100644
--- a/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/amd/sourcerootUrlSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/amd/sourcerootUrlSubfolderSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/node/sourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/node/sourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt
new file mode 100644
index 0000000000000..e54ea39b3abb1
--- /dev/null
+++ b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/node/sourcerootUrlSubfolderSpecifyOutputDirectory.errors.txt
@@ -0,0 +1,29 @@
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+
+
+==== ref/m1.ts (0 errors) ====
+    var m1_a1 = 10;
+    class m1_c1 {
+        public m1_c1_p1: number;
+    }
+    
+    var m1_instance1 = new m1_c1();
+    function m1_f1() {
+        return m1_instance1;
+    }
+==== test.ts (2 errors) ====
+    /// <reference path='ref/m1.ts'/>
+    var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
+    class c1 {
+        public p1: number;
+    }
+    
+    var instance1 = new c1();
+    function f1() {
+        return instance1;
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/node/sourcerootUrlSubfolderSpecifyOutputDirectory.json b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/node/sourcerootUrlSubfolderSpecifyOutputDirectory.json
index 1f41e0112914c..9535da39ea87f 100644
--- a/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/node/sourcerootUrlSubfolderSpecifyOutputDirectory.json
+++ b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputDirectory/node/sourcerootUrlSubfolderSpecifyOutputDirectory.json
@@ -21,7 +21,6 @@
         "outdir/simple/ref/m1.js",
         "outdir/simple/ref/m1.d.ts",
         "outdir/simple/test.js.map",
-        "outdir/simple/test.js",
-        "outdir/simple/test.d.ts"
+        "outdir/simple/test.js"
     ]
 }
\ No newline at end of file
diff --git a/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputFile/amd/sourcerootUrlSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputFile/amd/sourcerootUrlSubfolderSpecifyOutputFile.errors.txt
index 9d44caf58785e..f2efcd555ce88 100644
--- a/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputFile/amd/sourcerootUrlSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputFile/amd/sourcerootUrlSubfolderSpecifyOutputFile.errors.txt
@@ -1,5 +1,6 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -14,9 +15,11 @@ error TS5102: Option 'out' has been removed. Please remove it from your configur
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputFile/node/sourcerootUrlSubfolderSpecifyOutputFile.errors.txt b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputFile/node/sourcerootUrlSubfolderSpecifyOutputFile.errors.txt
index 5b48bc2c2c178..938e038fd9114 100644
--- a/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputFile/node/sourcerootUrlSubfolderSpecifyOutputFile.errors.txt
+++ b/tests/baselines/reference/project/sourcerootUrlSubfolderSpecifyOutputFile/node/sourcerootUrlSubfolderSpecifyOutputFile.errors.txt
@@ -1,6 +1,7 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
+test.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
@@ -16,9 +17,11 @@ error TS6082: Only 'amd' and 'system' modules are supported alongside --out.
     function m1_f1() {
         return m1_instance1;
     }
-==== test.ts (0 errors) ====
+==== test.ts (1 errors) ====
     /// <reference path='ref/m1.ts'/>
     var a1 = 10;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"ref/m1.d.ts"'
     class c1 {
         public p1: number;
     }
diff --git a/tests/baselines/reference/reactTransitiveImportHasValidDeclaration.errors.txt b/tests/baselines/reference/reactTransitiveImportHasValidDeclaration.errors.txt
new file mode 100644
index 0000000000000..24215e10a3a59
--- /dev/null
+++ b/tests/baselines/reference/reactTransitiveImportHasValidDeclaration.errors.txt
@@ -0,0 +1,38 @@
+index.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"react"'
+
+
+==== node_modules/react/index.d.ts (0 errors) ====
+    declare namespace React {
+        export interface DetailedHTMLProps<T, U> {}
+        export interface HTMLAttributes<T> {}
+    }
+    export = React;
+    export as namespace React;
+==== node_modules/create-emotion-styled/types/react/index.d.ts (0 errors) ====
+    /// <reference types="react" />
+    declare module 'react' { // augment
+        interface HTMLAttributes<T> {
+            css?: unknown;
+        }
+    }
+    export interface StyledOtherComponentList {
+        "div": React.DetailedHTMLProps<React.HTMLAttributes<HTMLDivElement>, HTMLDivElement>
+    }
+    export interface StyledOtherComponent<A, B, C> {}
+    
+==== node_modules/create-emotion-styled/index.d.ts (0 errors) ====
+    export * from "./types/react";
+    
+==== node_modules/react-emotion/index.d.ts (0 errors) ====
+    import {StyledOtherComponent, StyledOtherComponentList} from "create-emotion-styled";
+    export default function styled(tag: string): (o: object) => StyledOtherComponent<{}, StyledOtherComponentList["div"], any>;
+    
+==== index.ts (1 errors) ====
+    import styled from "react-emotion"
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"react"'
+    
+    const Form = styled('div')({ color: "red" })
+    
+    export default Form
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/reactTransitiveImportHasValidDeclaration.js b/tests/baselines/reference/reactTransitiveImportHasValidDeclaration.js
index f01809cd633b9..8d349ee015717 100644
--- a/tests/baselines/reference/reactTransitiveImportHasValidDeclaration.js
+++ b/tests/baselines/reference/reactTransitiveImportHasValidDeclaration.js
@@ -40,9 +40,3 @@ Object.defineProperty(exports, "__esModule", { value: true });
 var react_emotion_1 = require("react-emotion");
 var Form = (0, react_emotion_1.default)('div')({ color: "red" });
 exports.default = Form;
-
-
-//// [index.d.ts]
-/// <reference types="react" />
-declare const Form: import("create-emotion-styled").StyledOtherComponent<{}, import("react").DetailedHTMLProps<import("react").HTMLAttributes<HTMLDivElement>, HTMLDivElement>, any>;
-export default Form;
diff --git a/tests/baselines/reference/reactTransitiveImportHasValidDeclaration.types b/tests/baselines/reference/reactTransitiveImportHasValidDeclaration.types
index c9df856b7d927..af09080db3ee8 100644
--- a/tests/baselines/reference/reactTransitiveImportHasValidDeclaration.types
+++ b/tests/baselines/reference/reactTransitiveImportHasValidDeclaration.types
@@ -9,12 +9,12 @@ export = React;
 >React : any
 
 export as namespace React;
->React : error
+>React : any
 
 === node_modules/create-emotion-styled/types/react/index.d.ts ===
 /// <reference types="react" />
 declare module 'react' { // augment
->'react' : error
+>'react' : any
 
     interface HTMLAttributes<T> {
         css?: unknown;
diff --git a/tests/baselines/reference/referenceTypesPreferedToPathIfPossible.errors.txt b/tests/baselines/reference/referenceTypesPreferedToPathIfPossible.errors.txt
new file mode 100644
index 0000000000000..a0bbd205d3060
--- /dev/null
+++ b/tests/baselines/reference/referenceTypesPreferedToPathIfPossible.errors.txt
@@ -0,0 +1,14 @@
+usage.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"node"'
+
+
+==== usage.ts (1 errors) ====
+    import { parse } from "url";
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"node"'
+    export const thing = () => parse();
+    
+==== node_modules/@types/node/index.d.ts (0 errors) ====
+    declare module "url" {
+        export class Url {}
+        export function parse(): Url; 
+    }
\ No newline at end of file
diff --git a/tests/baselines/reference/referenceTypesPreferedToPathIfPossible.js b/tests/baselines/reference/referenceTypesPreferedToPathIfPossible.js
index a14c0214aa046..eadd56fac38a1 100644
--- a/tests/baselines/reference/referenceTypesPreferedToPathIfPossible.js
+++ b/tests/baselines/reference/referenceTypesPreferedToPathIfPossible.js
@@ -17,8 +17,3 @@ exports.thing = void 0;
 var url_1 = require("url");
 var thing = function () { return (0, url_1.parse)(); };
 exports.thing = thing;
-
-
-//// [usage.d.ts]
-/// <reference types="node" />
-export declare const thing: () => import("url").Url;
diff --git a/tests/baselines/reference/sourceMapWithMultipleFilesWithCopyright.errors.txt b/tests/baselines/reference/sourceMapWithMultipleFilesWithCopyright.errors.txt
index 76f8b9c73fc1a..614fd4c02f18b 100644
--- a/tests/baselines/reference/sourceMapWithMultipleFilesWithCopyright.errors.txt
+++ b/tests/baselines/reference/sourceMapWithMultipleFilesWithCopyright.errors.txt
@@ -1,16 +1,19 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+b.ts(6,1): error TS18056: Declaration file contains synthesized file reference directives: '"a.d.ts"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
 !!! error TS5102:   Use 'outFile' instead.
-==== b.ts (0 errors) ====
+==== b.ts (1 errors) ====
     /*--------------------------------------------------------------------------
     Copyright 
     ---------------------------------------------------------------------------*/
     
     ///<reference path="a.ts"/>
     var y = x;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"a.d.ts"'
     
 ==== a.ts (0 errors) ====
     /*--------------------------------------------------------------------------
diff --git a/tests/baselines/reference/tsbuild/moduleResolution/type-reference-resolution-uses-correct-options-for-different-resolution-options-referenced-project.js b/tests/baselines/reference/tsbuild/moduleResolution/type-reference-resolution-uses-correct-options-for-different-resolution-options-referenced-project.js
index 38b754724cbe4..97c6f17e546ea 100644
--- a/tests/baselines/reference/tsbuild/moduleResolution/type-reference-resolution-uses-correct-options-for-different-resolution-options-referenced-project.js
+++ b/tests/baselines/reference/tsbuild/moduleResolution/type-reference-resolution-uses-correct-options-for-different-resolution-options-referenced-project.js
@@ -72,9 +72,14 @@ File '/src/packages/typeroot1/sometype/package.json' does not exist.
 File '/src/packages/typeroot1/sometype/index.d.ts' exists - use it as a name resolution result.
 Resolving real path for '/src/packages/typeroot1/sometype/index.d.ts', result '/src/packages/typeroot1/sometype/index.d.ts'.
 ======== Type reference directive 'sometype' was successfully resolved to '/src/packages/typeroot1/sometype/index.d.ts', primary: true. ========
-[12:00:25 AM] Project 'src/packages/pkg2.tsconfig.json' is out of date because output file 'src/packages/pkg2.tsconfig.tsbuildinfo' does not exist
+src/packages/pkg1_index.ts:1:1 - error TS18055: Declaration file contains synthesized type reference directives: '"sometype"'
 
-[12:00:26 AM] Building project '/src/packages/pkg2.tsconfig.json'...
+1 export const theNum: TheNum = "type1";
+  ~~~~~~
+
+[12:00:23 AM] Project 'src/packages/pkg2.tsconfig.json' is out of date because output file 'src/packages/pkg2.tsconfig.tsbuildinfo' does not exist
+
+[12:00:24 AM] Building project '/src/packages/pkg2.tsconfig.json'...
 
 ======== Resolving type reference directive 'sometype', containing file '/src/packages/__inferred type names__.ts', root directory '/src/packages/typeroot2'. ========
 Resolving with primary search path '/src/packages/typeroot2'.
@@ -83,11 +88,19 @@ File '/src/packages/typeroot2/sometype/package.json' does not exist.
 File '/src/packages/typeroot2/sometype/index.d.ts' exists - use it as a name resolution result.
 Resolving real path for '/src/packages/typeroot2/sometype/index.d.ts', result '/src/packages/typeroot2/sometype/index.d.ts'.
 ======== Type reference directive 'sometype' was successfully resolved to '/src/packages/typeroot2/sometype/index.d.ts', primary: true. ========
-exitCode:: ExitStatus.Success
+src/packages/pkg2_index.ts:1:1 - error TS18055: Declaration file contains synthesized type reference directives: '"sometype"'
+
+1 export const theNum: TheNum2 = "type2";
+  ~~~~~~
+
+
+Found 2 errors.
+
+exitCode:: ExitStatus.DiagnosticsPresent_OutputsSkipped
 
 
 //// [/src/packages/pkg1.tsconfig.tsbuildinfo]
-{"program":{"fileNames":["../../lib/lib.d.ts","./pkg1_index.ts","./typeroot1/sometype/index.d.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-9601687719-export const theNum: TheNum = \"type1\";","signature":"-105541926-/// <reference types=\"sometype\" />\nexport declare const theNum: TheNum;\n"},{"version":"-4557394441-declare type TheNum = \"type1\";","affectsGlobalScope":true}],"root":[2],"options":{"composite":true},"referencedMap":[],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,2,3],"latestChangedDtsFile":"./pkg1_index.d.ts"},"version":"FakeTSVersion"}
+{"program":{"fileNames":["../../lib/lib.d.ts","./pkg1_index.ts","./typeroot1/sometype/index.d.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},"-9601687719-export const theNum: TheNum = \"type1\";",{"version":"-4557394441-declare type TheNum = \"type1\";","affectsGlobalScope":true}],"root":[2],"options":{"composite":true},"referencedMap":[],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,2,3],"affectedFilesPendingEmit":[2],"emitSignatures":[2]},"version":"FakeTSVersion"}
 
 //// [/src/packages/pkg1.tsconfig.tsbuildinfo.readable.baseline.txt]
 {
@@ -108,12 +121,8 @@ exitCode:: ExitStatus.Success
         "affectsGlobalScope": true
       },
       "./pkg1_index.ts": {
-        "original": {
-          "version": "-9601687719-export const theNum: TheNum = \"type1\";",
-          "signature": "-105541926-/// <reference types=\"sometype\" />\nexport declare const theNum: TheNum;\n"
-        },
         "version": "-9601687719-export const theNum: TheNum = \"type1\";",
-        "signature": "-105541926-/// <reference types=\"sometype\" />\nexport declare const theNum: TheNum;\n"
+        "signature": "-9601687719-export const theNum: TheNum = \"type1\";"
       },
       "./typeroot1/sometype/index.d.ts": {
         "original": {
@@ -141,26 +150,22 @@ exitCode:: ExitStatus.Success
       "./pkg1_index.ts",
       "./typeroot1/sometype/index.d.ts"
     ],
-    "latestChangedDtsFile": "./pkg1_index.d.ts"
+    "affectedFilesPendingEmit": [
+      [
+        "./pkg1_index.ts",
+        "Js | Dts"
+      ]
+    ],
+    "emitSignatures": [
+      "./pkg1_index.ts"
+    ]
   },
   "version": "FakeTSVersion",
-  "size": 1036
+  "size": 931
 }
 
-//// [/src/packages/pkg1_index.d.ts]
-/// <reference types="sometype" />
-export declare const theNum: TheNum;
-
-
-//// [/src/packages/pkg1_index.js]
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.theNum = void 0;
-exports.theNum = "type1";
-
-
 //// [/src/packages/pkg2.tsconfig.tsbuildinfo]
-{"program":{"fileNames":["../../lib/lib.d.ts","./pkg2_index.ts","./typeroot2/sometype/index.d.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-12823281204-export const theNum: TheNum2 = \"type2\";","signature":"812075564-/// <reference types=\"sometype\" />\nexport declare const theNum: TheNum2;\n"},{"version":"-980425686-declare type TheNum2 = \"type2\";","affectsGlobalScope":true}],"root":[2],"options":{"composite":true},"referencedMap":[],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,2,3],"latestChangedDtsFile":"./pkg2_index.d.ts"},"version":"FakeTSVersion"}
+{"program":{"fileNames":["../../lib/lib.d.ts","./pkg2_index.ts","./typeroot2/sometype/index.d.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},"-12823281204-export const theNum: TheNum2 = \"type2\";",{"version":"-980425686-declare type TheNum2 = \"type2\";","affectsGlobalScope":true}],"root":[2],"options":{"composite":true},"referencedMap":[],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,2,3],"affectedFilesPendingEmit":[2],"emitSignatures":[2]},"version":"FakeTSVersion"}
 
 //// [/src/packages/pkg2.tsconfig.tsbuildinfo.readable.baseline.txt]
 {
@@ -181,12 +186,8 @@ exports.theNum = "type1";
         "affectsGlobalScope": true
       },
       "./pkg2_index.ts": {
-        "original": {
-          "version": "-12823281204-export const theNum: TheNum2 = \"type2\";",
-          "signature": "812075564-/// <reference types=\"sometype\" />\nexport declare const theNum: TheNum2;\n"
-        },
         "version": "-12823281204-export const theNum: TheNum2 = \"type2\";",
-        "signature": "812075564-/// <reference types=\"sometype\" />\nexport declare const theNum: TheNum2;\n"
+        "signature": "-12823281204-export const theNum: TheNum2 = \"type2\";"
       },
       "./typeroot2/sometype/index.d.ts": {
         "original": {
@@ -214,21 +215,17 @@ exports.theNum = "type1";
       "./pkg2_index.ts",
       "./typeroot2/sometype/index.d.ts"
     ],
-    "latestChangedDtsFile": "./pkg2_index.d.ts"
+    "affectedFilesPendingEmit": [
+      [
+        "./pkg2_index.ts",
+        "Js | Dts"
+      ]
+    ],
+    "emitSignatures": [
+      "./pkg2_index.ts"
+    ]
   },
   "version": "FakeTSVersion",
-  "size": 1038
+  "size": 933
 }
 
-//// [/src/packages/pkg2_index.d.ts]
-/// <reference types="sometype" />
-export declare const theNum: TheNum2;
-
-
-//// [/src/packages/pkg2_index.js]
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.theNum = void 0;
-exports.theNum = "type2";
-
-
diff --git a/tests/baselines/reference/tsc/incremental/when-global-file-is-added,-the-signatures-are-updated.js b/tests/baselines/reference/tsc/incremental/when-global-file-is-added,-the-signatures-are-updated.js
index ec5de18bf2d40..a99240c862aa5 100644
--- a/tests/baselines/reference/tsc/incremental/when-global-file-is-added,-the-signatures-are-updated.js
+++ b/tests/baselines/reference/tsc/incremental/when-global-file-is-added,-the-signatures-are-updated.js
@@ -49,18 +49,28 @@ Output::
 2 /// <reference path="./fileNotFound.ts"/>
                        ~~~~~~~~~~~~~~~~~
 
+src/project/src/anotherFileWithSameReferenes.ts:3:1 - error TS18056: Declaration file contains synthesized file reference directives: '"filePresent.d.ts"'
+
+3 function anotherFileWithSameReferenes() { }
+  ~~~~~~~~
+
 src/project/src/main.ts:2:22 - error TS6053: File '/src/project/src/fileNotFound.ts' not found.
 
 2 /// <reference path="./fileNotFound.ts"/>
                        ~~~~~~~~~~~~~~~~~
 
+src/project/src/main.ts:3:1 - error TS18056: Declaration file contains synthesized file reference directives: '"filePresent.d.ts"'
 
-Found 2 errors in 2 files.
+3 function main() { }
+  ~~~~~~~~
+
+
+Found 4 errors in 2 files.
 
 Errors  Files
-     1  src/project/src/anotherFileWithSameReferenes.ts:2
-     1  src/project/src/main.ts:2
-exitCode:: ExitStatus.DiagnosticsPresent_OutputsGenerated
+     2  src/project/src/anotherFileWithSameReferenes.ts:2
+     2  src/project/src/main.ts:2
+exitCode:: ExitStatus.DiagnosticsPresent_OutputsSkipped
 Program root files: [
   "/src/project/src/anotherFileWithSameReferenes.ts",
   "/src/project/src/filePresent.ts",
@@ -87,15 +97,10 @@ Semantic diagnostics in builder refreshed for::
 Shape signatures in builder refreshed for::
 /lib/lib.d.ts (used version)
 /src/project/src/filepresent.ts (computed .d.ts during emit)
-/src/project/src/anotherfilewithsamereferenes.ts (computed .d.ts during emit)
-/src/project/src/main.ts (computed .d.ts during emit)
+/src/project/src/anotherfilewithsamereferenes.ts (used version)
+/src/project/src/main.ts (used version)
 
 
-//// [/src/project/src/anotherFileWithSameReferenes.d.ts]
-/// <reference path="filePresent.d.ts" />
-declare function anotherFileWithSameReferenes(): void;
-
-
 //// [/src/project/src/anotherFileWithSameReferenes.js]
 /// <reference path="./filePresent.ts"/>
 /// <reference path="./fileNotFound.ts"/>
@@ -110,11 +115,6 @@ declare function something(): number;
 function something() { return 10; }
 
 
-//// [/src/project/src/main.d.ts]
-/// <reference path="filePresent.d.ts" />
-declare function main(): void;
-
-
 //// [/src/project/src/main.js]
 /// <reference path="./filePresent.ts"/>
 /// <reference path="./fileNotFound.ts"/>
@@ -122,7 +122,7 @@ function main() { }
 
 
 //// [/src/project/tsconfig.tsbuildinfo]
-{"program":{"fileNames":["../../lib/lib.d.ts","./src/filepresent.ts","./src/anotherfilewithsamereferenes.ts","./src/main.ts","./src/filenotfound.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-12346563362-function something() { return 10; }","signature":"-4903250974-declare function something(): number;\n","affectsGlobalScope":true},{"version":"-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n","signature":"4626929588-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n","affectsGlobalScope":true},{"version":"-21256825585-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\n","signature":"6884835015-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n","affectsGlobalScope":true}],"root":[[2,4]],"options":{"composite":true},"fileIdsList":[[2,5]],"referencedMap":[[3,1],[4,1]],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,3,2,4],"latestChangedDtsFile":"./src/main.d.ts"},"version":"FakeTSVersion"}
+{"program":{"fileNames":["../../lib/lib.d.ts","./src/filepresent.ts","./src/anotherfilewithsamereferenes.ts","./src/main.ts","./src/filenotfound.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-12346563362-function something() { return 10; }","signature":"-4903250974-declare function something(): number;\n","affectsGlobalScope":true},{"version":"-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n","affectsGlobalScope":true},{"version":"-21256825585-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\n","affectsGlobalScope":true}],"root":[[2,4]],"options":{"composite":true},"fileIdsList":[[2,5]],"referencedMap":[[3,1],[4,1]],"exportedModulesMap":[[3,1],[4,1]],"semanticDiagnosticsPerFile":[1,3,2,4],"emitDiagnosticsPerFile":[[3,[{"file":"./src/anotherfilewithsamereferenes.ts","start":83,"length":8,"messageText":"Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'","category":1,"code":18056}]],[4,[{"file":"./src/main.ts","start":83,"length":8,"messageText":"Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'","category":1,"code":18056}]]],"emitSignatures":[3,4],"latestChangedDtsFile":"./src/filePresent.d.ts"},"version":"FakeTSVersion"}
 
 //// [/src/project/tsconfig.tsbuildinfo.readable.baseline.txt]
 {
@@ -163,21 +163,19 @@ function main() { }
       "./src/anotherfilewithsamereferenes.ts": {
         "original": {
           "version": "-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n",
-          "signature": "4626929588-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n",
           "affectsGlobalScope": true
         },
         "version": "-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n",
-        "signature": "4626929588-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n",
+        "signature": "-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n",
         "affectsGlobalScope": true
       },
       "./src/main.ts": {
         "original": {
           "version": "-21256825585-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\n",
-          "signature": "6884835015-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n",
           "affectsGlobalScope": true
         },
         "version": "-21256825585-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\n",
-        "signature": "6884835015-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n",
+        "signature": "-21256825585-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\n",
         "affectsGlobalScope": true
       }
     },
@@ -207,17 +205,58 @@ function main() { }
         "./src/filenotfound.ts"
       ]
     },
-    "exportedModulesMap": {},
+    "exportedModulesMap": {
+      "./src/anotherfilewithsamereferenes.ts": [
+        "./src/filepresent.ts",
+        "./src/filenotfound.ts"
+      ],
+      "./src/main.ts": [
+        "./src/filepresent.ts",
+        "./src/filenotfound.ts"
+      ]
+    },
     "semanticDiagnosticsPerFile": [
       "../../lib/lib.d.ts",
       "./src/anotherfilewithsamereferenes.ts",
       "./src/filepresent.ts",
       "./src/main.ts"
     ],
-    "latestChangedDtsFile": "./src/main.d.ts"
+    "emitDiagnosticsPerFile": [
+      [
+        "./src/anotherfilewithsamereferenes.ts",
+        [
+          {
+            "file": "./src/anotherfilewithsamereferenes.ts",
+            "start": 83,
+            "length": 8,
+            "messageText": "Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
+            "category": 1,
+            "code": 18056
+          }
+        ]
+      ],
+      [
+        "./src/main.ts",
+        [
+          {
+            "file": "./src/main.ts",
+            "start": 83,
+            "length": 8,
+            "messageText": "Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
+            "category": 1,
+            "code": 18056
+          }
+        ]
+      ]
+    ],
+    "emitSignatures": [
+      "./src/anotherfilewithsamereferenes.ts",
+      "./src/main.ts"
+    ],
+    "latestChangedDtsFile": "./src/filePresent.d.ts"
   },
   "version": "FakeTSVersion",
-  "size": 1607
+  "size": 1835
 }
 
 
@@ -233,18 +272,28 @@ Output::
 2 /// <reference path="./fileNotFound.ts"/>
                        ~~~~~~~~~~~~~~~~~
 
+src/project/src/anotherFileWithSameReferenes.ts:3:1 - error TS18056: Declaration file contains synthesized file reference directives: '"filePresent.d.ts"'
+
+3 function anotherFileWithSameReferenes() { }
+  ~~~~~~~~
+
 src/project/src/main.ts:2:22 - error TS6053: File '/src/project/src/fileNotFound.ts' not found.
 
 2 /// <reference path="./fileNotFound.ts"/>
                        ~~~~~~~~~~~~~~~~~
 
+src/project/src/main.ts:3:1 - error TS18056: Declaration file contains synthesized file reference directives: '"filePresent.d.ts"'
+
+3 function main() { }
+  ~~~~~~~~
 
-Found 2 errors in 2 files.
+
+Found 4 errors in 2 files.
 
 Errors  Files
-     1  src/project/src/anotherFileWithSameReferenes.ts:2
-     1  src/project/src/main.ts:2
-exitCode:: ExitStatus.DiagnosticsPresent_OutputsGenerated
+     2  src/project/src/anotherFileWithSameReferenes.ts:2
+     2  src/project/src/main.ts:2
+exitCode:: ExitStatus.DiagnosticsPresent_OutputsSkipped
 Program root files: [
   "/src/project/src/anotherFileWithSameReferenes.ts",
   "/src/project/src/filePresent.ts",
@@ -286,18 +335,28 @@ Output::
 2 /// <reference path="./fileNotFound.ts"/>
                        ~~~~~~~~~~~~~~~~~
 
+src/project/src/anotherFileWithSameReferenes.ts:3:1 - error TS18056: Declaration file contains synthesized file reference directives: '"filePresent.d.ts"'
+
+3 function anotherFileWithSameReferenes() { }
+  ~~~~~~~~
+
 src/project/src/main.ts:2:22 - error TS6053: File '/src/project/src/fileNotFound.ts' not found.
 
 2 /// <reference path="./fileNotFound.ts"/>
                        ~~~~~~~~~~~~~~~~~
 
+src/project/src/main.ts:3:1 - error TS18056: Declaration file contains synthesized file reference directives: '"filePresent.d.ts"'
+
+3 function main() { }
+  ~~~~~~~~
 
-Found 2 errors in 2 files.
+
+Found 4 errors in 2 files.
 
 Errors  Files
-     1  src/project/src/anotherFileWithSameReferenes.ts:2
-     1  src/project/src/main.ts:2
-exitCode:: ExitStatus.DiagnosticsPresent_OutputsGenerated
+     2  src/project/src/anotherFileWithSameReferenes.ts:2
+     2  src/project/src/main.ts:2
+exitCode:: ExitStatus.DiagnosticsPresent_OutputsSkipped
 Program root files: [
   "/src/project/src/anotherFileWithSameReferenes.ts",
   "/src/project/src/filePresent.ts",
@@ -316,12 +375,19 @@ Program files::
 /src/project/src/main.ts
 
 Semantic diagnostics in builder refreshed for::
+/lib/lib.d.ts
+/src/project/src/filePresent.ts
+/src/project/src/anotherFileWithSameReferenes.ts
 /src/project/src/main.ts
 
 Shape signatures in builder refreshed for::
 /src/project/src/main.ts (computed .d.ts)
+/src/project/src/filepresent.ts (computed .d.ts)
+/src/project/src/anotherfilewithsamereferenes.ts (computed .d.ts)
 
 
+//// [/src/project/src/anotherFileWithSameReferenes.js] file written with same contents
+//// [/src/project/src/filePresent.js] file written with same contents
 //// [/src/project/src/main.js]
 /// <reference path="./filePresent.ts"/>
 /// <reference path="./fileNotFound.ts"/>
@@ -330,7 +396,7 @@ something();
 
 
 //// [/src/project/tsconfig.tsbuildinfo]
-{"program":{"fileNames":["../../lib/lib.d.ts","./src/filepresent.ts","./src/anotherfilewithsamereferenes.ts","./src/main.ts","./src/filenotfound.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-12346563362-function something() { return 10; }","signature":"-4903250974-declare function something(): number;\n","affectsGlobalScope":true},{"version":"-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n","signature":"4626929588-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n","affectsGlobalScope":true},{"version":"-24702349751-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();","signature":"6884835015-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n","affectsGlobalScope":true}],"root":[[2,4]],"options":{"composite":true},"fileIdsList":[[2,5]],"referencedMap":[[3,1],[4,1]],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,3,2,4],"latestChangedDtsFile":"./src/main.d.ts"},"version":"FakeTSVersion"}
+{"program":{"fileNames":["../../lib/lib.d.ts","./src/filepresent.ts","./src/anotherfilewithsamereferenes.ts","./src/main.ts","./src/filenotfound.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-12346563362-function something() { return 10; }","signature":"-4903250974-declare function something(): number;\n","affectsGlobalScope":true},{"version":"-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n","signature":"19965656560-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'","affectsGlobalScope":true},{"version":"-24702349751-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();","signature":"20858779043-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'","affectsGlobalScope":true}],"root":[[2,4]],"options":{"composite":true},"fileIdsList":[[2,5]],"referencedMap":[[3,1],[4,1]],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,3,2,4],"emitDiagnosticsPerFile":[[3,[{"file":"./src/anotherfilewithsamereferenes.ts","start":83,"length":8,"messageText":"Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'","category":1,"code":18056}]],[4,[{"file":"./src/main.ts","start":83,"length":8,"messageText":"Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'","category":1,"code":18056}]]],"emitSignatures":[3,4],"latestChangedDtsFile":"./src/filePresent.d.ts"},"version":"FakeTSVersion"}
 
 //// [/src/project/tsconfig.tsbuildinfo.readable.baseline.txt]
 {
@@ -371,21 +437,21 @@ something();
       "./src/anotherfilewithsamereferenes.ts": {
         "original": {
           "version": "-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n",
-          "signature": "4626929588-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n",
+          "signature": "19965656560-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
           "affectsGlobalScope": true
         },
         "version": "-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n",
-        "signature": "4626929588-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n",
+        "signature": "19965656560-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
         "affectsGlobalScope": true
       },
       "./src/main.ts": {
         "original": {
           "version": "-24702349751-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();",
-          "signature": "6884835015-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n",
+          "signature": "20858779043-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
           "affectsGlobalScope": true
         },
         "version": "-24702349751-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();",
-        "signature": "6884835015-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n",
+        "signature": "20858779043-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
         "affectsGlobalScope": true
       }
     },
@@ -422,10 +488,42 @@ something();
       "./src/filepresent.ts",
       "./src/main.ts"
     ],
-    "latestChangedDtsFile": "./src/main.d.ts"
+    "emitDiagnosticsPerFile": [
+      [
+        "./src/anotherfilewithsamereferenes.ts",
+        [
+          {
+            "file": "./src/anotherfilewithsamereferenes.ts",
+            "start": 83,
+            "length": 8,
+            "messageText": "Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
+            "category": 1,
+            "code": 18056
+          }
+        ]
+      ],
+      [
+        "./src/main.ts",
+        [
+          {
+            "file": "./src/main.ts",
+            "start": 83,
+            "length": 8,
+            "messageText": "Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
+            "category": 1,
+            "code": 18056
+          }
+        ]
+      ]
+    ],
+    "emitSignatures": [
+      "./src/anotherfilewithsamereferenes.ts",
+      "./src/main.ts"
+    ],
+    "latestChangedDtsFile": "./src/filePresent.d.ts"
   },
   "version": "FakeTSVersion",
-  "size": 1619
+  "size": 2278
 }
 
 
@@ -447,18 +545,28 @@ Output::
 2 /// <reference path="./fileNotFound.ts"/>
                        ~~~~~~~~~~~~~~~~~
 
+src/project/src/anotherFileWithSameReferenes.ts:3:1 - error TS18056: Declaration file contains synthesized file reference directives: '"filePresent.d.ts"'
+
+3 function anotherFileWithSameReferenes() { }
+  ~~~~~~~~
+
 src/project/src/main.ts:2:22 - error TS6053: File '/src/project/src/fileNotFound.ts' not found.
 
 2 /// <reference path="./fileNotFound.ts"/>
                        ~~~~~~~~~~~~~~~~~
 
+src/project/src/main.ts:3:1 - error TS18056: Declaration file contains synthesized file reference directives: '"filePresent.d.ts"'
+
+3 function main() { }
+  ~~~~~~~~
 
-Found 2 errors in 2 files.
+
+Found 4 errors in 2 files.
 
 Errors  Files
-     1  src/project/src/anotherFileWithSameReferenes.ts:2
-     1  src/project/src/main.ts:2
-exitCode:: ExitStatus.DiagnosticsPresent_OutputsGenerated
+     2  src/project/src/anotherFileWithSameReferenes.ts:2
+     2  src/project/src/main.ts:2
+exitCode:: ExitStatus.DiagnosticsPresent_OutputsSkipped
 Program root files: [
   "/src/project/src/anotherFileWithSameReferenes.ts",
   "/src/project/src/filePresent.ts",
@@ -492,7 +600,7 @@ something();
 
 
 //// [/src/project/tsconfig.tsbuildinfo]
-{"program":{"fileNames":["../../lib/lib.d.ts","./src/filepresent.ts","./src/anotherfilewithsamereferenes.ts","./src/main.ts","./src/filenotfound.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-12346563362-function something() { return 10; }","signature":"-4903250974-declare function something(): number;\n","affectsGlobalScope":true},{"version":"-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n","signature":"4626929588-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n","affectsGlobalScope":true},{"version":"-20086051197-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();","signature":"6884835015-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n","affectsGlobalScope":true}],"root":[[2,4]],"options":{"composite":true},"fileIdsList":[[2,5]],"referencedMap":[[3,1],[4,1]],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,3,2,4],"latestChangedDtsFile":"./src/main.d.ts"},"version":"FakeTSVersion"}
+{"program":{"fileNames":["../../lib/lib.d.ts","./src/filepresent.ts","./src/anotherfilewithsamereferenes.ts","./src/main.ts","./src/filenotfound.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-12346563362-function something() { return 10; }","signature":"-4903250974-declare function something(): number;\n","affectsGlobalScope":true},{"version":"-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n","signature":"19965656560-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'","affectsGlobalScope":true},{"version":"-20086051197-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();","signature":"20858779043-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'","affectsGlobalScope":true}],"root":[[2,4]],"options":{"composite":true},"fileIdsList":[[2,5]],"referencedMap":[[3,1],[4,1]],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,3,2,4],"emitDiagnosticsPerFile":[[3,[{"file":"./src/anotherfilewithsamereferenes.ts","start":83,"length":8,"messageText":"Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'","category":1,"code":18056}]],[4,[{"file":"./src/main.ts","start":83,"length":8,"messageText":"Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'","category":1,"code":18056}]]],"emitSignatures":[3,4],"latestChangedDtsFile":"./src/filePresent.d.ts"},"version":"FakeTSVersion"}
 
 //// [/src/project/tsconfig.tsbuildinfo.readable.baseline.txt]
 {
@@ -533,21 +641,21 @@ something();
       "./src/anotherfilewithsamereferenes.ts": {
         "original": {
           "version": "-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n",
-          "signature": "4626929588-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n",
+          "signature": "19965656560-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
           "affectsGlobalScope": true
         },
         "version": "-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n",
-        "signature": "4626929588-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n",
+        "signature": "19965656560-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
         "affectsGlobalScope": true
       },
       "./src/main.ts": {
         "original": {
           "version": "-20086051197-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();",
-          "signature": "6884835015-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n",
+          "signature": "20858779043-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
           "affectsGlobalScope": true
         },
         "version": "-20086051197-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();",
-        "signature": "6884835015-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n",
+        "signature": "20858779043-/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
         "affectsGlobalScope": true
       }
     },
@@ -584,10 +692,42 @@ something();
       "./src/filepresent.ts",
       "./src/main.ts"
     ],
-    "latestChangedDtsFile": "./src/main.d.ts"
+    "emitDiagnosticsPerFile": [
+      [
+        "./src/anotherfilewithsamereferenes.ts",
+        [
+          {
+            "file": "./src/anotherfilewithsamereferenes.ts",
+            "start": 83,
+            "length": 8,
+            "messageText": "Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
+            "category": 1,
+            "code": 18056
+          }
+        ]
+      ],
+      [
+        "./src/main.ts",
+        [
+          {
+            "file": "./src/main.ts",
+            "start": 83,
+            "length": 8,
+            "messageText": "Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
+            "category": 1,
+            "code": 18056
+          }
+        ]
+      ]
+    ],
+    "emitSignatures": [
+      "./src/anotherfilewithsamereferenes.ts",
+      "./src/main.ts"
+    ],
+    "latestChangedDtsFile": "./src/filePresent.d.ts"
   },
   "version": "FakeTSVersion",
-  "size": 1631
+  "size": 2290
 }
 
 
@@ -613,18 +753,28 @@ Output::
 2 /// <reference path="./fileNotFound.ts"/>
                        ~~~~~~~~~~~~~~~~~
 
+src/project/src/anotherFileWithSameReferenes.ts:3:1 - error TS18056: Declaration file contains synthesized file reference directives: '"filePresent.d.ts"'
+
+3 function anotherFileWithSameReferenes() { }
+  ~~~~~~~~
+
 src/project/src/main.ts:3:22 - error TS6053: File '/src/project/src/fileNotFound.ts' not found.
 
 3 /// <reference path="./fileNotFound.ts"/>
                        ~~~~~~~~~~~~~~~~~
 
+src/project/src/main.ts:4:1 - error TS18056: Declaration file contains synthesized file reference directives: '"newFile.d.ts", "filePresent.d.ts"'
 
-Found 2 errors in 2 files.
+4 function main() { }
+  ~~~~~~~~
+
+
+Found 4 errors in 2 files.
 
 Errors  Files
-     1  src/project/src/anotherFileWithSameReferenes.ts:2
-     1  src/project/src/main.ts:3
-exitCode:: ExitStatus.DiagnosticsPresent_OutputsGenerated
+     2  src/project/src/anotherFileWithSameReferenes.ts:2
+     2  src/project/src/main.ts:3
+exitCode:: ExitStatus.DiagnosticsPresent_OutputsSkipped
 Program root files: [
   "/src/project/src/anotherFileWithSameReferenes.ts",
   "/src/project/src/filePresent.ts",
@@ -660,12 +810,6 @@ Shape signatures in builder refreshed for::
 
 //// [/src/project/src/anotherFileWithSameReferenes.js] file written with same contents
 //// [/src/project/src/filePresent.js] file written with same contents
-//// [/src/project/src/main.d.ts]
-/// <reference path="newFile.d.ts" />
-/// <reference path="filePresent.d.ts" />
-declare function main(): void;
-
-
 //// [/src/project/src/main.js]
 /// <reference path="./newFile.ts"/>
 /// <reference path="./filePresent.ts"/>
@@ -685,7 +829,7 @@ function foo() { return 20; }
 
 
 //// [/src/project/tsconfig.tsbuildinfo]
-{"program":{"fileNames":["../../lib/lib.d.ts","./src/filepresent.ts","./src/anotherfilewithsamereferenes.ts","./src/newfile.ts","./src/main.ts","./src/filenotfound.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-12346563362-function something() { return 10; }","signature":"-4903250974-declare function something(): number;\n","affectsGlobalScope":true},{"version":"-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n","signature":"4626929588-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n","affectsGlobalScope":true},{"version":"5451387573-function foo() { return 20; }","signature":"517738360-declare function foo(): number;\n","affectsGlobalScope":true},{"version":"-3581559188-/// <reference path=\"./newFile.ts\"/>\n/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();foo();","signature":"-1842835947-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n","affectsGlobalScope":true}],"root":[[2,5]],"options":{"composite":true},"fileIdsList":[[2,6],[2,4,6]],"referencedMap":[[3,1],[5,2]],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,3,2,5,4],"latestChangedDtsFile":"./src/main.d.ts"},"version":"FakeTSVersion"}
+{"program":{"fileNames":["../../lib/lib.d.ts","./src/filepresent.ts","./src/anotherfilewithsamereferenes.ts","./src/newfile.ts","./src/main.ts","./src/filenotfound.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-12346563362-function something() { return 10; }","signature":"-4903250974-declare function something(): number;\n","affectsGlobalScope":true},{"version":"-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n","signature":"19965656560-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'","affectsGlobalScope":true},{"version":"5451387573-function foo() { return 20; }","signature":"517738360-declare function foo(): number;\n","affectsGlobalScope":true},{"version":"-3581559188-/// <reference path=\"./newFile.ts\"/>\n/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();foo();","signature":"-5534159910-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n(120,8)Error18056: Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\"'","affectsGlobalScope":true}],"root":[[2,5]],"options":{"composite":true},"fileIdsList":[[2,6],[2,4,6]],"referencedMap":[[3,1],[5,2]],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,3,2,5,4],"emitDiagnosticsPerFile":[[3,[{"file":"./src/anotherfilewithsamereferenes.ts","start":83,"length":8,"messageText":"Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'","category":1,"code":18056}]],[5,[{"file":"./src/main.ts","start":120,"length":8,"messageText":"Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\"'","category":1,"code":18056}]]],"emitSignatures":[3,5],"latestChangedDtsFile":"./src/newFile.d.ts"},"version":"FakeTSVersion"}
 
 //// [/src/project/tsconfig.tsbuildinfo.readable.baseline.txt]
 {
@@ -732,11 +876,11 @@ function foo() { return 20; }
       "./src/anotherfilewithsamereferenes.ts": {
         "original": {
           "version": "-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n",
-          "signature": "4626929588-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n",
+          "signature": "19965656560-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
           "affectsGlobalScope": true
         },
         "version": "-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n",
-        "signature": "4626929588-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n",
+        "signature": "19965656560-/// <reference path=\"filePresent.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
         "affectsGlobalScope": true
       },
       "./src/newfile.ts": {
@@ -752,11 +896,11 @@ function foo() { return 20; }
       "./src/main.ts": {
         "original": {
           "version": "-3581559188-/// <reference path=\"./newFile.ts\"/>\n/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();foo();",
-          "signature": "-1842835947-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n",
+          "signature": "-5534159910-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n(120,8)Error18056: Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\"'",
           "affectsGlobalScope": true
         },
         "version": "-3581559188-/// <reference path=\"./newFile.ts\"/>\n/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();foo();",
-        "signature": "-1842835947-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n",
+        "signature": "-5534159910-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\ndeclare function main(): void;\n(120,8)Error18056: Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\"'",
         "affectsGlobalScope": true
       }
     },
@@ -796,10 +940,42 @@ function foo() { return 20; }
       "./src/main.ts",
       "./src/newfile.ts"
     ],
-    "latestChangedDtsFile": "./src/main.d.ts"
+    "emitDiagnosticsPerFile": [
+      [
+        "./src/anotherfilewithsamereferenes.ts",
+        [
+          {
+            "file": "./src/anotherfilewithsamereferenes.ts",
+            "start": 83,
+            "length": 8,
+            "messageText": "Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\"'",
+            "category": 1,
+            "code": 18056
+          }
+        ]
+      ],
+      [
+        "./src/main.ts",
+        [
+          {
+            "file": "./src/main.ts",
+            "start": 120,
+            "length": 8,
+            "messageText": "Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\"'",
+            "category": 1,
+            "code": 18056
+          }
+        ]
+      ]
+    ],
+    "emitSignatures": [
+      "./src/anotherfilewithsamereferenes.ts",
+      "./src/main.ts"
+    ],
+    "latestChangedDtsFile": "./src/newFile.d.ts"
   },
   "version": "FakeTSVersion",
-  "size": 1886
+  "size": 2578
 }
 
 
@@ -813,7 +989,23 @@ function something2() { return 20; }
 
 Output::
 /lib/tsc --p src/project
-exitCode:: ExitStatus.Success
+src/project/src/anotherFileWithSameReferenes.ts:3:1 - error TS18056: Declaration file contains synthesized file reference directives: '"filePresent.d.ts", "fileNotFound.d.ts"'
+
+3 function anotherFileWithSameReferenes() { }
+  ~~~~~~~~
+
+src/project/src/main.ts:4:1 - error TS18056: Declaration file contains synthesized file reference directives: '"newFile.d.ts", "filePresent.d.ts", "fileNotFound.d.ts"'
+
+4 function main() { }
+  ~~~~~~~~
+
+
+Found 2 errors in 2 files.
+
+Errors  Files
+     1  src/project/src/anotherFileWithSameReferenes.ts:3
+     1  src/project/src/main.ts:4
+exitCode:: ExitStatus.DiagnosticsPresent_OutputsSkipped
 Program root files: [
   "/src/project/src/anotherFileWithSameReferenes.ts",
   "/src/project/src/fileNotFound.ts",
@@ -851,12 +1043,6 @@ Shape signatures in builder refreshed for::
 /src/project/src/main.ts (computed .d.ts)
 
 
-//// [/src/project/src/anotherFileWithSameReferenes.d.ts]
-/// <reference path="filePresent.d.ts" />
-/// <reference path="fileNotFound.d.ts" />
-declare function anotherFileWithSameReferenes(): void;
-
-
 //// [/src/project/src/anotherFileWithSameReferenes.js] file written with same contents
 //// [/src/project/src/fileNotFound.d.ts]
 declare function something2(): number;
@@ -867,17 +1053,10 @@ function something2() { return 20; }
 
 
 //// [/src/project/src/filePresent.js] file written with same contents
-//// [/src/project/src/main.d.ts]
-/// <reference path="newFile.d.ts" />
-/// <reference path="filePresent.d.ts" />
-/// <reference path="fileNotFound.d.ts" />
-declare function main(): void;
-
-
 //// [/src/project/src/main.js] file written with same contents
 //// [/src/project/src/newFile.js] file written with same contents
 //// [/src/project/tsconfig.tsbuildinfo]
-{"program":{"fileNames":["../../lib/lib.d.ts","./src/filepresent.ts","./src/filenotfound.ts","./src/anotherfilewithsamereferenes.ts","./src/newfile.ts","./src/main.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-12346563362-function something() { return 10; }","signature":"-4903250974-declare function something(): number;\n","affectsGlobalScope":true},{"version":"-9011934479-function something2() { return 20; }","signature":"-11412869068-declare function something2(): number;\n","affectsGlobalScope":true},{"version":"-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n","signature":"-18213659-/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n","affectsGlobalScope":true},{"version":"5451387573-function foo() { return 20; }","signature":"517738360-declare function foo(): number;\n","affectsGlobalScope":true},{"version":"-3581559188-/// <reference path=\"./newFile.ts\"/>\n/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();foo();","signature":"5698040710-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function main(): void;\n","affectsGlobalScope":true}],"root":[[2,6]],"options":{"composite":true},"fileIdsList":[[2,3],[2,3,5]],"referencedMap":[[4,1],[6,2]],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,4,3,2,6,5],"latestChangedDtsFile":"./src/main.d.ts"},"version":"FakeTSVersion"}
+{"program":{"fileNames":["../../lib/lib.d.ts","./src/filepresent.ts","./src/filenotfound.ts","./src/anotherfilewithsamereferenes.ts","./src/newfile.ts","./src/main.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-12346563362-function something() { return 10; }","signature":"-4903250974-declare function something(): number;\n","affectsGlobalScope":true},{"version":"-9011934479-function something2() { return 20; }","signature":"-11412869068-declare function something2(): number;\n","affectsGlobalScope":true},{"version":"-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n","signature":"-17669273851-/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\", \"fileNotFound.d.ts\"'","affectsGlobalScope":true},{"version":"5451387573-function foo() { return 20; }","signature":"517738360-declare function foo(): number;\n","affectsGlobalScope":true},{"version":"-3581559188-/// <reference path=\"./newFile.ts\"/>\n/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();foo();","signature":"1320858511-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function main(): void;\n(120,8)Error18056: Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\", \"fileNotFound.d.ts\"'","affectsGlobalScope":true}],"root":[[2,6]],"options":{"composite":true},"fileIdsList":[[2,3],[2,3,5]],"referencedMap":[[4,1],[6,2]],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,4,3,2,6,5],"emitDiagnosticsPerFile":[[4,[{"file":"./src/anotherfilewithsamereferenes.ts","start":83,"length":8,"messageText":"Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\", \"fileNotFound.d.ts\"'","category":1,"code":18056}]],[6,[{"file":"./src/main.ts","start":120,"length":8,"messageText":"Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\", \"fileNotFound.d.ts\"'","category":1,"code":18056}]]],"emitSignatures":[4,6],"latestChangedDtsFile":"./src/fileNotFound.d.ts"},"version":"FakeTSVersion"}
 
 //// [/src/project/tsconfig.tsbuildinfo.readable.baseline.txt]
 {
@@ -934,11 +1113,11 @@ declare function main(): void;
       "./src/anotherfilewithsamereferenes.ts": {
         "original": {
           "version": "-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n",
-          "signature": "-18213659-/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n",
+          "signature": "-17669273851-/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\", \"fileNotFound.d.ts\"'",
           "affectsGlobalScope": true
         },
         "version": "-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n",
-        "signature": "-18213659-/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n",
+        "signature": "-17669273851-/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\", \"fileNotFound.d.ts\"'",
         "affectsGlobalScope": true
       },
       "./src/newfile.ts": {
@@ -954,11 +1133,11 @@ declare function main(): void;
       "./src/main.ts": {
         "original": {
           "version": "-3581559188-/// <reference path=\"./newFile.ts\"/>\n/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();foo();",
-          "signature": "5698040710-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function main(): void;\n",
+          "signature": "1320858511-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function main(): void;\n(120,8)Error18056: Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\", \"fileNotFound.d.ts\"'",
           "affectsGlobalScope": true
         },
         "version": "-3581559188-/// <reference path=\"./newFile.ts\"/>\n/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();foo();",
-        "signature": "5698040710-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function main(): void;\n",
+        "signature": "1320858511-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function main(): void;\n(120,8)Error18056: Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\", \"fileNotFound.d.ts\"'",
         "affectsGlobalScope": true
       }
     },
@@ -1000,10 +1179,42 @@ declare function main(): void;
       "./src/main.ts",
       "./src/newfile.ts"
     ],
-    "latestChangedDtsFile": "./src/main.d.ts"
+    "emitDiagnosticsPerFile": [
+      [
+        "./src/anotherfilewithsamereferenes.ts",
+        [
+          {
+            "file": "./src/anotherfilewithsamereferenes.ts",
+            "start": 83,
+            "length": 8,
+            "messageText": "Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\", \"fileNotFound.d.ts\"'",
+            "category": 1,
+            "code": 18056
+          }
+        ]
+      ],
+      [
+        "./src/main.ts",
+        [
+          {
+            "file": "./src/main.ts",
+            "start": 120,
+            "length": 8,
+            "messageText": "Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\", \"fileNotFound.d.ts\"'",
+            "category": 1,
+            "code": 18056
+          }
+        ]
+      ]
+    ],
+    "emitSignatures": [
+      "./src/anotherfilewithsamereferenes.ts",
+      "./src/main.ts"
+    ],
+    "latestChangedDtsFile": "./src/fileNotFound.d.ts"
   },
   "version": "FakeTSVersion",
-  "size": 2135
+  "size": 2926
 }
 
 
@@ -1021,7 +1232,23 @@ something();something();foo();something();
 
 Output::
 /lib/tsc --p src/project
-exitCode:: ExitStatus.Success
+src/project/src/anotherFileWithSameReferenes.ts:3:1 - error TS18056: Declaration file contains synthesized file reference directives: '"filePresent.d.ts", "fileNotFound.d.ts"'
+
+3 function anotherFileWithSameReferenes() { }
+  ~~~~~~~~
+
+src/project/src/main.ts:4:1 - error TS18056: Declaration file contains synthesized file reference directives: '"newFile.d.ts", "filePresent.d.ts", "fileNotFound.d.ts"'
+
+4 function main() { }
+  ~~~~~~~~
+
+
+Found 2 errors in 2 files.
+
+Errors  Files
+     1  src/project/src/anotherFileWithSameReferenes.ts:3
+     1  src/project/src/main.ts:4
+exitCode:: ExitStatus.DiagnosticsPresent_OutputsSkipped
 Program root files: [
   "/src/project/src/anotherFileWithSameReferenes.ts",
   "/src/project/src/fileNotFound.ts",
@@ -1062,7 +1289,7 @@ something();
 
 
 //// [/src/project/tsconfig.tsbuildinfo]
-{"program":{"fileNames":["../../lib/lib.d.ts","./src/filepresent.ts","./src/filenotfound.ts","./src/anotherfilewithsamereferenes.ts","./src/newfile.ts","./src/main.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-12346563362-function something() { return 10; }","signature":"-4903250974-declare function something(): number;\n","affectsGlobalScope":true},{"version":"-9011934479-function something2() { return 20; }","signature":"-11412869068-declare function something2(): number;\n","affectsGlobalScope":true},{"version":"-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n","signature":"-18213659-/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n","affectsGlobalScope":true},{"version":"5451387573-function foo() { return 20; }","signature":"517738360-declare function foo(): number;\n","affectsGlobalScope":true},{"version":"3987942182-/// <reference path=\"./newFile.ts\"/>\n/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();foo();something();","signature":"5698040710-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function main(): void;\n","affectsGlobalScope":true}],"root":[[2,6]],"options":{"composite":true},"fileIdsList":[[2,3],[2,3,5]],"referencedMap":[[4,1],[6,2]],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,4,3,2,6,5],"latestChangedDtsFile":"./src/main.d.ts"},"version":"FakeTSVersion"}
+{"program":{"fileNames":["../../lib/lib.d.ts","./src/filepresent.ts","./src/filenotfound.ts","./src/anotherfilewithsamereferenes.ts","./src/newfile.ts","./src/main.ts"],"fileInfos":[{"version":"3858781397-/// <reference no-default-lib=\"true\"/>\ninterface Boolean {}\ninterface Function {}\ninterface CallableFunction {}\ninterface NewableFunction {}\ninterface IArguments {}\ninterface Number { toExponential: any; }\ninterface Object {}\ninterface RegExp {}\ninterface String { charAt: any; }\ninterface Array<T> { length: number; [n: number]: T; }\ninterface ReadonlyArray<T> {}\ndeclare const console: { log(msg: any): void; };","affectsGlobalScope":true},{"version":"-12346563362-function something() { return 10; }","signature":"-4903250974-declare function something(): number;\n","affectsGlobalScope":true},{"version":"-9011934479-function something2() { return 20; }","signature":"-11412869068-declare function something2(): number;\n","affectsGlobalScope":true},{"version":"-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n","signature":"-17669273851-/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\", \"fileNotFound.d.ts\"'","affectsGlobalScope":true},{"version":"5451387573-function foo() { return 20; }","signature":"517738360-declare function foo(): number;\n","affectsGlobalScope":true},{"version":"3987942182-/// <reference path=\"./newFile.ts\"/>\n/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();foo();something();","signature":"1320858511-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function main(): void;\n(120,8)Error18056: Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\", \"fileNotFound.d.ts\"'","affectsGlobalScope":true}],"root":[[2,6]],"options":{"composite":true},"fileIdsList":[[2,3],[2,3,5]],"referencedMap":[[4,1],[6,2]],"exportedModulesMap":[],"semanticDiagnosticsPerFile":[1,4,3,2,6,5],"emitDiagnosticsPerFile":[[4,[{"file":"./src/anotherfilewithsamereferenes.ts","start":83,"length":8,"messageText":"Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\", \"fileNotFound.d.ts\"'","category":1,"code":18056}]],[6,[{"file":"./src/main.ts","start":120,"length":8,"messageText":"Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\", \"fileNotFound.d.ts\"'","category":1,"code":18056}]]],"emitSignatures":[4,6],"latestChangedDtsFile":"./src/fileNotFound.d.ts"},"version":"FakeTSVersion"}
 
 //// [/src/project/tsconfig.tsbuildinfo.readable.baseline.txt]
 {
@@ -1119,11 +1346,11 @@ something();
       "./src/anotherfilewithsamereferenes.ts": {
         "original": {
           "version": "-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n",
-          "signature": "-18213659-/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n",
+          "signature": "-17669273851-/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\", \"fileNotFound.d.ts\"'",
           "affectsGlobalScope": true
         },
         "version": "-28237004260-/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction anotherFileWithSameReferenes() { }\n",
-        "signature": "-18213659-/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n",
+        "signature": "-17669273851-/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function anotherFileWithSameReferenes(): void;\n(83,8)Error18056: Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\", \"fileNotFound.d.ts\"'",
         "affectsGlobalScope": true
       },
       "./src/newfile.ts": {
@@ -1139,11 +1366,11 @@ something();
       "./src/main.ts": {
         "original": {
           "version": "3987942182-/// <reference path=\"./newFile.ts\"/>\n/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();foo();something();",
-          "signature": "5698040710-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function main(): void;\n",
+          "signature": "1320858511-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function main(): void;\n(120,8)Error18056: Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\", \"fileNotFound.d.ts\"'",
           "affectsGlobalScope": true
         },
         "version": "3987942182-/// <reference path=\"./newFile.ts\"/>\n/// <reference path=\"./filePresent.ts\"/>\n/// <reference path=\"./fileNotFound.ts\"/>\nfunction main() { }\nsomething();something();foo();something();",
-        "signature": "5698040710-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function main(): void;\n",
+        "signature": "1320858511-/// <reference path=\"newFile.d.ts\" />\n/// <reference path=\"filePresent.d.ts\" />\n/// <reference path=\"fileNotFound.d.ts\" />\ndeclare function main(): void;\n(120,8)Error18056: Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\", \"fileNotFound.d.ts\"'",
         "affectsGlobalScope": true
       }
     },
@@ -1185,9 +1412,41 @@ something();
       "./src/main.ts",
       "./src/newfile.ts"
     ],
-    "latestChangedDtsFile": "./src/main.d.ts"
+    "emitDiagnosticsPerFile": [
+      [
+        "./src/anotherfilewithsamereferenes.ts",
+        [
+          {
+            "file": "./src/anotherfilewithsamereferenes.ts",
+            "start": 83,
+            "length": 8,
+            "messageText": "Declaration file contains synthesized file reference directives: '\"filePresent.d.ts\", \"fileNotFound.d.ts\"'",
+            "category": 1,
+            "code": 18056
+          }
+        ]
+      ],
+      [
+        "./src/main.ts",
+        [
+          {
+            "file": "./src/main.ts",
+            "start": 120,
+            "length": 8,
+            "messageText": "Declaration file contains synthesized file reference directives: '\"newFile.d.ts\", \"filePresent.d.ts\", \"fileNotFound.d.ts\"'",
+            "category": 1,
+            "code": 18056
+          }
+        ]
+      ]
+    ],
+    "emitSignatures": [
+      "./src/anotherfilewithsamereferenes.ts",
+      "./src/main.ts"
+    ],
+    "latestChangedDtsFile": "./src/fileNotFound.d.ts"
   },
   "version": "FakeTSVersion",
-  "size": 2146
+  "size": 2937
 }
 
diff --git a/tests/baselines/reference/typeReferenceDirectives11.errors.txt b/tests/baselines/reference/typeReferenceDirectives11.errors.txt
index b28f67c06959d..4299bd527fdeb 100644
--- a/tests/baselines/reference/typeReferenceDirectives11.errors.txt
+++ b/tests/baselines/reference/typeReferenceDirectives11.errors.txt
@@ -1,19 +1,25 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
+/mod1.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
 /mod1.ts(1,17): error TS6131: Cannot compile modules using option 'out' unless the '--module' flag is 'amd' or 'system'.
+/mod2.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
 !!! error TS5102:   Use 'outFile' instead.
-==== /mod2.ts (0 errors) ====
+==== /mod2.ts (1 errors) ====
     import {foo} from "./mod1";
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
     export const bar = foo();
     
 ==== /types/lib/index.d.ts (0 errors) ====
     interface Lib { x }
     
-==== /mod1.ts (1 errors) ====
+==== /mod1.ts (2 errors) ====
     export function foo(): Lib { return {x: 1} }
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
                     ~~~
 !!! error TS6131: Cannot compile modules using option 'out' unless the '--module' flag is 'amd' or 'system'.
     
\ No newline at end of file
diff --git a/tests/baselines/reference/typeReferenceDirectives12.errors.txt b/tests/baselines/reference/typeReferenceDirectives12.errors.txt
index e2917374c95ea..df21fc95e6816 100644
--- a/tests/baselines/reference/typeReferenceDirectives12.errors.txt
+++ b/tests/baselines/reference/typeReferenceDirectives12.errors.txt
@@ -1,12 +1,15 @@
 error TS5102: Option 'out' has been removed. Please remove it from your configuration.
   Use 'outFile' instead.
 /main.ts(1,14): error TS6131: Cannot compile modules using option 'out' unless the '--module' flag is 'amd' or 'system'.
+/mod2.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
 
 
 !!! error TS5102: Option 'out' has been removed. Please remove it from your configuration.
 !!! error TS5102:   Use 'outFile' instead.
-==== /mod2.ts (0 errors) ====
+==== /mod2.ts (1 errors) ====
     import { Cls } from "./main";
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
     import "./mod1";
     
     export const cls = Cls;
diff --git a/tests/baselines/reference/typeReferenceDirectives2.errors.txt b/tests/baselines/reference/typeReferenceDirectives2.errors.txt
new file mode 100644
index 0000000000000..33e6a9d265aff
--- /dev/null
+++ b/tests/baselines/reference/typeReferenceDirectives2.errors.txt
@@ -0,0 +1,12 @@
+/app.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
+
+
+==== /app.ts (1 errors) ====
+    interface A {
+    ~~~~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
+        x: $
+    }
+==== /types/lib/index.d.ts (0 errors) ====
+    interface $ { x }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/typeReferenceDirectives2.js b/tests/baselines/reference/typeReferenceDirectives2.js
index 3e9decbdfdae5..0e5de149bb71a 100644
--- a/tests/baselines/reference/typeReferenceDirectives2.js
+++ b/tests/baselines/reference/typeReferenceDirectives2.js
@@ -9,10 +9,3 @@ interface A {
 }
 
 //// [app.js]
-
-
-//// [app.d.ts]
-/// <reference types="lib" />
-interface A {
-    x: $;
-}
diff --git a/tests/baselines/reference/typeReferenceDirectives8.errors.txt b/tests/baselines/reference/typeReferenceDirectives8.errors.txt
new file mode 100644
index 0000000000000..0f08eea880d2a
--- /dev/null
+++ b/tests/baselines/reference/typeReferenceDirectives8.errors.txt
@@ -0,0 +1,17 @@
+/mod1.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
+/mod2.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
+
+
+==== /mod2.ts (1 errors) ====
+    import {foo} from "./mod1";
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
+    export const bar = foo();
+==== /types/lib/index.d.ts (0 errors) ====
+    interface Lib { x }
+    
+==== /mod1.ts (1 errors) ====
+    export function foo(): Lib { return {x: 1} }
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/typeReferenceDirectives8.js b/tests/baselines/reference/typeReferenceDirectives8.js
index 8526b26ed7b5f..b3a8a9e66790b 100644
--- a/tests/baselines/reference/typeReferenceDirectives8.js
+++ b/tests/baselines/reference/typeReferenceDirectives8.js
@@ -22,11 +22,3 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.bar = void 0;
 var mod1_1 = require("./mod1");
 exports.bar = (0, mod1_1.foo)();
-
-
-//// [mod1.d.ts]
-/// <reference types="lib" />
-export declare function foo(): Lib;
-//// [mod2.d.ts]
-/// <reference types="lib" />
-export declare const bar: Lib;
diff --git a/tests/baselines/reference/typeReferenceDirectives9.errors.txt b/tests/baselines/reference/typeReferenceDirectives9.errors.txt
new file mode 100644
index 0000000000000..7dc23b792beaa
--- /dev/null
+++ b/tests/baselines/reference/typeReferenceDirectives9.errors.txt
@@ -0,0 +1,35 @@
+/mod2.ts(1,1): error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
+
+
+==== /mod2.ts (1 errors) ====
+    import { Cls } from "./main";
+    ~~~~~~
+!!! error TS18055: Declaration file contains synthesized type reference directives: '"lib"'
+    import "./mod1";
+    
+    export const cls = Cls;
+    export const foo = new Cls().foo();
+    export const bar = Cls.bar();
+==== /types/lib/index.d.ts (0 errors) ====
+    interface Lib { x }
+    
+==== /main.ts (0 errors) ====
+    export class Cls {
+        x
+    }
+    
+==== /mod1.ts (0 errors) ====
+    /// <reference types="lib" />
+    
+    import {Cls} from "./main";
+    Cls.prototype.foo = function() { return undefined; }
+    
+    declare module "./main" {
+        interface Cls {
+            foo(): Lib;
+        }
+        namespace Cls {
+            function bar(): Lib;
+        }
+    }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/typeReferenceDirectives9.js b/tests/baselines/reference/typeReferenceDirectives9.js
index 625eae1646a54..9ceae4db2407a 100644
--- a/tests/baselines/reference/typeReferenceDirectives9.js
+++ b/tests/baselines/reference/typeReferenceDirectives9.js
@@ -73,10 +73,3 @@ declare module "./main" {
     }
 }
 export {};
-//// [mod2.d.ts]
-/// <reference types="lib" />
-import { Cls } from "./main";
-import "./mod1";
-export declare const cls: typeof Cls;
-export declare const foo: Lib;
-export declare const bar: Lib;
diff --git a/tests/baselines/reference/withImportDecl.errors.txt b/tests/baselines/reference/withImportDecl.errors.txt
new file mode 100644
index 0000000000000..849d154940382
--- /dev/null
+++ b/tests/baselines/reference/withImportDecl.errors.txt
@@ -0,0 +1,47 @@
+withImportDecl_1.ts(2,1): error TS18056: Declaration file contains synthesized file reference directives: '"withImportDecl_0.d.ts"'
+
+
+==== withImportDecl_1.ts (1 errors) ====
+    ///<reference path='withImportDecl_0.ts'/>
+    var simpleVar;
+    ~~~
+!!! error TS18056: Declaration file contains synthesized file reference directives: '"withImportDecl_0.d.ts"'
+    
+    var anotherVar: any;
+    var varWithSimpleType: number;
+    var varWithArrayType: number[];
+    
+    var varWithInitialValue = 30;
+    
+    var withComplicatedValue = { x: 30, y: 70, desc: "position" };
+    
+    declare var declaredVar;
+    declare var declareVar2
+    
+    declare var declaredVar;
+    declare var deckareVarWithType: number;
+    
+    var arrayVar: string[] = ['a', 'b'];
+    
+    
+    function simpleFunction() {
+        return {
+            x: "Hello",
+            y: "word",
+            n: 2
+        };
+    }
+    
+    module m1 {
+        export function foo() {
+            return "Hello";
+        }
+    }
+    
+    import m3 = require("withImportDecl_0");
+    
+    var b = new m3.A();
+    b.foo;
+==== withImportDecl_0.ts (0 errors) ====
+    export class A { foo: string; }
+    
\ No newline at end of file
diff --git a/tests/baselines/reference/withImportDecl.js b/tests/baselines/reference/withImportDecl.js
index 24f1c1bcb8032..beaa505266df4 100644
--- a/tests/baselines/reference/withImportDecl.js
+++ b/tests/baselines/reference/withImportDecl.js
@@ -90,6 +90,3 @@ define(["require", "exports", "withImportDecl_0"], function (require, exports, m
 export declare class A {
     foo: string;
 }
-//// [withImportDecl_1.d.ts]
-/// <reference path="withImportDecl_0.d.ts" />
-export {};