From 5be6ca2d0bb78a97e78c9e0e90d2a01a090fc08e Mon Sep 17 00:00:00 2001
From: Alexandre Archambault <alexandre.archambault@gmail.com>
Date: Wed, 24 Oct 2018 16:09:03 +0200
Subject: [PATCH 1/9] Allow to fetch both default and source or javadoc
 artifacts

Pass --classifer _ along --sources or --javadoc
---
 .../scala-2.12/coursier/cli/Bootstrap.scala   |  6 ++---
 .../main/scala-2.12/coursier/cli/Fetch.scala  |  3 ++-
 .../main/scala-2.12/coursier/cli/Helper.scala | 19 +++++++++++---
 .../scala-2.12/coursier/cli/SparkSubmit.scala |  8 +++---
 .../cli/options/ArtifactOptions.scala         | 12 +++++----
 .../cli/CliFetchIntegrationTest.scala         | 26 +++++++++++++++++++
 6 files changed, 57 insertions(+), 17 deletions(-)

diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala b/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
index 8fede6c593..2dc83871d5 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
@@ -27,7 +27,7 @@ object Bootstrap extends CaseApp[BootstrapOptions] {
     val files = helper.fetch(
       sources = false,
       javadoc = false,
-      artifactTypes = options.artifactOptions.artifactTypes(sources = false, javadoc = false)
+      artifactTypes = options.artifactOptions.artifactTypes()
     )
 
     val log: String => Unit =
@@ -168,7 +168,7 @@ object Bootstrap extends CaseApp[BootstrapOptions] {
           val m = helper.fetchMap(
             sources = false,
             javadoc = false,
-            artifactTypes = options.artifactOptions.artifactTypes(sources = false, javadoc = false),
+            artifactTypes = options.artifactOptions.artifactTypes(),
             subset = isolatedDeps.getOrElse(target, Seq.empty).toSet
           )
 
@@ -353,7 +353,7 @@ object Bootstrap extends CaseApp[BootstrapOptions] {
         helper.fetchMap(
           sources = false,
           javadoc = false,
-          artifactTypes = options.artifactOptions.artifactTypes(sources = false, javadoc = false)
+          artifactTypes = options.artifactOptions.artifactTypes()
         ).toList.foldLeft((List.empty[String], List.empty[File])){
           case ((urls, files), (url, file)) =>
             if (options.options.assembly || options.options.standalone) (urls, file :: files)
diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala b/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala
index 01684383bc..ae580c309c 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala
@@ -16,7 +16,8 @@ final class Fetch(options: FetchOptions, args: RemainingArgs) {
     javadoc = options.javadoc,
     artifactTypes = options.artifactOptions.artifactTypes(
       options.sources || options.common.classifier0(Classifier.sources),
-      options.javadoc || options.common.classifier0(Classifier.javadoc)
+      options.javadoc || options.common.classifier0(Classifier.javadoc),
+      (!options.sources && !options.javadoc) || options.common.classifier0(Classifier("_"))
     )
   )
 
diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/Helper.scala b/modules/cli/src/main/scala-2.12/coursier/cli/Helper.scala
index fd09977978..a5506dd670 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/Helper.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/Helper.scala
@@ -599,11 +599,22 @@ class Helper(
   }
 
   private def getDepArtifactsForClassifier(sources: Boolean, javadoc: Boolean, res0: Resolution): Seq[(Dependency, Attributes, Artifact)] = {
+
     val raw =
-      if (hasOverrideClassifiers(sources, javadoc))
-        //TODO: this function somehow gives duplicated things
-        res0.dependencyArtifacts(Some(overrideClassifiers(sources, javadoc).toVector.sorted))
-      else
+      if (hasOverrideClassifiers(sources, javadoc)) {
+        val classifiers = overrideClassifiers(sources, javadoc)
+
+        val baseArtifacts =
+          if (classifiers(Classifier("_")))
+            res0.dependencyArtifacts(None)
+          else
+            Nil
+
+        val classifierArtifacts =
+          res0.dependencyArtifacts(Some(classifiers.filter(_ != Classifier("_")).toVector.sorted))
+
+        baseArtifacts ++ classifierArtifacts
+      } else
         res0.dependencyArtifacts(None)
 
     raw.map {
diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/SparkSubmit.scala b/modules/cli/src/main/scala-2.12/coursier/cli/SparkSubmit.scala
index 9baf518366..80838872ec 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/SparkSubmit.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/SparkSubmit.scala
@@ -65,7 +65,7 @@ object SparkSubmit extends CaseApp[SparkSubmitOptions] {
       helper.fetch(
         sources = false,
         javadoc = false,
-        artifactTypes = options.artifactOptions.artifactTypes(sources = false, javadoc = false)
+        artifactTypes = options.artifactOptions.artifactTypes()
       ) ++ options.extraJars.map(new File(_))
 
     val (scalaVersion, sparkVersion) =
@@ -93,7 +93,7 @@ object SparkSubmit extends CaseApp[SparkSubmitOptions] {
           options.assemblyDependencies.flatMap(_.split(",")).filter(_.nonEmpty) ++
             options.sparkAssemblyDependencies.flatMap(_.split(",")).filter(_.nonEmpty).map(_ + s":$sparkVersion"),
           options.common,
-          options.artifactOptions.artifactTypes(sources = false, javadoc = false)
+          options.artifactOptions.artifactTypes()
         )
 
         val extraConf =
@@ -115,7 +115,7 @@ object SparkSubmit extends CaseApp[SparkSubmitOptions] {
           options.assemblyDependencies.flatMap(_.split(",")).filter(_.nonEmpty) ++
             options.sparkAssemblyDependencies.flatMap(_.split(",")).filter(_.nonEmpty).map(_ + s":$sparkVersion"),
           options.common,
-          options.artifactOptions.artifactTypes(sources = false, javadoc = false)
+          options.artifactOptions.artifactTypes()
         )
 
         val (assembly, assemblyJars) = assemblyAndJarsOrError match {
@@ -191,7 +191,7 @@ object SparkSubmit extends CaseApp[SparkSubmitOptions] {
       sparkVersion,
       options.noDefaultSubmitDependencies,
       options.submitDependencies.flatMap(_.split(",")).filter(_.nonEmpty),
-      options.artifactOptions.artifactTypes(sources = false, javadoc = false),
+      options.artifactOptions.artifactTypes(),
       options.common
     )
 
diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala b/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala
index 63092684bb..50a89f4916 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala
@@ -18,7 +18,9 @@ final case class ArtifactOptions(
   @Help("Fetch artifacts even if the resolution is errored")
     force: Boolean = false
 ) {
-  def artifactTypes(sources: Boolean, javadoc: Boolean): Set[Type] = {
+  def artifactTypes(): Set[Type] =
+    artifactTypes(sources = false, javadoc = false, default = true)
+  def artifactTypes(sources: Boolean, javadoc: Boolean, default: Boolean): Set[Type] = {
 
     val types0 = artifactType
       .flatMap(_.split(','))
@@ -27,10 +29,10 @@ final case class ArtifactOptions(
       .toSet
 
     if (types0.isEmpty) {
-      if (sources || javadoc)
-        Some(Type.source).filter(_ => sources).toSet ++ Some(Type.doc).filter(_ => javadoc)
-      else
-        ArtifactOptions.defaultArtifactTypes
+      val sourceTypes = Some(Type.source).filter(_ => sources).toSet
+      val javadocTypes = Some(Type.doc).filter(_ => javadoc).toSet
+      val defaultTypes = if (default) ArtifactOptions.defaultArtifactTypes else Set()
+      sourceTypes ++ javadocTypes ++ defaultTypes
     } else if (types0(Type("*")))
       Set(Type("*"))
     else
diff --git a/modules/cli/src/test/scala-2.12/coursier/cli/CliFetchIntegrationTest.scala b/modules/cli/src/test/scala-2.12/coursier/cli/CliFetchIntegrationTest.scala
index 850525cf11..f5a47fc2a9 100644
--- a/modules/cli/src/test/scala-2.12/coursier/cli/CliFetchIntegrationTest.scala
+++ b/modules/cli/src/test/scala-2.12/coursier/cli/CliFetchIntegrationTest.scala
@@ -42,6 +42,32 @@ class CliFetchIntegrationTest extends FlatSpec with CliTestLib with Matchers {
     assert(fetch.files0.map(_.getName).toSet.equals(Set("junit-4.12.jar", "hamcrest-core-1.3.jar")))
   }
 
+  "Underscore classifier" should "fetch default files" in {
+    val commonOpt = CommonOptions(
+      classifier = List("_")
+    )
+    val fetchOpt = FetchOptions(common = commonOpt)
+    val fetch = Fetch(fetchOpt, RemainingArgs(Seq("junit:junit:4.12"), Seq()))
+    assert(fetch.files0.map(_.getName).toSet.equals(Set("junit-4.12.jar", "hamcrest-core-1.3.jar")))
+  }
+
+  "Underscore and source classifier" should "fetch default and source files" in {
+    val commonOpt = CommonOptions(
+      classifier = List("_")
+    )
+    val fetchOpt = FetchOptions(
+      common = commonOpt,
+      sources = true
+    )
+    val fetch = Fetch(fetchOpt, RemainingArgs(Seq("junit:junit:4.12"), Seq()))
+    assert(fetch.files0.map(_.getName).toSet.equals(Set(
+      "junit-4.12.jar",
+      "junit-4.12-sources.jar",
+      "hamcrest-core-1.3.jar",
+      "hamcrest-core-1.3-sources.jar"
+    )))
+  }
+
   "scalafmt-cli fetch" should "discover all main classes" in {
     val fetchOpt = FetchOptions(common = CommonOptions())
     val fetch = Fetch(fetchOpt, RemainingArgs(Seq("com.geirsson:scalafmt-cli_2.12:1.4.0"), Seq()))

From b8b9fb5e47eee0850c430b491572ebb3b233fc6a Mon Sep 17 00:00:00 2001
From: Alexandre Archambault <alexandre.archambault@gmail.com>
Date: Wed, 24 Oct 2018 16:29:17 +0200
Subject: [PATCH 2/9] Accept --default option to get default artifacts along
 --sources

---
 .../scala-2.12/coursier/cli/Bootstrap.scala   |  3 ++
 .../main/scala-2.12/coursier/cli/Fetch.scala  |  8 +++-
 .../main/scala-2.12/coursier/cli/Helper.scala | 48 ++++++++++++++-----
 .../scala-2.12/coursier/cli/SparkSubmit.scala |  1 +
 .../coursier/cli/options/FetchOptions.scala   |  2 +
 .../coursier/cli/spark/SparkAssembly.scala    |  6 +--
 .../coursier/cli/spark/Submit.scala           |  1 +
 .../cli/CliFetchIntegrationTest.scala         | 15 ++++++
 8 files changed, 69 insertions(+), 15 deletions(-)

diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala b/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
index 2dc83871d5..2eb868ad4d 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
@@ -27,6 +27,7 @@ object Bootstrap extends CaseApp[BootstrapOptions] {
     val files = helper.fetch(
       sources = false,
       javadoc = false,
+      default = true,
       artifactTypes = options.artifactOptions.artifactTypes()
     )
 
@@ -168,6 +169,7 @@ object Bootstrap extends CaseApp[BootstrapOptions] {
           val m = helper.fetchMap(
             sources = false,
             javadoc = false,
+            default = true,
             artifactTypes = options.artifactOptions.artifactTypes(),
             subset = isolatedDeps.getOrElse(target, Seq.empty).toSet
           )
@@ -353,6 +355,7 @@ object Bootstrap extends CaseApp[BootstrapOptions] {
         helper.fetchMap(
           sources = false,
           javadoc = false,
+          default = true,
           artifactTypes = options.artifactOptions.artifactTypes()
         ).toList.foldLeft((List.empty[String], List.empty[File])){
           case ((urls, files), (url, file)) =>
diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala b/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala
index ae580c309c..8ae21a3a95 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala
@@ -11,13 +11,19 @@ final class Fetch(options: FetchOptions, args: RemainingArgs) {
 
   val helper = new Helper(options.common, args.all, ignoreErrors = options.artifactOptions.force)
 
+  val default = options.default.getOrElse {
+    (!options.sources && !options.javadoc && options.common.classifier0.isEmpty) ||
+      options.common.classifier0(Classifier("_"))
+  }
+
   val files0 = helper.fetch(
     sources = options.sources,
     javadoc = options.javadoc,
+    default = default,
     artifactTypes = options.artifactOptions.artifactTypes(
       options.sources || options.common.classifier0(Classifier.sources),
       options.javadoc || options.common.classifier0(Classifier.javadoc),
-      (!options.sources && !options.javadoc) || options.common.classifier0(Classifier("_"))
+      default
     )
   )
 
diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/Helper.scala b/modules/cli/src/main/scala-2.12/coursier/cli/Helper.scala
index a5506dd670..6bb793efd8 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/Helper.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/Helper.scala
@@ -564,6 +564,7 @@ class Helper(
   def artifacts(
     sources: Boolean,
     javadoc: Boolean,
+    default: Boolean,
     artifactTypes: Set[Type],
     subset: Set[Dependency] = null
   ): Seq[Artifact] = {
@@ -587,7 +588,7 @@ class Helper(
 
     val res0 = Option(subset).fold(res)(res.subset)
 
-    val artifacts0 = getDepArtifactsForClassifier(sources, javadoc, res0).map(t => (t._2, t._3))
+    val artifacts0 = getDepArtifactsForClassifier(sources, javadoc, default, res0).map(t => (t._2, t._3))
 
     if (artifactTypes(Type("*")))
       artifacts0.map(_._2)
@@ -598,11 +599,16 @@ class Helper(
       }
   }
 
-  private def getDepArtifactsForClassifier(sources: Boolean, javadoc: Boolean, res0: Resolution): Seq[(Dependency, Attributes, Artifact)] = {
+  private def getDepArtifactsForClassifier(
+    sources: Boolean,
+    javadoc: Boolean,
+    default: Boolean,
+    res0: Resolution
+  ): Seq[(Dependency, Attributes, Artifact)] = {
 
     val raw =
       if (hasOverrideClassifiers(sources, javadoc)) {
-        val classifiers = overrideClassifiers(sources, javadoc)
+        val classifiers = overrideClassifiers(sources, javadoc, default)
 
         val baseArtifacts =
           if (classifiers(Classifier("_")))
@@ -628,12 +634,18 @@ class Helper(
     }
   }
 
-  private def overrideClassifiers(sources: Boolean, javadoc:Boolean): Set[Classifier] = {
+  private def overrideClassifiers(
+    sources: Boolean,
+    javadoc: Boolean,
+    default: Boolean
+  ): Set[Classifier] = {
     var classifiers = classifier0
     if (sources)
       classifiers = classifiers + Classifier.sources
     if (javadoc)
       classifiers = classifiers + Classifier.javadoc
+    if (default)
+      classifiers = classifiers + Classifier("_")
     classifiers
   }
 
@@ -644,11 +656,12 @@ class Helper(
   def fetchMap(
     sources: Boolean,
     javadoc: Boolean,
+    default: Boolean,
     artifactTypes: Set[Type],
     subset: Set[Dependency] = null
   ): Map[String, File] = {
 
-    val artifacts0 = artifacts(sources, javadoc, artifactTypes, subset).distinct
+    val artifacts0 = artifacts(sources, javadoc, default, artifactTypes, subset).distinct
 
     val logger =
       if (common.verbosityLevel >= 0)
@@ -729,13 +742,13 @@ class Helper(
     }
 
     val depToArtifacts: Map[Dependency, Vector[(Attributes, Artifact)]] =
-      getDepArtifactsForClassifier(sources, javadoc, res).groupBy(_._1).mapValues(_.map(t => (t._2, t._3)).toVector)
+      getDepArtifactsForClassifier(sources, javadoc, default, res).groupBy(_._1).mapValues(_.map(t => (t._2, t._3)).toVector)
 
 
     if (!jsonOutputFile.isEmpty) {
       // TODO(wisechengyi): This is not exactly the root dependencies we are asking for on the command line, but it should be
       // a strict super set.
-      val deps: Seq[Dependency] = Set(getDepArtifactsForClassifier(sources, javadoc, res).map(_._1): _*).toSeq
+      val deps: Seq[Dependency] = Set(getDepArtifactsForClassifier(sources, javadoc, default, res).map(_._1): _*).toSeq
 
       // A map from requested org:name:version to reconciled org:name:version
       val conflictResolutionForRoots: Map[String, String] = allDependencies.map({ dep =>
@@ -754,7 +767,18 @@ class Helper(
       }
 
       val jsonReq = JsonPrintRequirement(artifactToFile, depToArtifacts)
-      val roots = deps.toVector.map(JsonElem(_, artifacts, Option(jsonReq), res, printExclusions = common.verbosityLevel >= 1, excluded = false, colors = false, overrideClassifiers = overrideClassifiers(sources, javadoc)))
+      val roots = deps.toVector.map(d =>
+        JsonElem(
+          d,
+          artifacts,
+          Option(jsonReq),
+          res,
+          printExclusions = common.verbosityLevel >= 1,
+          excluded = false,
+          colors = false,
+          overrideClassifiers = overrideClassifiers(sources, javadoc, default)
+        )
+      )
       val jsonStr = JsonReport(
         roots,
         conflictResolutionForRoots
@@ -774,11 +798,11 @@ class Helper(
   def fetch(
     sources: Boolean,
     javadoc: Boolean,
+    default: Boolean,
     artifactTypes: Set[Type],
     subset: Set[Dependency] = null
-  ): Seq[File] = {
-    fetchMap(sources, javadoc, artifactTypes, subset).values.toSeq
-  }
+  ): Seq[File] =
+    fetchMap(sources, javadoc, default, artifactTypes, subset).values.toSeq
 
   def contextLoader = Thread.currentThread().getContextClassLoader
 
@@ -803,6 +827,7 @@ class Helper(
     val files0 = fetch(
       sources = false,
       javadoc = false,
+      default = true,
       artifactTypes = artifactTypes
     )
 
@@ -819,6 +844,7 @@ class Helper(
           val isolatedFiles = fetch(
             sources = false,
             javadoc = false,
+            default = true,
             artifactTypes = artifactTypes,
             subset = isolatedDeps.getOrElse(target, Seq.empty).toSet
           )
diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/SparkSubmit.scala b/modules/cli/src/main/scala-2.12/coursier/cli/SparkSubmit.scala
index 80838872ec..6bb200c3ac 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/SparkSubmit.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/SparkSubmit.scala
@@ -65,6 +65,7 @@ object SparkSubmit extends CaseApp[SparkSubmitOptions] {
       helper.fetch(
         sources = false,
         javadoc = false,
+        default = true,
         artifactTypes = options.artifactOptions.artifactTypes()
       ) ++ options.extraJars.map(new File(_))
 
diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/options/FetchOptions.scala b/modules/cli/src/main/scala-2.12/coursier/cli/options/FetchOptions.scala
index 59fa5daebe..19bb2e9804 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/options/FetchOptions.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/options/FetchOptions.scala
@@ -9,6 +9,8 @@ final case class FetchOptions(
   @Help("Fetch javadoc artifacts")
   @Short("D")
     javadoc: Boolean = false,
+  @Help("Fetch default artifacts (default: false if --sources or --javadoc or --classifier are passed, true else)")
+    default: Option[Boolean] = None,
   @Help("Print java -cp compatible output")
   @Short("p")
     classpath: Boolean = false,
diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/spark/SparkAssembly.scala b/modules/cli/src/main/scala-2.12/coursier/cli/spark/SparkAssembly.scala
index 72685e8eef..8b18b4be29 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/spark/SparkAssembly.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/spark/SparkAssembly.scala
@@ -82,7 +82,7 @@ object SparkAssembly {
 
     val helper = sparkJarsHelper(scalaVersion, sparkVersion, yarnVersion, default, extraDependencies, options)
 
-    helper.fetch(sources = false, javadoc = false, artifactTypes = artifactTypes)
+    helper.fetch(sources = false, javadoc = false, default = true, artifactTypes = artifactTypes)
   }
 
   def spark(
@@ -99,8 +99,8 @@ object SparkAssembly {
 
     val helper = sparkJarsHelper(scalaVersion, sparkVersion, yarnVersion, default, extraDependencies, options)
 
-    val artifacts = helper.artifacts(sources = false, javadoc = false, artifactTypes = artifactTypes)
-    val jars = helper.fetch(sources = false, javadoc = false, artifactTypes = artifactTypes)
+    val artifacts = helper.artifacts(sources = false, javadoc = false, default = true, artifactTypes = artifactTypes)
+    val jars = helper.fetch(sources = false, javadoc = false, default = true, artifactTypes = artifactTypes)
 
     val checksums = artifacts.map { a =>
       val f = a.checksumUrls.get("SHA-1") match {
diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/spark/Submit.scala b/modules/cli/src/main/scala-2.12/coursier/cli/spark/Submit.scala
index 8e52bf3207..160ed970a2 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/spark/Submit.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/spark/Submit.scala
@@ -51,6 +51,7 @@ object Submit {
     helper.fetch(
       sources = false,
       javadoc = false,
+      default = true,
       artifactTypes = artifactTypes
     ) ++ extraCp
   }
diff --git a/modules/cli/src/test/scala-2.12/coursier/cli/CliFetchIntegrationTest.scala b/modules/cli/src/test/scala-2.12/coursier/cli/CliFetchIntegrationTest.scala
index f5a47fc2a9..6c530c63d3 100644
--- a/modules/cli/src/test/scala-2.12/coursier/cli/CliFetchIntegrationTest.scala
+++ b/modules/cli/src/test/scala-2.12/coursier/cli/CliFetchIntegrationTest.scala
@@ -68,6 +68,21 @@ class CliFetchIntegrationTest extends FlatSpec with CliTestLib with Matchers {
     )))
   }
 
+  "Default and source options" should "fetch default and source files" in {
+    val fetchOpt = FetchOptions(
+      common = CommonOptions(),
+      default = Some(true),
+      sources = true
+    )
+    val fetch = Fetch(fetchOpt, RemainingArgs(Seq("junit:junit:4.12"), Seq()))
+    assert(fetch.files0.map(_.getName).toSet.equals(Set(
+      "junit-4.12.jar",
+      "junit-4.12-sources.jar",
+      "hamcrest-core-1.3.jar",
+      "hamcrest-core-1.3-sources.jar"
+    )))
+  }
+
   "scalafmt-cli fetch" should "discover all main classes" in {
     val fetchOpt = FetchOptions(common = CommonOptions())
     val fetch = Fetch(fetchOpt, RemainingArgs(Seq("com.geirsson:scalafmt-cli_2.12:1.4.0"), Seq()))

From b0a3d1ef1a5a9388a7f5dd356b14f6716b0de6c3 Mon Sep 17 00:00:00 2001
From: Alexandre Archambault <alexandre.archambault@gmail.com>
Date: Wed, 24 Oct 2018 16:36:36 +0200
Subject: [PATCH 3/9] Move --sources / --javadoc / --default options to
 ArtifactOptions

So that they can be taken into account from other commands
---
 .../src/main/scala-2.12/coursier/cli/Fetch.scala  | 12 ++++++------
 .../coursier/cli/options/ArtifactOptions.scala    |  8 ++++++++
 .../coursier/cli/options/FetchOptions.scala       |  8 --------
 .../coursier/cli/CliFetchIntegrationTest.scala    | 15 +++++++++++----
 4 files changed, 25 insertions(+), 18 deletions(-)

diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala b/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala
index 8ae21a3a95..48379d37e9 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala
@@ -11,18 +11,18 @@ final class Fetch(options: FetchOptions, args: RemainingArgs) {
 
   val helper = new Helper(options.common, args.all, ignoreErrors = options.artifactOptions.force)
 
-  val default = options.default.getOrElse {
-    (!options.sources && !options.javadoc && options.common.classifier0.isEmpty) ||
+  val default = options.artifactOptions.default.getOrElse {
+    (!options.artifactOptions.sources && !options.artifactOptions.javadoc && options.common.classifier0.isEmpty) ||
       options.common.classifier0(Classifier("_"))
   }
 
   val files0 = helper.fetch(
-    sources = options.sources,
-    javadoc = options.javadoc,
+    sources = options.artifactOptions.sources,
+    javadoc = options.artifactOptions.javadoc,
     default = default,
     artifactTypes = options.artifactOptions.artifactTypes(
-      options.sources || options.common.classifier0(Classifier.sources),
-      options.javadoc || options.common.classifier0(Classifier.javadoc),
+      options.artifactOptions.sources || options.common.classifier0(Classifier.sources),
+      options.artifactOptions.javadoc || options.common.classifier0(Classifier.javadoc),
       default
     )
   )
diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala b/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala
index 50a89f4916..711f2e4ea7 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala
@@ -11,6 +11,14 @@ object ArtifactOptions {
 }
 
 final case class ArtifactOptions(
+  @Help("Fetch source artifacts")
+  @Short("S")
+    sources: Boolean = false,
+  @Help("Fetch javadoc artifacts")
+  @Short("D")
+    javadoc: Boolean = false,
+  @Help("Fetch default artifacts (default: false if --sources or --javadoc or --classifier are passed, true else)")
+    default: Option[Boolean] = None,
   @Help("Artifact types that should be retained (e.g. jar, src, doc, etc.) - defaults to jar,bundle")
   @Value("type1,type2,...")
   @Short("A")
diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/options/FetchOptions.scala b/modules/cli/src/main/scala-2.12/coursier/cli/options/FetchOptions.scala
index 19bb2e9804..3e5a94a10c 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/options/FetchOptions.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/options/FetchOptions.scala
@@ -3,14 +3,6 @@ package coursier.cli.options
 import caseapp.{ HelpMessage => Help, ExtraName => Short, _ }
 
 final case class FetchOptions(
-  @Help("Fetch source artifacts")
-  @Short("S")
-    sources: Boolean = false,
-  @Help("Fetch javadoc artifacts")
-  @Short("D")
-    javadoc: Boolean = false,
-  @Help("Fetch default artifacts (default: false if --sources or --javadoc or --classifier are passed, true else)")
-    default: Option[Boolean] = None,
   @Help("Print java -cp compatible output")
   @Short("p")
     classpath: Boolean = false,
diff --git a/modules/cli/src/test/scala-2.12/coursier/cli/CliFetchIntegrationTest.scala b/modules/cli/src/test/scala-2.12/coursier/cli/CliFetchIntegrationTest.scala
index 6c530c63d3..91696ac3d0 100644
--- a/modules/cli/src/test/scala-2.12/coursier/cli/CliFetchIntegrationTest.scala
+++ b/modules/cli/src/test/scala-2.12/coursier/cli/CliFetchIntegrationTest.scala
@@ -55,9 +55,12 @@ class CliFetchIntegrationTest extends FlatSpec with CliTestLib with Matchers {
     val commonOpt = CommonOptions(
       classifier = List("_")
     )
+    val artifactOpt = ArtifactOptions(
+      sources = true
+    )
     val fetchOpt = FetchOptions(
       common = commonOpt,
-      sources = true
+      artifactOptions = artifactOpt
     )
     val fetch = Fetch(fetchOpt, RemainingArgs(Seq("junit:junit:4.12"), Seq()))
     assert(fetch.files0.map(_.getName).toSet.equals(Set(
@@ -69,11 +72,14 @@ class CliFetchIntegrationTest extends FlatSpec with CliTestLib with Matchers {
   }
 
   "Default and source options" should "fetch default and source files" in {
-    val fetchOpt = FetchOptions(
-      common = CommonOptions(),
+    val artifactOpt = ArtifactOptions(
       default = Some(true),
       sources = true
     )
+    val fetchOpt = FetchOptions(
+      common = CommonOptions(),
+      artifactOptions = artifactOpt
+    )
     val fetch = Fetch(fetchOpt, RemainingArgs(Seq("junit:junit:4.12"), Seq()))
     assert(fetch.files0.map(_.getName).toSet.equals(Set(
       "junit-4.12.jar",
@@ -722,7 +728,8 @@ class CliFetchIntegrationTest extends FlatSpec with CliTestLib with Matchers {
   "classifier sources" should "fetch sources jar" in withFile() {
     (jsonFile, _) => {
       val commonOpt = CommonOptions(jsonOutputFile = jsonFile.getPath)
-      val fetchOpt = FetchOptions(common = commonOpt, sources=true)
+      val artifactOpt = ArtifactOptions(sources = true)
+      val fetchOpt = FetchOptions(common = commonOpt, artifactOptions = artifactOpt)
 
       // encode path to different jar than requested
 

From ebf4ce3f4538fed596981a3ece2dde6195c71835 Mon Sep 17 00:00:00 2001
From: Alexandre Archambault <alexandre.archambault@gmail.com>
Date: Wed, 24 Oct 2018 16:41:47 +0200
Subject: [PATCH 4/9] Move some helper methods around

---
 .../main/scala-2.12/coursier/cli/Fetch.scala  | 11 ++---------
 .../cli/options/ArtifactOptions.scala         | 19 +++++++++++++------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala b/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala
index 48379d37e9..6d1a9a7823 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/Fetch.scala
@@ -11,20 +11,13 @@ final class Fetch(options: FetchOptions, args: RemainingArgs) {
 
   val helper = new Helper(options.common, args.all, ignoreErrors = options.artifactOptions.force)
 
-  val default = options.artifactOptions.default.getOrElse {
-    (!options.artifactOptions.sources && !options.artifactOptions.javadoc && options.common.classifier0.isEmpty) ||
-      options.common.classifier0(Classifier("_"))
-  }
+  val default = options.artifactOptions.default0(options.common.classifier0)
 
   val files0 = helper.fetch(
     sources = options.artifactOptions.sources,
     javadoc = options.artifactOptions.javadoc,
     default = default,
-    artifactTypes = options.artifactOptions.artifactTypes(
-      options.artifactOptions.sources || options.common.classifier0(Classifier.sources),
-      options.artifactOptions.javadoc || options.common.classifier0(Classifier.javadoc),
-      default
-    )
+    artifactTypes = options.artifactOptions.artifactTypes(options.common.classifier0)
   )
 
 }
diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala b/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala
index 711f2e4ea7..503f49f145 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala
@@ -1,7 +1,7 @@
 package coursier.cli.options
 
 import caseapp.{ExtraName => Short, HelpMessage => Help, ValueDescription => Value, _}
-import coursier.core.{Resolution, Type}
+import coursier.core.{Classifier, Resolution, Type}
 
 object ArtifactOptions {
   def defaultArtifactTypes = Resolution.defaultTypes
@@ -26,9 +26,16 @@ final case class ArtifactOptions(
   @Help("Fetch artifacts even if the resolution is errored")
     force: Boolean = false
 ) {
+
+  def default0(classifiers: Set[Classifier]): Boolean =
+    default.getOrElse {
+      (!sources && !javadoc && classifiers.isEmpty) ||
+        classifiers(Classifier("_"))
+    }
+
   def artifactTypes(): Set[Type] =
-    artifactTypes(sources = false, javadoc = false, default = true)
-  def artifactTypes(sources: Boolean, javadoc: Boolean, default: Boolean): Set[Type] = {
+    artifactTypes(Set())
+  def artifactTypes(classifiers: Set[Classifier]): Set[Type] = {
 
     val types0 = artifactType
       .flatMap(_.split(','))
@@ -37,9 +44,9 @@ final case class ArtifactOptions(
       .toSet
 
     if (types0.isEmpty) {
-      val sourceTypes = Some(Type.source).filter(_ => sources).toSet
-      val javadocTypes = Some(Type.doc).filter(_ => javadoc).toSet
-      val defaultTypes = if (default) ArtifactOptions.defaultArtifactTypes else Set()
+      val sourceTypes = Some(Type.source).filter(_ => sources || classifiers(Classifier.sources)).toSet
+      val javadocTypes = Some(Type.doc).filter(_ => javadoc || classifiers(Classifier.javadoc)).toSet
+      val defaultTypes = if (default0(classifiers)) ArtifactOptions.defaultArtifactTypes else Set()
       sourceTypes ++ javadocTypes ++ defaultTypes
     } else if (types0(Type("*")))
       Set(Type("*"))

From 345492b60c8885afe711eb6adca35da2ffe1e448 Mon Sep 17 00:00:00 2001
From: Alexandre Archambault <alexandre.archambault@gmail.com>
Date: Wed, 24 Oct 2018 16:43:50 +0200
Subject: [PATCH 5/9] Allow to add classifier artifacts in bootstraps

Source JARs in particular
---
 .../scala-2.12/coursier/cli/Bootstrap.scala   | 16 ++--
 .../cli/CliBootstrapIntegrationTest.scala     | 90 +++++++++++++------
 scripts/generate-launcher.sh                  |  1 +
 3 files changed, 71 insertions(+), 36 deletions(-)

diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala b/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
index 2eb868ad4d..7dc9c0019f 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
@@ -25,10 +25,10 @@ object Bootstrap extends CaseApp[BootstrapOptions] {
   ): Unit = {
 
     val files = helper.fetch(
-      sources = false,
-      javadoc = false,
-      default = true,
-      artifactTypes = options.artifactOptions.artifactTypes()
+      sources = options.artifactOptions.sources,
+      javadoc = options.artifactOptions.javadoc,
+      default = options.artifactOptions.default0(options.options.common.classifier0),
+      artifactTypes = options.artifactOptions.artifactTypes(options.options.common.classifier0)
     )
 
     val log: String => Unit =
@@ -353,10 +353,10 @@ object Bootstrap extends CaseApp[BootstrapOptions] {
 
       val (urls, files) =
         helper.fetchMap(
-          sources = false,
-          javadoc = false,
-          default = true,
-          artifactTypes = options.artifactOptions.artifactTypes()
+          sources = options.artifactOptions.sources,
+          javadoc = options.artifactOptions.javadoc,
+          default = options.artifactOptions.default0(options.options.common.classifier0),
+          artifactTypes = options.artifactOptions.artifactTypes(options.options.common.classifier0)
         ).toList.foldLeft((List.empty[String], List.empty[File])){
           case ((urls, files), (url, file)) =>
             if (options.options.assembly || options.options.standalone) (urls, file :: files)
diff --git a/modules/cli/src/test/scala-2.12/coursier/cli/CliBootstrapIntegrationTest.scala b/modules/cli/src/test/scala-2.12/coursier/cli/CliBootstrapIntegrationTest.scala
index 0913391843..00b77e6bba 100644
--- a/modules/cli/src/test/scala-2.12/coursier/cli/CliBootstrapIntegrationTest.scala
+++ b/modules/cli/src/test/scala-2.12/coursier/cli/CliBootstrapIntegrationTest.scala
@@ -17,18 +17,37 @@ import org.scalatest.junit.JUnitRunner
 @RunWith(classOf[JUnitRunner])
 class CliBootstrapIntegrationTest extends FlatSpec with CliTestLib {
 
-  "bootstrap" should "not add POMs to the classpath" in withFile() {
+  private def zipEntryContent(zis: ZipInputStream, path: String): Array[Byte] = {
+    val e = zis.getNextEntry
+    if (e == null)
+      throw new NoSuchElementException(s"Entry $path in zip file")
+    else if (e.getName == path)
+      coursier.internal.FileUtil.readFully(zis)
+    else
+      zipEntryContent(zis, path)
+  }
+
+  private def actualContent(file: File) = {
 
-    def zipEntryContent(zis: ZipInputStream, path: String): Array[Byte] = {
-      val e = zis.getNextEntry
-      if (e == null)
-        throw new NoSuchElementException(s"Entry $path in zip file")
-      else if (e.getName == path)
-        coursier.internal.FileUtil.readFully(zis)
-      else
-        zipEntryContent(zis, path)
+    var fis: InputStream = null
+
+    val content = try {
+      fis = new FileInputStream(file)
+      coursier.internal.FileUtil.readFully(fis)
+    } finally {
+      if (fis != null) fis.close()
     }
 
+    val header = Seq[Byte](0x50, 0x4b, 0x03, 0x04)
+    val idx = content.indexOfSlice(header)
+    if (idx < 0)
+      throw new Exception(s"ZIP header not found in ${file.getPath}")
+    else
+      content.drop(idx)
+  }
+
+  "bootstrap" should "not add POMs to the classpath" in withFile() {
+
     (bootstrapFile, _) =>
       val repositoryOpt = RepositoryOptions(repository = List("bintray:scalameta/maven"))
       val artifactOptions = ArtifactOptions()
@@ -52,25 +71,7 @@ class CliBootstrapIntegrationTest extends FlatSpec with CliTestLib {
         RemainingArgs(Seq("com.geirsson:scalafmt-cli_2.12:1.4.0"), Seq())
       )
 
-      var fis: InputStream = null
-
-      val content = try {
-        fis = new FileInputStream(bootstrapFile)
-        coursier.internal.FileUtil.readFully(fis)
-      } finally {
-        if (fis != null) fis.close()
-      }
-
-      val actualContent = {
-        val header = Seq[Byte](0x50, 0x4b, 0x03, 0x04)
-        val idx = content.indexOfSlice(header)
-        if (idx < 0)
-          throw new Exception(s"ZIP header not found in ${bootstrapFile.getPath}")
-        else
-          content.drop(idx)
-      }
-
-      val zis = new ZipInputStream(new ByteArrayInputStream(actualContent))
+      val zis = new ZipInputStream(new ByteArrayInputStream(actualContent(bootstrapFile)))
 
       val lines = new String(zipEntryContent(zis, "bootstrap-isolation-foo-jar-urls"), UTF_8).lines.toVector
 
@@ -86,4 +87,37 @@ class CliBootstrapIntegrationTest extends FlatSpec with CliTestLib {
 
       assert(extensions == Set("jar"))
   }
+
+  "bootstrap" should "add standard and source JARs to the classpath" in withFile() {
+
+    (bootstrapFile, _) =>
+      val repositoryOpt = RepositoryOptions(repository = List("bintray:scalameta/maven"))
+      val artifactOptions = ArtifactOptions(
+        sources = true,
+        default = Some(true)
+      )
+      val common = CommonOptions(
+        repositoryOptions = repositoryOpt
+      )
+      val bootstrapSpecificOptions = BootstrapSpecificOptions(
+        output = bootstrapFile.getPath,
+        force = true,
+        common = common
+      )
+      val bootstrapOptions = BootstrapOptions(artifactOptions, bootstrapSpecificOptions)
+
+      Bootstrap.run(
+        bootstrapOptions,
+        RemainingArgs(Seq("com.geirsson:scalafmt-cli_2.12:1.4.0"), Seq())
+      )
+
+      val zis = new ZipInputStream(new ByteArrayInputStream(actualContent(bootstrapFile)))
+
+      val lines = new String(zipEntryContent(zis, "bootstrap-jar-urls"), UTF_8)
+        .lines
+        .toVector
+
+      assert(lines.exists(_.endsWith("/scalaparse_2.12-0.4.2.jar")))
+      assert(lines.exists(_.endsWith("/scalaparse_2.12-0.4.2-sources.jar")))
+  }
 }
diff --git a/scripts/generate-launcher.sh b/scripts/generate-launcher.sh
index 9e7dedf26c..c1d5c94201 100755
--- a/scripts/generate-launcher.sh
+++ b/scripts/generate-launcher.sh
@@ -16,6 +16,7 @@ fi
 "$SBTPACK_LAUNCHER" bootstrap \
   --intransitive "io.get-coursier::coursier-cli:$ACTUAL_VERSION" \
   --classifier standalone \
+  -A jar \
   -J "-noverify" \
   --no-default \
   -r central \

From 00638a4982922191e7bc83aad33586618d44f4c7 Mon Sep 17 00:00:00 2001
From: Alexandre Archambault <alexandre.archambault@gmail.com>
Date: Wed, 24 Oct 2018 17:22:58 +0200
Subject: [PATCH 6/9] Disable -S and -D short options for --sources and
 --javadoc

The first one now conflicts with --native in the bootstrap options, and
the second one with the Java property handling.
---
 .../main/scala-2.12/coursier/cli/options/ArtifactOptions.scala  | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala b/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala
index 503f49f145..8d0d89a41b 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/options/ArtifactOptions.scala
@@ -12,10 +12,8 @@ object ArtifactOptions {
 
 final case class ArtifactOptions(
   @Help("Fetch source artifacts")
-  @Short("S")
     sources: Boolean = false,
   @Help("Fetch javadoc artifacts")
-  @Short("D")
     javadoc: Boolean = false,
   @Help("Fetch default artifacts (default: false if --sources or --javadoc or --classifier are passed, true else)")
     default: Option[Boolean] = None,

From 136423b1ff51c65922c01e0d779fad1dca225ba6 Mon Sep 17 00:00:00 2001
From: Alexandre Archambault <alexandre.archambault@gmail.com>
Date: Wed, 24 Oct 2018 17:24:06 +0200
Subject: [PATCH 7/9] Switch to latest case-app

---
 project/Deps.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/project/Deps.scala b/project/Deps.scala
index b94bd0d063..474eeeae24 100644
--- a/project/Deps.scala
+++ b/project/Deps.scala
@@ -12,7 +12,7 @@ object Deps {
   def jsoup = "org.jsoup" % "jsoup" % "1.10.3"
   def scalaXml = "org.scala-lang.modules" %% "scala-xml" % "1.1.0"
   def scalazConcurrent = "org.scalaz" %% "scalaz-concurrent" % SharedVersions.scalaz
-  def caseApp = "com.github.alexarchambault" %% "case-app" % "2.0.0-M3"
+  def caseApp = "com.github.alexarchambault" %% "case-app" % "2.0.0-M5"
   def okhttpUrlConnection = "com.squareup.okhttp" % "okhttp-urlconnection" % "2.7.5"
   def argonautShapeless = "com.github.alexarchambault" %% "argonaut-shapeless_6.2" % "1.2.0-M8"
   def scalatest = "org.scalatest" %% "scalatest" % "3.0.5"

From 2cc187040baec7e24dd1ed2eca77297162a30ccb Mon Sep 17 00:00:00 2001
From: Alexandre Archambault <alexandre.archambault@gmail.com>
Date: Wed, 24 Oct 2018 18:11:40 +0200
Subject: [PATCH 8/9] Ensure bootstrap with classloader isolation don't
 duplicate JARs in the classpath

---
 .../scala-2.12/coursier/cli/Bootstrap.scala   | 22 +++++++++----------
 .../cli/CliBootstrapIntegrationTest.scala     | 13 ++++++++---
 2 files changed, 21 insertions(+), 14 deletions(-)

diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala b/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
index 7dc9c0019f..112a29f9ff 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
@@ -160,8 +160,8 @@ object Bootstrap extends CaseApp[BootstrapOptions] {
 
     val isolatedDeps = options.options.isolated.isolatedDeps(options.options.common.resolutionOptions.scalaVersion)
 
-    val (_, isolatedArtifactFiles) =
-      options.options.isolated.targets.foldLeft((Vector.empty[String], Map.empty[String, (Seq[String], Seq[File])])) {
+    val (done, isolatedArtifactFiles) =
+      options.options.isolated.targets.foldLeft((Set.empty[String], Map.empty[String, (Seq[String], Seq[File])])) {
         case ((done, acc), target) =>
 
           // TODO Add non regression test checking that optional artifacts indeed land in the isolated loader URLs
@@ -174,14 +174,14 @@ object Bootstrap extends CaseApp[BootstrapOptions] {
             subset = isolatedDeps.getOrElse(target, Seq.empty).toSet
           )
 
-          val (done0, subUrls, subFiles) =
-            if (options.options.standalone) {
-              val subFiles0 = m.values.toSeq
-              (done, Nil, subFiles0)
-            } else {
-              val filteredSubArtifacts = m.keys.toSeq.diff(done)
-              (done ++ filteredSubArtifacts, filteredSubArtifacts, Nil)
-            }
+          val m0 = m.filterKeys(url => !done(url))
+          val done0 = done ++ m0.keys
+
+          val (subUrls, subFiles) =
+            if (options.options.standalone)
+              (Nil, m0.values.toSeq)
+            else
+              (m0.keys.toSeq, Nil)
 
           val updatedAcc = acc + (target -> (subUrls, subFiles))
 
@@ -223,7 +223,7 @@ object Bootstrap extends CaseApp[BootstrapOptions] {
       outputZip.closeEntry()
     }
 
-    putStringEntry("bootstrap-jar-urls", urls.mkString("\n"))
+    putStringEntry("bootstrap-jar-urls", urls.filterNot(done).mkString("\n"))
 
     if (options.options.isolated.anyIsolatedDep) {
       putStringEntry("bootstrap-isolation-ids", options.options.isolated.targets.mkString("\n"))
diff --git a/modules/cli/src/test/scala-2.12/coursier/cli/CliBootstrapIntegrationTest.scala b/modules/cli/src/test/scala-2.12/coursier/cli/CliBootstrapIntegrationTest.scala
index 00b77e6bba..3148814c1c 100644
--- a/modules/cli/src/test/scala-2.12/coursier/cli/CliBootstrapIntegrationTest.scala
+++ b/modules/cli/src/test/scala-2.12/coursier/cli/CliBootstrapIntegrationTest.scala
@@ -71,11 +71,18 @@ class CliBootstrapIntegrationTest extends FlatSpec with CliTestLib {
         RemainingArgs(Seq("com.geirsson:scalafmt-cli_2.12:1.4.0"), Seq())
       )
 
-      val zis = new ZipInputStream(new ByteArrayInputStream(actualContent(bootstrapFile)))
+      def zis = new ZipInputStream(new ByteArrayInputStream(actualContent(bootstrapFile)))
+
+      val fooLines = new String(zipEntryContent(zis, "bootstrap-isolation-foo-jar-urls"), UTF_8).lines.toVector
+      val lines = new String(zipEntryContent(zis, "bootstrap-jar-urls"), UTF_8).lines.toVector
+
+      assert(fooLines.exists(_.endsWith("/scalaparse_2.12-0.4.2.jar")))
+      assert(!lines.exists(_.endsWith("/scalaparse_2.12-0.4.2.jar")))
 
-      val lines = new String(zipEntryContent(zis, "bootstrap-isolation-foo-jar-urls"), UTF_8).lines.toVector
+      assert(!fooLines.exists(_.endsWith("/scalameta_2.12-1.7.0.jar")))
+      assert(lines.exists(_.endsWith("/scalameta_2.12-1.7.0.jar")))
 
-      val extensions = lines
+      val extensions = fooLines
         .map { l =>
           val idx = l.lastIndexOf('.')
           if (idx < 0)

From d3bf181785403609ebdaf89d31c823403a5ac77a Mon Sep 17 00:00:00 2001
From: Alexandre Archambault <alexandre.archambault@gmail.com>
Date: Wed, 24 Oct 2018 18:18:00 +0200
Subject: [PATCH 9/9] Take classifiers into account for bootstraps with
 classloader isolation

---
 .../scala-2.12/coursier/cli/Bootstrap.scala   |  8 +--
 .../cli/CliBootstrapIntegrationTest.scala     | 50 +++++++++++++++++++
 2 files changed, 54 insertions(+), 4 deletions(-)

diff --git a/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala b/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
index 112a29f9ff..051f532827 100644
--- a/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
+++ b/modules/cli/src/main/scala-2.12/coursier/cli/Bootstrap.scala
@@ -167,10 +167,10 @@ object Bootstrap extends CaseApp[BootstrapOptions] {
           // TODO Add non regression test checking that optional artifacts indeed land in the isolated loader URLs
 
           val m = helper.fetchMap(
-            sources = false,
-            javadoc = false,
-            default = true,
-            artifactTypes = options.artifactOptions.artifactTypes(),
+            sources = options.artifactOptions.sources,
+            javadoc = options.artifactOptions.javadoc,
+            default = options.artifactOptions.default0(options.options.common.classifier0),
+            artifactTypes = options.artifactOptions.artifactTypes(options.options.common.classifier0),
             subset = isolatedDeps.getOrElse(target, Seq.empty).toSet
           )
 
diff --git a/modules/cli/src/test/scala-2.12/coursier/cli/CliBootstrapIntegrationTest.scala b/modules/cli/src/test/scala-2.12/coursier/cli/CliBootstrapIntegrationTest.scala
index 3148814c1c..c0f3e950b0 100644
--- a/modules/cli/src/test/scala-2.12/coursier/cli/CliBootstrapIntegrationTest.scala
+++ b/modules/cli/src/test/scala-2.12/coursier/cli/CliBootstrapIntegrationTest.scala
@@ -82,6 +82,12 @@ class CliBootstrapIntegrationTest extends FlatSpec with CliTestLib {
       assert(!fooLines.exists(_.endsWith("/scalameta_2.12-1.7.0.jar")))
       assert(lines.exists(_.endsWith("/scalameta_2.12-1.7.0.jar")))
 
+      // checking that there are no sources just in case…
+      assert(!fooLines.exists(_.endsWith("/scalaparse_2.12-0.4.2-sources.jar")))
+      assert(!lines.exists(_.endsWith("/scalaparse_2.12-0.4.2-sources.jar")))
+      assert(!fooLines.exists(_.endsWith("/scalameta_2.12-1.7.0-sources.jar")))
+      assert(!lines.exists(_.endsWith("/scalameta_2.12-1.7.0-sources.jar")))
+
       val extensions = fooLines
         .map { l =>
           val idx = l.lastIndexOf('.')
@@ -127,4 +133,48 @@ class CliBootstrapIntegrationTest extends FlatSpec with CliTestLib {
       assert(lines.exists(_.endsWith("/scalaparse_2.12-0.4.2.jar")))
       assert(lines.exists(_.endsWith("/scalaparse_2.12-0.4.2-sources.jar")))
   }
+
+  "bootstrap" should "add standard and source JARs to the classpath with classloader isolation" in withFile() {
+
+    (bootstrapFile, _) =>
+      val repositoryOpt = RepositoryOptions(repository = List("bintray:scalameta/maven"))
+      val artifactOptions = ArtifactOptions(
+        sources = true,
+        default = Some(true)
+      )
+      val common = CommonOptions(
+        repositoryOptions = repositoryOpt
+      )
+      val isolatedLoaderOptions = IsolatedLoaderOptions(
+        isolateTarget = List("foo"),
+        isolated = List("foo:org.scalameta:trees_2.12:1.7.0")
+      )
+      val bootstrapSpecificOptions = BootstrapSpecificOptions(
+        output = bootstrapFile.getPath,
+        isolated = isolatedLoaderOptions,
+        force = true,
+        common = common
+      )
+      val bootstrapOptions = BootstrapOptions(artifactOptions, bootstrapSpecificOptions)
+
+      Bootstrap.run(
+        bootstrapOptions,
+        RemainingArgs(Seq("com.geirsson:scalafmt-cli_2.12:1.4.0"), Seq())
+      )
+
+      def zis = new ZipInputStream(new ByteArrayInputStream(actualContent(bootstrapFile)))
+
+      val fooLines = new String(zipEntryContent(zis, "bootstrap-isolation-foo-jar-urls"), UTF_8).lines.toVector
+      val lines = new String(zipEntryContent(zis, "bootstrap-jar-urls"), UTF_8).lines.toVector
+
+      assert(fooLines.exists(_.endsWith("/scalaparse_2.12-0.4.2.jar")))
+      assert(fooLines.exists(_.endsWith("/scalaparse_2.12-0.4.2-sources.jar")))
+      assert(!lines.exists(_.endsWith("/scalaparse_2.12-0.4.2.jar")))
+      assert(!lines.exists(_.endsWith("/scalaparse_2.12-0.4.2-sources.jar")))
+
+      assert(!fooLines.exists(_.endsWith("/scalameta_2.12-1.7.0.jar")))
+      assert(!fooLines.exists(_.endsWith("/scalameta_2.12-1.7.0-sources.jar")))
+      assert(lines.exists(_.endsWith("/scalameta_2.12-1.7.0.jar")))
+      assert(lines.exists(_.endsWith("/scalameta_2.12-1.7.0-sources.jar")))
+  }
 }