diff --git a/lib/analyze-action-post.js b/lib/analyze-action-post.js
index 99d289f8f0..c2fcd9c1bc 100644
--- a/lib/analyze-action-post.js
+++ b/lib/analyze-action-post.js
@@ -117921,15 +117921,6 @@ var featureConfig = {
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
-var defaultAugmentationProperties = {
-  queriesInputCombines: false,
-  packsInputCombines: false,
-  packsInput: void 0,
-  queriesInput: void 0,
-  extraQueryExclusions: [],
-  overlayDatabaseMode: "none" /* None */,
-  useOverlayDatabaseCaching: false
-};
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
@@ -117973,38 +117964,10 @@ async function getConfig(tempDir, logger) {
   logger.debug(configString);
   return JSON.parse(configString);
 }
-function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
-  const augmentedConfig = cloneObject(originalUserInput);
-  if (augmentationProperties.queriesInput) {
-    if (augmentationProperties.queriesInputCombines) {
-      augmentedConfig.queries = (augmentedConfig.queries || []).concat(
-        augmentationProperties.queriesInput
-      );
-    } else {
-      augmentedConfig.queries = augmentationProperties.queriesInput;
-    }
-  }
-  if (augmentedConfig.queries?.length === 0) {
-    delete augmentedConfig.queries;
-  }
-  if (augmentationProperties.packsInput) {
-    if (augmentationProperties.packsInputCombines) {
-      if (Array.isArray(augmentedConfig.packs)) {
-        augmentedConfig.packs = (augmentedConfig.packs || []).concat(
-          augmentationProperties.packsInput
-        );
-      } else if (!augmentedConfig.packs) {
-        augmentedConfig.packs = augmentationProperties.packsInput;
-      } else {
-        const language = Object.keys(augmentedConfig.packs)[0];
-        augmentedConfig.packs[language] = augmentedConfig.packs[language].concat(augmentationProperties.packsInput);
-      }
-    } else {
-      augmentedConfig.packs = augmentationProperties.packsInput;
-    }
-  }
-  if (Array.isArray(augmentedConfig.packs) && !augmentedConfig.packs.length) {
-    delete augmentedConfig.packs;
+function appendExtraQueryExclusions(extraQueryExclusions, cliConfig) {
+  const augmentedConfig = cloneObject(cliConfig);
+  if (extraQueryExclusions.length === 0) {
+    return augmentedConfig;
   }
   augmentedConfig["query-filters"] = [
     // Ordering matters. If the first filter is an inclusion, it implicitly
@@ -118012,7 +117975,7 @@ function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
     // it implicitly includes all queries that are not excluded. So user
     // filters (if any) should always be first to preserve intent.
     ...augmentedConfig["query-filters"] || [],
-    ...augmentationProperties.extraQueryExclusions
+    ...extraQueryExclusions
   ];
   if (augmentedConfig["query-filters"]?.length === 0) {
     delete augmentedConfig["query-filters"];
@@ -118134,7 +118097,7 @@ async function getCodeQLForCmd(cmd, checkVersion) {
         await this.getVersion(),
         "forceOverwrite" /* ForceOverwrite */
       ) ? "--force-overwrite" : "--overwrite";
-      const overlayDatabaseMode = config.augmentationProperties.overlayDatabaseMode;
+      const overlayDatabaseMode = config.overlayDatabaseMode;
       if (overlayDatabaseMode === "overlay" /* Overlay */) {
         const overlayChangesFile = await writeOverlayChangesFile(
           config,
@@ -118548,9 +118511,9 @@ async function runCli(cmd, args = [], opts = {}) {
 }
 async function writeCodeScanningConfigFile(config, logger) {
   const codeScanningConfigFile = getGeneratedCodeScanningConfigPath(config);
-  const augmentedConfig = generateCodeScanningConfig(
-    config.originalUserInput,
-    config.augmentationProperties
+  const augmentedConfig = appendExtraQueryExclusions(
+    config.extraQueryExclusions,
+    config.computedConfig
   );
   logger.info(
     `Writing augmented user configuration file to ${codeScanningConfigFile}`
diff --git a/lib/analyze-action.js b/lib/analyze-action.js
index 29aef44a7a..f8ba08884a 100644
--- a/lib/analyze-action.js
+++ b/lib/analyze-action.js
@@ -90863,14 +90863,14 @@ function checkOverlayBaseDatabase(config, logger, warningPrefix) {
   return true;
 }
 async function uploadOverlayBaseDatabaseToCache(codeql, config, logger) {
-  const overlayDatabaseMode = config.augmentationProperties.overlayDatabaseMode;
+  const overlayDatabaseMode = config.overlayDatabaseMode;
   if (overlayDatabaseMode !== "overlay-base" /* OverlayBase */) {
     logger.debug(
       `Overlay database mode is ${overlayDatabaseMode}. Skip uploading overlay-base database to cache.`
     );
     return false;
   }
-  if (!config.augmentationProperties.useOverlayDatabaseCaching) {
+  if (!config.useOverlayDatabaseCaching) {
     logger.debug(
       "Overlay database caching is disabled. Skip uploading overlay-base database to cache."
     );
@@ -91542,15 +91542,6 @@ async function cachePrefix(codeql, language) {
 }
 
 // src/config-utils.ts
-var defaultAugmentationProperties = {
-  queriesInputCombines: false,
-  packsInputCombines: false,
-  packsInput: void 0,
-  queriesInput: void 0,
-  extraQueryExclusions: [],
-  overlayDatabaseMode: "none" /* None */,
-  useOverlayDatabaseCaching: false
-};
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
@@ -91594,38 +91585,10 @@ async function getConfig(tempDir, logger) {
   logger.debug(configString);
   return JSON.parse(configString);
 }
-function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
-  const augmentedConfig = cloneObject(originalUserInput);
-  if (augmentationProperties.queriesInput) {
-    if (augmentationProperties.queriesInputCombines) {
-      augmentedConfig.queries = (augmentedConfig.queries || []).concat(
-        augmentationProperties.queriesInput
-      );
-    } else {
-      augmentedConfig.queries = augmentationProperties.queriesInput;
-    }
-  }
-  if (augmentedConfig.queries?.length === 0) {
-    delete augmentedConfig.queries;
-  }
-  if (augmentationProperties.packsInput) {
-    if (augmentationProperties.packsInputCombines) {
-      if (Array.isArray(augmentedConfig.packs)) {
-        augmentedConfig.packs = (augmentedConfig.packs || []).concat(
-          augmentationProperties.packsInput
-        );
-      } else if (!augmentedConfig.packs) {
-        augmentedConfig.packs = augmentationProperties.packsInput;
-      } else {
-        const language = Object.keys(augmentedConfig.packs)[0];
-        augmentedConfig.packs[language] = augmentedConfig.packs[language].concat(augmentationProperties.packsInput);
-      }
-    } else {
-      augmentedConfig.packs = augmentationProperties.packsInput;
-    }
-  }
-  if (Array.isArray(augmentedConfig.packs) && !augmentedConfig.packs.length) {
-    delete augmentedConfig.packs;
+function appendExtraQueryExclusions(extraQueryExclusions, cliConfig) {
+  const augmentedConfig = cloneObject(cliConfig);
+  if (extraQueryExclusions.length === 0) {
+    return augmentedConfig;
   }
   augmentedConfig["query-filters"] = [
     // Ordering matters. If the first filter is an inclusion, it implicitly
@@ -91633,7 +91596,7 @@ function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
     // it implicitly includes all queries that are not excluded. So user
     // filters (if any) should always be first to preserve intent.
     ...augmentedConfig["query-filters"] || [],
-    ...augmentationProperties.extraQueryExclusions
+    ...extraQueryExclusions
   ];
   if (augmentedConfig["query-filters"]?.length === 0) {
     delete augmentedConfig["query-filters"];
@@ -92646,7 +92609,7 @@ async function getCodeQLForCmd(cmd, checkVersion) {
         await this.getVersion(),
         "forceOverwrite" /* ForceOverwrite */
       ) ? "--force-overwrite" : "--overwrite";
-      const overlayDatabaseMode = config.augmentationProperties.overlayDatabaseMode;
+      const overlayDatabaseMode = config.overlayDatabaseMode;
       if (overlayDatabaseMode === "overlay" /* Overlay */) {
         const overlayChangesFile = await writeOverlayChangesFile(
           config,
@@ -93060,9 +93023,9 @@ async function runCli(cmd, args = [], opts = {}) {
 }
 async function writeCodeScanningConfigFile(config, logger) {
   const codeScanningConfigFile = getGeneratedCodeScanningConfigPath(config);
-  const augmentedConfig = generateCodeScanningConfig(
-    config.originalUserInput,
-    config.augmentationProperties
+  const augmentedConfig = appendExtraQueryExclusions(
+    config.extraQueryExclusions,
+    config.computedConfig
   );
   logger.info(
     `Writing augmented user configuration file to ${codeScanningConfigFile}`
@@ -93603,7 +93566,7 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
   const statusReport = {};
   const queryFlags = [memoryFlag, threadsFlag];
   const incrementalMode = [];
-  if (config.augmentationProperties.overlayDatabaseMode !== "overlay-base" /* OverlayBase */) {
+  if (config.overlayDatabaseMode !== "overlay-base" /* OverlayBase */) {
     queryFlags.push("--expect-discarded-cache");
   }
   statusReport.analysis_is_diff_informed = diffRangePackDir !== void 0;
@@ -93612,9 +93575,9 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
     queryFlags.push("--extension-packs=codeql-action/pr-diff-range");
     incrementalMode.push("diff-informed");
   }
-  statusReport.analysis_is_overlay = config.augmentationProperties.overlayDatabaseMode === "overlay" /* Overlay */;
-  statusReport.analysis_builds_overlay_base_database = config.augmentationProperties.overlayDatabaseMode === "overlay-base" /* OverlayBase */;
-  if (config.augmentationProperties.overlayDatabaseMode === "overlay" /* Overlay */) {
+  statusReport.analysis_is_overlay = config.overlayDatabaseMode === "overlay" /* Overlay */;
+  statusReport.analysis_builds_overlay_base_database = config.overlayDatabaseMode === "overlay-base" /* OverlayBase */;
+  if (config.overlayDatabaseMode === "overlay" /* Overlay */) {
     incrementalMode.push("overlay");
   }
   const sarifRunPropertyFlag = incrementalMode.length > 0 ? `--sarif-run-property=incrementalMode=${incrementalMode.join(",")}` : void 0;
diff --git a/lib/autobuild-action.js b/lib/autobuild-action.js
index ca18e315a4..c2d8f0d0ea 100644
--- a/lib/autobuild-action.js
+++ b/lib/autobuild-action.js
@@ -78923,15 +78923,6 @@ var GitHubFeatureFlags = class {
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
-var defaultAugmentationProperties = {
-  queriesInputCombines: false,
-  packsInputCombines: false,
-  packsInput: void 0,
-  queriesInput: void 0,
-  extraQueryExclusions: [],
-  overlayDatabaseMode: "none" /* None */,
-  useOverlayDatabaseCaching: false
-};
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
@@ -78975,38 +78966,10 @@ async function getConfig(tempDir, logger) {
   logger.debug(configString);
   return JSON.parse(configString);
 }
-function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
-  const augmentedConfig = cloneObject(originalUserInput);
-  if (augmentationProperties.queriesInput) {
-    if (augmentationProperties.queriesInputCombines) {
-      augmentedConfig.queries = (augmentedConfig.queries || []).concat(
-        augmentationProperties.queriesInput
-      );
-    } else {
-      augmentedConfig.queries = augmentationProperties.queriesInput;
-    }
-  }
-  if (augmentedConfig.queries?.length === 0) {
-    delete augmentedConfig.queries;
-  }
-  if (augmentationProperties.packsInput) {
-    if (augmentationProperties.packsInputCombines) {
-      if (Array.isArray(augmentedConfig.packs)) {
-        augmentedConfig.packs = (augmentedConfig.packs || []).concat(
-          augmentationProperties.packsInput
-        );
-      } else if (!augmentedConfig.packs) {
-        augmentedConfig.packs = augmentationProperties.packsInput;
-      } else {
-        const language = Object.keys(augmentedConfig.packs)[0];
-        augmentedConfig.packs[language] = augmentedConfig.packs[language].concat(augmentationProperties.packsInput);
-      }
-    } else {
-      augmentedConfig.packs = augmentationProperties.packsInput;
-    }
-  }
-  if (Array.isArray(augmentedConfig.packs) && !augmentedConfig.packs.length) {
-    delete augmentedConfig.packs;
+function appendExtraQueryExclusions(extraQueryExclusions, cliConfig) {
+  const augmentedConfig = cloneObject(cliConfig);
+  if (extraQueryExclusions.length === 0) {
+    return augmentedConfig;
   }
   augmentedConfig["query-filters"] = [
     // Ordering matters. If the first filter is an inclusion, it implicitly
@@ -79014,7 +78977,7 @@ function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
     // it implicitly includes all queries that are not excluded. So user
     // filters (if any) should always be first to preserve intent.
     ...augmentedConfig["query-filters"] || [],
-    ...augmentationProperties.extraQueryExclusions
+    ...extraQueryExclusions
   ];
   if (augmentedConfig["query-filters"]?.length === 0) {
     delete augmentedConfig["query-filters"];
@@ -79169,7 +79132,7 @@ async function getCodeQLForCmd(cmd, checkVersion) {
         await this.getVersion(),
         "forceOverwrite" /* ForceOverwrite */
       ) ? "--force-overwrite" : "--overwrite";
-      const overlayDatabaseMode = config.augmentationProperties.overlayDatabaseMode;
+      const overlayDatabaseMode = config.overlayDatabaseMode;
       if (overlayDatabaseMode === "overlay" /* Overlay */) {
         const overlayChangesFile = await writeOverlayChangesFile(
           config,
@@ -79583,9 +79546,9 @@ async function runCli(cmd, args = [], opts = {}) {
 }
 async function writeCodeScanningConfigFile(config, logger) {
   const codeScanningConfigFile = getGeneratedCodeScanningConfigPath(config);
-  const augmentedConfig = generateCodeScanningConfig(
-    config.originalUserInput,
-    config.augmentationProperties
+  const augmentedConfig = appendExtraQueryExclusions(
+    config.extraQueryExclusions,
+    config.computedConfig
   );
   logger.info(
     `Writing augmented user configuration file to ${codeScanningConfigFile}`
diff --git a/lib/init-action-post.js b/lib/init-action-post.js
index 1995591edc..f4117f9ada 100644
--- a/lib/init-action-post.js
+++ b/lib/init-action-post.js
@@ -129520,15 +129520,6 @@ ${jsonContents}`
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
-var defaultAugmentationProperties = {
-  queriesInputCombines: false,
-  packsInputCombines: false,
-  packsInput: void 0,
-  queriesInput: void 0,
-  extraQueryExclusions: [],
-  overlayDatabaseMode: "none" /* None */,
-  useOverlayDatabaseCaching: false
-};
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
@@ -129572,38 +129563,10 @@ async function getConfig(tempDir, logger) {
   logger.debug(configString);
   return JSON.parse(configString);
 }
-function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
-  const augmentedConfig = cloneObject(originalUserInput);
-  if (augmentationProperties.queriesInput) {
-    if (augmentationProperties.queriesInputCombines) {
-      augmentedConfig.queries = (augmentedConfig.queries || []).concat(
-        augmentationProperties.queriesInput
-      );
-    } else {
-      augmentedConfig.queries = augmentationProperties.queriesInput;
-    }
-  }
-  if (augmentedConfig.queries?.length === 0) {
-    delete augmentedConfig.queries;
-  }
-  if (augmentationProperties.packsInput) {
-    if (augmentationProperties.packsInputCombines) {
-      if (Array.isArray(augmentedConfig.packs)) {
-        augmentedConfig.packs = (augmentedConfig.packs || []).concat(
-          augmentationProperties.packsInput
-        );
-      } else if (!augmentedConfig.packs) {
-        augmentedConfig.packs = augmentationProperties.packsInput;
-      } else {
-        const language = Object.keys(augmentedConfig.packs)[0];
-        augmentedConfig.packs[language] = augmentedConfig.packs[language].concat(augmentationProperties.packsInput);
-      }
-    } else {
-      augmentedConfig.packs = augmentationProperties.packsInput;
-    }
-  }
-  if (Array.isArray(augmentedConfig.packs) && !augmentedConfig.packs.length) {
-    delete augmentedConfig.packs;
+function appendExtraQueryExclusions(extraQueryExclusions, cliConfig) {
+  const augmentedConfig = cloneObject(cliConfig);
+  if (extraQueryExclusions.length === 0) {
+    return augmentedConfig;
   }
   augmentedConfig["query-filters"] = [
     // Ordering matters. If the first filter is an inclusion, it implicitly
@@ -129611,7 +129574,7 @@ function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
     // it implicitly includes all queries that are not excluded. So user
     // filters (if any) should always be first to preserve intent.
     ...augmentedConfig["query-filters"] || [],
-    ...augmentationProperties.extraQueryExclusions
+    ...extraQueryExclusions
   ];
   if (augmentedConfig["query-filters"]?.length === 0) {
     delete augmentedConfig["query-filters"];
@@ -130588,7 +130551,7 @@ async function getCodeQLForCmd(cmd, checkVersion) {
         await this.getVersion(),
         "forceOverwrite" /* ForceOverwrite */
       ) ? "--force-overwrite" : "--overwrite";
-      const overlayDatabaseMode = config.augmentationProperties.overlayDatabaseMode;
+      const overlayDatabaseMode = config.overlayDatabaseMode;
       if (overlayDatabaseMode === "overlay" /* Overlay */) {
         const overlayChangesFile = await writeOverlayChangesFile(
           config,
@@ -131002,9 +130965,9 @@ async function runCli(cmd, args = [], opts = {}) {
 }
 async function writeCodeScanningConfigFile(config, logger) {
   const codeScanningConfigFile = getGeneratedCodeScanningConfigPath(config);
-  const augmentedConfig = generateCodeScanningConfig(
-    config.originalUserInput,
-    config.augmentationProperties
+  const augmentedConfig = appendExtraQueryExclusions(
+    config.extraQueryExclusions,
+    config.computedConfig
   );
   logger.info(
     `Writing augmented user configuration file to ${codeScanningConfigFile}`
diff --git a/lib/init-action.js b/lib/init-action.js
index 2edef19804..bedab733cf 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -86458,14 +86458,14 @@ function checkOverlayBaseDatabase(config, logger, warningPrefix) {
   return true;
 }
 async function downloadOverlayBaseDatabaseFromCache(codeql, config, logger) {
-  const overlayDatabaseMode = config.augmentationProperties.overlayDatabaseMode;
+  const overlayDatabaseMode = config.overlayDatabaseMode;
   if (overlayDatabaseMode !== "overlay" /* Overlay */) {
     logger.debug(
       `Overlay database mode is ${overlayDatabaseMode}. Skip downloading overlay-base database from cache.`
     );
     return void 0;
   }
-  if (!config.augmentationProperties.useOverlayDatabaseCaching) {
+  if (!config.useOverlayDatabaseCaching) {
     logger.debug(
       "Overlay database caching is disabled. Skip downloading overlay-base database from cache."
     );
@@ -87116,15 +87116,6 @@ async function cachePrefix(codeql, language) {
 
 // src/config-utils.ts
 var PACKS_PROPERTY = "packs";
-var defaultAugmentationProperties = {
-  queriesInputCombines: false,
-  packsInputCombines: false,
-  packsInput: void 0,
-  queriesInput: void 0,
-  extraQueryExclusions: [],
-  overlayDatabaseMode: "none" /* None */,
-  useOverlayDatabaseCaching: false
-};
 function getPacksStrInvalid(packStr, configFile) {
   return configFile ? getConfigFilePropertyError(
     configFile,
@@ -87301,6 +87292,7 @@ async function getDefaultConfig({
     languages,
     buildMode,
     originalUserInput: {},
+    computedConfig: {},
     tempDir,
     codeQLCmd: codeql.getPath(),
     gitHubVersion: githubVersion,
@@ -87311,7 +87303,10 @@ async function getDefaultConfig({
     augmentationProperties,
     trapCaches,
     trapCacheDownloadTime,
-    dependencyCachingEnabled: getCachingKind(dependencyCachingEnabled)
+    dependencyCachingEnabled: getCachingKind(dependencyCachingEnabled),
+    extraQueryExclusions: [],
+    overlayDatabaseMode: "none" /* None */,
+    useOverlayDatabaseCaching: false
   };
 }
 async function downloadCacheWithTime(trapCachingEnabled, codeQL, languages, logger) {
@@ -87355,10 +87350,7 @@ async function calculateAugmentation(rawPacksInput, rawQueriesInput, languages)
     packsInputCombines,
     packsInput: packsInput?.[languages[0]],
     queriesInput,
-    queriesInputCombines,
-    extraQueryExclusions: [],
-    overlayDatabaseMode: "none" /* None */,
-    useOverlayDatabaseCaching: false
+    queriesInputCombines
   };
 }
 function parseQueriesFromInput(rawQueriesInput, queriesInputCombines) {
@@ -87610,8 +87602,11 @@ async function initConfig(inputs) {
     );
   }
   const config = await getDefaultConfig(inputs);
-  const augmentationProperties = config.augmentationProperties;
   config.originalUserInput = userConfig;
+  config.computedConfig = generateCodeScanningConfig(
+    userConfig,
+    config.augmentationProperties
+  );
   const { overlayDatabaseMode, useOverlayDatabaseCaching } = await getOverlayDatabaseMode(
     inputs.codeql,
     inputs.repository,
@@ -87619,20 +87614,20 @@ async function initConfig(inputs) {
     config.languages,
     inputs.sourceRoot,
     config.buildMode,
-    generateCodeScanningConfig(userConfig, augmentationProperties),
+    config.computedConfig,
     logger
   );
   logger.info(
     `Using overlay database mode: ${overlayDatabaseMode} ${useOverlayDatabaseCaching ? "with" : "without"} caching.`
   );
-  augmentationProperties.overlayDatabaseMode = overlayDatabaseMode;
-  augmentationProperties.useOverlayDatabaseCaching = useOverlayDatabaseCaching;
+  config.overlayDatabaseMode = overlayDatabaseMode;
+  config.useOverlayDatabaseCaching = useOverlayDatabaseCaching;
   if (overlayDatabaseMode === "overlay" /* Overlay */ || await shouldPerformDiffInformedAnalysis(
     inputs.codeql,
     inputs.features,
     logger
   )) {
-    augmentationProperties.extraQueryExclusions.push({
+    config.extraQueryExclusions.push({
       exclude: { tags: "exclude-from-incremental" }
     });
   }
@@ -87825,13 +87820,20 @@ function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
   if (Array.isArray(augmentedConfig.packs) && !augmentedConfig.packs.length) {
     delete augmentedConfig.packs;
   }
+  return augmentedConfig;
+}
+function appendExtraQueryExclusions(extraQueryExclusions, cliConfig) {
+  const augmentedConfig = cloneObject(cliConfig);
+  if (extraQueryExclusions.length === 0) {
+    return augmentedConfig;
+  }
   augmentedConfig["query-filters"] = [
     // Ordering matters. If the first filter is an inclusion, it implicitly
     // excludes all queries that are not included. If it is an exclusion,
     // it implicitly includes all queries that are not excluded. So user
     // filters (if any) should always be first to preserve intent.
     ...augmentedConfig["query-filters"] || [],
-    ...augmentationProperties.extraQueryExclusions
+    ...extraQueryExclusions
   ];
   if (augmentedConfig["query-filters"]?.length === 0) {
     delete augmentedConfig["query-filters"];
@@ -89192,7 +89194,7 @@ async function getCodeQLForCmd(cmd, checkVersion) {
         await this.getVersion(),
         "forceOverwrite" /* ForceOverwrite */
       ) ? "--force-overwrite" : "--overwrite";
-      const overlayDatabaseMode = config.augmentationProperties.overlayDatabaseMode;
+      const overlayDatabaseMode = config.overlayDatabaseMode;
       if (overlayDatabaseMode === "overlay" /* Overlay */) {
         const overlayChangesFile = await writeOverlayChangesFile(
           config,
@@ -89606,9 +89608,9 @@ async function runCli(cmd, args = [], opts = {}) {
 }
 async function writeCodeScanningConfigFile(config, logger) {
   const codeScanningConfigFile = getGeneratedCodeScanningConfigPath(config);
-  const augmentedConfig = generateCodeScanningConfig(
-    config.originalUserInput,
-    config.augmentationProperties
+  const augmentedConfig = appendExtraQueryExclusions(
+    config.extraQueryExclusions,
+    config.computedConfig
   );
   logger.info(
     `Writing augmented user configuration file to ${codeScanningConfigFile}`
@@ -90391,20 +90393,20 @@ async function run() {
   }
   let overlayBaseDatabaseStats;
   try {
-    if (config.augmentationProperties.overlayDatabaseMode === "overlay" /* Overlay */ && config.augmentationProperties.useOverlayDatabaseCaching) {
+    if (config.overlayDatabaseMode === "overlay" /* Overlay */ && config.useOverlayDatabaseCaching) {
       overlayBaseDatabaseStats = await downloadOverlayBaseDatabaseFromCache(
         codeql,
         config,
         logger
       );
       if (!overlayBaseDatabaseStats) {
-        config.augmentationProperties.overlayDatabaseMode = "none" /* None */;
+        config.overlayDatabaseMode = "none" /* None */;
         logger.info(
           `No overlay-base database found in cache, reverting overlay database mode to ${"none" /* None */}.`
         );
       }
     }
-    if (config.augmentationProperties.overlayDatabaseMode !== "overlay" /* Overlay */) {
+    if (config.overlayDatabaseMode !== "overlay" /* Overlay */) {
       cleanupDatabaseClusterDirectory(config, logger);
     }
     if (zstdAvailability) {
@@ -90581,11 +90583,11 @@ exec ${goBinaryPath} "$@"`
       qlconfigFile,
       logger
     );
-    if (config.augmentationProperties.overlayDatabaseMode !== "none" /* None */ && !await checkPacksForOverlayCompatibility(codeql, config, logger)) {
+    if (config.overlayDatabaseMode !== "none" /* None */ && !await checkPacksForOverlayCompatibility(codeql, config, logger)) {
       logger.info(
         "Reverting overlay database mode to None due to incompatible packs."
       );
-      config.augmentationProperties.overlayDatabaseMode = "none" /* None */;
+      config.overlayDatabaseMode = "none" /* None */;
       cleanupDatabaseClusterDirectory(config, logger, {
         disableExistingDirectoryWarning: true
       });
diff --git a/lib/resolve-environment-action.js b/lib/resolve-environment-action.js
index 7c46b8092b..11761c618f 100644
--- a/lib/resolve-environment-action.js
+++ b/lib/resolve-environment-action.js
@@ -78650,15 +78650,6 @@ var featureConfig = {
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
-var defaultAugmentationProperties = {
-  queriesInputCombines: false,
-  packsInputCombines: false,
-  packsInput: void 0,
-  queriesInput: void 0,
-  extraQueryExclusions: [],
-  overlayDatabaseMode: "none" /* None */,
-  useOverlayDatabaseCaching: false
-};
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
@@ -78702,38 +78693,10 @@ async function getConfig(tempDir, logger) {
   logger.debug(configString);
   return JSON.parse(configString);
 }
-function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
-  const augmentedConfig = cloneObject(originalUserInput);
-  if (augmentationProperties.queriesInput) {
-    if (augmentationProperties.queriesInputCombines) {
-      augmentedConfig.queries = (augmentedConfig.queries || []).concat(
-        augmentationProperties.queriesInput
-      );
-    } else {
-      augmentedConfig.queries = augmentationProperties.queriesInput;
-    }
-  }
-  if (augmentedConfig.queries?.length === 0) {
-    delete augmentedConfig.queries;
-  }
-  if (augmentationProperties.packsInput) {
-    if (augmentationProperties.packsInputCombines) {
-      if (Array.isArray(augmentedConfig.packs)) {
-        augmentedConfig.packs = (augmentedConfig.packs || []).concat(
-          augmentationProperties.packsInput
-        );
-      } else if (!augmentedConfig.packs) {
-        augmentedConfig.packs = augmentationProperties.packsInput;
-      } else {
-        const language = Object.keys(augmentedConfig.packs)[0];
-        augmentedConfig.packs[language] = augmentedConfig.packs[language].concat(augmentationProperties.packsInput);
-      }
-    } else {
-      augmentedConfig.packs = augmentationProperties.packsInput;
-    }
-  }
-  if (Array.isArray(augmentedConfig.packs) && !augmentedConfig.packs.length) {
-    delete augmentedConfig.packs;
+function appendExtraQueryExclusions(extraQueryExclusions, cliConfig) {
+  const augmentedConfig = cloneObject(cliConfig);
+  if (extraQueryExclusions.length === 0) {
+    return augmentedConfig;
   }
   augmentedConfig["query-filters"] = [
     // Ordering matters. If the first filter is an inclusion, it implicitly
@@ -78741,7 +78704,7 @@ function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
     // it implicitly includes all queries that are not excluded. So user
     // filters (if any) should always be first to preserve intent.
     ...augmentedConfig["query-filters"] || [],
-    ...augmentationProperties.extraQueryExclusions
+    ...extraQueryExclusions
   ];
   if (augmentedConfig["query-filters"]?.length === 0) {
     delete augmentedConfig["query-filters"];
@@ -78869,7 +78832,7 @@ async function getCodeQLForCmd(cmd, checkVersion) {
         await this.getVersion(),
         "forceOverwrite" /* ForceOverwrite */
       ) ? "--force-overwrite" : "--overwrite";
-      const overlayDatabaseMode = config.augmentationProperties.overlayDatabaseMode;
+      const overlayDatabaseMode = config.overlayDatabaseMode;
       if (overlayDatabaseMode === "overlay" /* Overlay */) {
         const overlayChangesFile = await writeOverlayChangesFile(
           config,
@@ -79283,9 +79246,9 @@ async function runCli(cmd, args = [], opts = {}) {
 }
 async function writeCodeScanningConfigFile(config, logger) {
   const codeScanningConfigFile = getGeneratedCodeScanningConfigPath(config);
-  const augmentedConfig = generateCodeScanningConfig(
-    config.originalUserInput,
-    config.augmentationProperties
+  const augmentedConfig = appendExtraQueryExclusions(
+    config.extraQueryExclusions,
+    config.computedConfig
   );
   logger.info(
     `Writing augmented user configuration file to ${codeScanningConfigFile}`
diff --git a/lib/start-proxy-action-post.js b/lib/start-proxy-action-post.js
index c9317c4cd2..a203807e9c 100644
--- a/lib/start-proxy-action-post.js
+++ b/lib/start-proxy-action-post.js
@@ -117330,15 +117330,6 @@ var featureConfig = {
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
-var defaultAugmentationProperties = {
-  queriesInputCombines: false,
-  packsInputCombines: false,
-  packsInput: void 0,
-  queriesInput: void 0,
-  extraQueryExclusions: [],
-  overlayDatabaseMode: "none" /* None */,
-  useOverlayDatabaseCaching: false
-};
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
diff --git a/lib/upload-lib.js b/lib/upload-lib.js
index 825744e8d4..ff2f43e49f 100644
--- a/lib/upload-lib.js
+++ b/lib/upload-lib.js
@@ -89367,15 +89367,6 @@ ${jsonContents}`
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
-var defaultAugmentationProperties = {
-  queriesInputCombines: false,
-  packsInputCombines: false,
-  packsInput: void 0,
-  queriesInput: void 0,
-  extraQueryExclusions: [],
-  overlayDatabaseMode: "none" /* None */,
-  useOverlayDatabaseCaching: false
-};
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
@@ -89419,38 +89410,10 @@ async function getConfig(tempDir, logger) {
   logger.debug(configString);
   return JSON.parse(configString);
 }
-function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
-  const augmentedConfig = cloneObject(originalUserInput);
-  if (augmentationProperties.queriesInput) {
-    if (augmentationProperties.queriesInputCombines) {
-      augmentedConfig.queries = (augmentedConfig.queries || []).concat(
-        augmentationProperties.queriesInput
-      );
-    } else {
-      augmentedConfig.queries = augmentationProperties.queriesInput;
-    }
-  }
-  if (augmentedConfig.queries?.length === 0) {
-    delete augmentedConfig.queries;
-  }
-  if (augmentationProperties.packsInput) {
-    if (augmentationProperties.packsInputCombines) {
-      if (Array.isArray(augmentedConfig.packs)) {
-        augmentedConfig.packs = (augmentedConfig.packs || []).concat(
-          augmentationProperties.packsInput
-        );
-      } else if (!augmentedConfig.packs) {
-        augmentedConfig.packs = augmentationProperties.packsInput;
-      } else {
-        const language = Object.keys(augmentedConfig.packs)[0];
-        augmentedConfig.packs[language] = augmentedConfig.packs[language].concat(augmentationProperties.packsInput);
-      }
-    } else {
-      augmentedConfig.packs = augmentationProperties.packsInput;
-    }
-  }
-  if (Array.isArray(augmentedConfig.packs) && !augmentedConfig.packs.length) {
-    delete augmentedConfig.packs;
+function appendExtraQueryExclusions(extraQueryExclusions, cliConfig) {
+  const augmentedConfig = cloneObject(cliConfig);
+  if (extraQueryExclusions.length === 0) {
+    return augmentedConfig;
   }
   augmentedConfig["query-filters"] = [
     // Ordering matters. If the first filter is an inclusion, it implicitly
@@ -89458,7 +89421,7 @@ function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
     // it implicitly includes all queries that are not excluded. So user
     // filters (if any) should always be first to preserve intent.
     ...augmentedConfig["query-filters"] || [],
-    ...augmentationProperties.extraQueryExclusions
+    ...extraQueryExclusions
   ];
   if (augmentedConfig["query-filters"]?.length === 0) {
     delete augmentedConfig["query-filters"];
@@ -90435,7 +90398,7 @@ async function getCodeQLForCmd(cmd, checkVersion) {
         await this.getVersion(),
         "forceOverwrite" /* ForceOverwrite */
       ) ? "--force-overwrite" : "--overwrite";
-      const overlayDatabaseMode = config.augmentationProperties.overlayDatabaseMode;
+      const overlayDatabaseMode = config.overlayDatabaseMode;
       if (overlayDatabaseMode === "overlay" /* Overlay */) {
         const overlayChangesFile = await writeOverlayChangesFile(
           config,
@@ -90849,9 +90812,9 @@ async function runCli(cmd, args = [], opts = {}) {
 }
 async function writeCodeScanningConfigFile(config, logger) {
   const codeScanningConfigFile = getGeneratedCodeScanningConfigPath(config);
-  const augmentedConfig = generateCodeScanningConfig(
-    config.originalUserInput,
-    config.augmentationProperties
+  const augmentedConfig = appendExtraQueryExclusions(
+    config.extraQueryExclusions,
+    config.computedConfig
   );
   logger.info(
     `Writing augmented user configuration file to ${codeScanningConfigFile}`
diff --git a/lib/upload-sarif-action-post.js b/lib/upload-sarif-action-post.js
index 4e569eb512..cb13fd3c6c 100644
--- a/lib/upload-sarif-action-post.js
+++ b/lib/upload-sarif-action-post.js
@@ -117495,15 +117495,6 @@ var featureConfig = {
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
-var defaultAugmentationProperties = {
-  queriesInputCombines: false,
-  packsInputCombines: false,
-  packsInput: void 0,
-  queriesInput: void 0,
-  extraQueryExclusions: [],
-  overlayDatabaseMode: "none" /* None */,
-  useOverlayDatabaseCaching: false
-};
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
diff --git a/lib/upload-sarif-action.js b/lib/upload-sarif-action.js
index e785cef377..a1ba491b14 100644
--- a/lib/upload-sarif-action.js
+++ b/lib/upload-sarif-action.js
@@ -90047,15 +90047,6 @@ ${jsonContents}`
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
-var defaultAugmentationProperties = {
-  queriesInputCombines: false,
-  packsInputCombines: false,
-  packsInput: void 0,
-  queriesInput: void 0,
-  extraQueryExclusions: [],
-  overlayDatabaseMode: "none" /* None */,
-  useOverlayDatabaseCaching: false
-};
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
@@ -90099,38 +90090,10 @@ async function getConfig(tempDir, logger) {
   logger.debug(configString);
   return JSON.parse(configString);
 }
-function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
-  const augmentedConfig = cloneObject(originalUserInput);
-  if (augmentationProperties.queriesInput) {
-    if (augmentationProperties.queriesInputCombines) {
-      augmentedConfig.queries = (augmentedConfig.queries || []).concat(
-        augmentationProperties.queriesInput
-      );
-    } else {
-      augmentedConfig.queries = augmentationProperties.queriesInput;
-    }
-  }
-  if (augmentedConfig.queries?.length === 0) {
-    delete augmentedConfig.queries;
-  }
-  if (augmentationProperties.packsInput) {
-    if (augmentationProperties.packsInputCombines) {
-      if (Array.isArray(augmentedConfig.packs)) {
-        augmentedConfig.packs = (augmentedConfig.packs || []).concat(
-          augmentationProperties.packsInput
-        );
-      } else if (!augmentedConfig.packs) {
-        augmentedConfig.packs = augmentationProperties.packsInput;
-      } else {
-        const language = Object.keys(augmentedConfig.packs)[0];
-        augmentedConfig.packs[language] = augmentedConfig.packs[language].concat(augmentationProperties.packsInput);
-      }
-    } else {
-      augmentedConfig.packs = augmentationProperties.packsInput;
-    }
-  }
-  if (Array.isArray(augmentedConfig.packs) && !augmentedConfig.packs.length) {
-    delete augmentedConfig.packs;
+function appendExtraQueryExclusions(extraQueryExclusions, cliConfig) {
+  const augmentedConfig = cloneObject(cliConfig);
+  if (extraQueryExclusions.length === 0) {
+    return augmentedConfig;
   }
   augmentedConfig["query-filters"] = [
     // Ordering matters. If the first filter is an inclusion, it implicitly
@@ -90138,7 +90101,7 @@ function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
     // it implicitly includes all queries that are not excluded. So user
     // filters (if any) should always be first to preserve intent.
     ...augmentedConfig["query-filters"] || [],
-    ...augmentationProperties.extraQueryExclusions
+    ...extraQueryExclusions
   ];
   if (augmentedConfig["query-filters"]?.length === 0) {
     delete augmentedConfig["query-filters"];
@@ -91115,7 +91078,7 @@ async function getCodeQLForCmd(cmd, checkVersion) {
         await this.getVersion(),
         "forceOverwrite" /* ForceOverwrite */
       ) ? "--force-overwrite" : "--overwrite";
-      const overlayDatabaseMode = config.augmentationProperties.overlayDatabaseMode;
+      const overlayDatabaseMode = config.overlayDatabaseMode;
       if (overlayDatabaseMode === "overlay" /* Overlay */) {
         const overlayChangesFile = await writeOverlayChangesFile(
           config,
@@ -91529,9 +91492,9 @@ async function runCli(cmd, args = [], opts = {}) {
 }
 async function writeCodeScanningConfigFile(config, logger) {
   const codeScanningConfigFile = getGeneratedCodeScanningConfigPath(config);
-  const augmentedConfig = generateCodeScanningConfig(
-    config.originalUserInput,
-    config.augmentationProperties
+  const augmentedConfig = appendExtraQueryExclusions(
+    config.extraQueryExclusions,
+    config.computedConfig
   );
   logger.info(
     `Writing augmented user configuration file to ${codeScanningConfigFile}`
diff --git a/src/analyze.ts b/src/analyze.ts
index 19bfcf028f..a8ab5ca91d 100644
--- a/src/analyze.ts
+++ b/src/analyze.ts
@@ -626,10 +626,7 @@ export async function runQueries(
   const incrementalMode: string[] = [];
 
   // Preserve cached intermediate results for overlay-base databases.
-  if (
-    config.augmentationProperties.overlayDatabaseMode !==
-    OverlayDatabaseMode.OverlayBase
-  ) {
+  if (config.overlayDatabaseMode !== OverlayDatabaseMode.OverlayBase) {
     queryFlags.push("--expect-discarded-cache");
   }
 
@@ -641,15 +638,10 @@ export async function runQueries(
   }
 
   statusReport.analysis_is_overlay =
-    config.augmentationProperties.overlayDatabaseMode ===
-    OverlayDatabaseMode.Overlay;
+    config.overlayDatabaseMode === OverlayDatabaseMode.Overlay;
   statusReport.analysis_builds_overlay_base_database =
-    config.augmentationProperties.overlayDatabaseMode ===
-    OverlayDatabaseMode.OverlayBase;
-  if (
-    config.augmentationProperties.overlayDatabaseMode ===
-    OverlayDatabaseMode.Overlay
-  ) {
+    config.overlayDatabaseMode === OverlayDatabaseMode.OverlayBase;
+  if (config.overlayDatabaseMode === OverlayDatabaseMode.Overlay) {
     incrementalMode.push("overlay");
   }
 
diff --git a/src/codeql.test.ts b/src/codeql.test.ts
index 29e4b27ef3..e6df746c73 100644
--- a/src/codeql.test.ts
+++ b/src/codeql.test.ts
@@ -18,6 +18,7 @@ import {
   AugmentationProperties,
   Config,
   defaultAugmentationProperties,
+  generateCodeScanningConfig,
 } from "./config-utils";
 import * as defaults from "./defaults.json";
 import { DocUrl } from "./doc-url";
@@ -504,6 +505,10 @@ const injectedConfigMacro = test.macro({
         tempDir,
         augmentationProperties,
       };
+      thisStubConfig.computedConfig = generateCodeScanningConfig(
+        thisStubConfig.originalUserInput,
+        thisStubConfig.augmentationProperties,
+      );
 
       await codeqlObject.databaseInitCluster(
         thisStubConfig,
diff --git a/src/codeql.ts b/src/codeql.ts
index 81c8e3decd..567eb80875 100644
--- a/src/codeql.ts
+++ b/src/codeql.ts
@@ -13,7 +13,7 @@ import {
 } from "./actions-util";
 import * as api from "./api-client";
 import { CliError, wrapCliConfigurationError } from "./cli-errors";
-import { generateCodeScanningConfig, type Config } from "./config-utils";
+import { appendExtraQueryExclusions, type Config } from "./config-utils";
 import { DocUrl } from "./doc-url";
 import { EnvVar } from "./environment";
 import {
@@ -593,8 +593,7 @@ export async function getCodeQLForCmd(
         ? "--force-overwrite"
         : "--overwrite";
 
-      const overlayDatabaseMode =
-        config.augmentationProperties.overlayDatabaseMode;
+      const overlayDatabaseMode = config.overlayDatabaseMode;
       if (overlayDatabaseMode === OverlayDatabaseMode.Overlay) {
         const overlayChangesFile = await writeOverlayChangesFile(
           config,
@@ -1150,20 +1149,26 @@ async function runCli(
 }
 
 /**
- * Generates a code scanning configuration that is to be used for a scan.
+ * Writes the code scanning configuration that is to be used by the CLI.
  *
  * @param codeql The CodeQL object to use.
- * @param config The configuration to use.
- * @returns the path to the generated user configuration file.
+ * @param config The CodeQL Action state to use.
+ * @returns The path to the generated user configuration file.
  */
 async function writeCodeScanningConfigFile(
   config: Config,
   logger: Logger,
 ): Promise<string> {
   const codeScanningConfigFile = getGeneratedCodeScanningConfigPath(config);
-  const augmentedConfig = generateCodeScanningConfig(
-    config.originalUserInput,
-    config.augmentationProperties,
+
+  // Apply the `extraQueryExclusions` from the CodeQL Action state to the CLI configuration.
+  // We do this here at the latest possible point before passing the CLI configuration on to
+  // the CLI so that the `extraQueryExclusions` appear after all user-configured `query-filters`.
+  // See the comment in `applyExtraQueryExclusions` for more information, as well as
+  // https://github.com/github/codeql-action/pull/2938
+  const augmentedConfig = appendExtraQueryExclusions(
+    config.extraQueryExclusions,
+    config.computedConfig,
   );
 
   logger.info(
diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index e57cb5f6f4..b133f500bc 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -322,18 +322,21 @@ test("load non-empty input", async (t) => {
 
     fs.mkdirSync(path.join(tempDir, "foo"));
 
+    const userConfig: configUtils.UserConfig = {
+      name: "my config",
+      "disable-default-queries": true,
+      queries: [{ uses: "./foo" }],
+      "paths-ignore": ["a", "b"],
+      paths: ["c/d"],
+    };
+
     // And the config we expect it to parse to
     const expectedConfig: configUtils.Config = {
       analysisKinds: [AnalysisKind.CodeScanning],
       languages: [KnownLanguage.javascript],
       buildMode: BuildMode.None,
-      originalUserInput: {
-        name: "my config",
-        "disable-default-queries": true,
-        queries: [{ uses: "./foo" }],
-        "paths-ignore": ["a", "b"],
-        paths: ["c/d"],
-      },
+      originalUserInput: userConfig,
+      computedConfig: userConfig,
       tempDir,
       codeQLCmd: codeql.getPath(),
       gitHubVersion: githubVersion,
@@ -345,6 +348,9 @@ test("load non-empty input", async (t) => {
       trapCaches: {},
       trapCacheDownloadTime: 0,
       dependencyCachingEnabled: CachingKind.None,
+      extraQueryExclusions: [],
+      overlayDatabaseMode: OverlayDatabaseMode.None,
+      useOverlayDatabaseCaching: false,
     };
 
     const languagesInput = "javascript";
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 477cb20e6c..64a1c93b9d 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -145,8 +145,17 @@ export interface Config {
    */
   debugDatabaseName: string;
 
+  /**
+   * Describes how to augment the user configuration with inputs from the action.
+   */
   augmentationProperties: AugmentationProperties;
 
+  /**
+   * The configuration we computed by combining `originalUserInput` with `augmentationProperties`,
+   * as well as adjustments made to it based on unsupported or required options.
+   */
+  computedConfig: UserConfig;
+
   /**
    * Partial map from languages to locations of TRAP caches for that language.
    * If a key is omitted, then TRAP caching should not be used for that language.
@@ -160,6 +169,28 @@ export interface Config {
 
   /** A value indicating how dependency caching should be used. */
   dependencyCachingEnabled: CachingKind;
+
+  /**
+   * Extra query exclusions to append to the config.
+   */
+  extraQueryExclusions: ExcludeQueryFilter[];
+
+  /**
+   * The overlay database mode to use.
+   */
+  overlayDatabaseMode: OverlayDatabaseMode;
+
+  /**
+   * Whether to use caching for overlay databases. If it is true, the action
+   * will upload the created overlay-base database to the actions cache, and
+   * download an overlay-base database from the actions cache before it creates
+   * a new overlay database. If it is false, the action assumes that the
+   * workflow will be responsible for managing database storage and retrieval.
+   *
+   * This property has no effect unless `overlayDatabaseMode` is `Overlay` or
+   * `OverlayBase`.
+   */
+  useOverlayDatabaseCaching: boolean;
 }
 
 /**
@@ -192,28 +223,6 @@ export interface AugmentationProperties {
    * The packs input from the `with` block of the action declaration
    */
   packsInput?: string[];
-
-  /**
-   * Extra query exclusions to append to the config.
-   */
-  extraQueryExclusions: ExcludeQueryFilter[];
-
-  /**
-   * The overlay database mode to use.
-   */
-  overlayDatabaseMode: OverlayDatabaseMode;
-
-  /**
-   * Whether to use caching for overlay databases. If it is true, the action
-   * will upload the created overlay-base database to the actions cache, and
-   * download an overlay-base database from the actions cache before it creates
-   * a new overlay database. If it is false, the action assumes that the
-   * workflow will be responsible for managing database storage and retrieval.
-   *
-   * This property has no effect unless `overlayDatabaseMode` is `Overlay` or
-   * `OverlayBase`.
-   */
-  useOverlayDatabaseCaching: boolean;
 }
 
 /**
@@ -225,9 +234,6 @@ export const defaultAugmentationProperties: AugmentationProperties = {
   packsInputCombines: false,
   packsInput: undefined,
   queriesInput: undefined,
-  extraQueryExclusions: [],
-  overlayDatabaseMode: OverlayDatabaseMode.None,
-  useOverlayDatabaseCaching: false,
 };
 export type Packs = Partial<Record<Language, string[]>>;
 
@@ -576,6 +582,7 @@ export async function getDefaultConfig({
     languages,
     buildMode,
     originalUserInput: {},
+    computedConfig: {},
     tempDir,
     codeQLCmd: codeql.getPath(),
     gitHubVersion: githubVersion,
@@ -587,6 +594,9 @@ export async function getDefaultConfig({
     trapCaches,
     trapCacheDownloadTime,
     dependencyCachingEnabled: getCachingKind(dependencyCachingEnabled),
+    extraQueryExclusions: [],
+    overlayDatabaseMode: OverlayDatabaseMode.None,
+    useOverlayDatabaseCaching: false,
   };
 }
 
@@ -673,9 +683,6 @@ export async function calculateAugmentation(
     packsInput: packsInput?.[languages[0]],
     queriesInput,
     queriesInputCombines,
-    extraQueryExclusions: [],
-    overlayDatabaseMode: OverlayDatabaseMode.None,
-    useOverlayDatabaseCaching: false,
   };
 }
 
@@ -1098,9 +1105,15 @@ export async function initConfig(inputs: InitConfigInputs): Promise<Config> {
   }
 
   const config = await getDefaultConfig(inputs);
-  const augmentationProperties = config.augmentationProperties;
   config.originalUserInput = userConfig;
 
+  // Compute the full Code Scanning configuration that combines the configuration from the
+  // configuration file / `config` input with other inputs, such as `queries`.
+  config.computedConfig = generateCodeScanningConfig(
+    userConfig,
+    config.augmentationProperties,
+  );
+
   // The choice of overlay database mode depends on the selection of languages
   // and queries, which in turn depends on the user config and the augmentation
   // properties. So we need to calculate the overlay database mode after the
@@ -1113,15 +1126,15 @@ export async function initConfig(inputs: InitConfigInputs): Promise<Config> {
       config.languages,
       inputs.sourceRoot,
       config.buildMode,
-      generateCodeScanningConfig(userConfig, augmentationProperties),
+      config.computedConfig,
       logger,
     );
   logger.info(
     `Using overlay database mode: ${overlayDatabaseMode} ` +
       `${useOverlayDatabaseCaching ? "with" : "without"} caching.`,
   );
-  augmentationProperties.overlayDatabaseMode = overlayDatabaseMode;
-  augmentationProperties.useOverlayDatabaseCaching = useOverlayDatabaseCaching;
+  config.overlayDatabaseMode = overlayDatabaseMode;
+  config.useOverlayDatabaseCaching = useOverlayDatabaseCaching;
 
   if (
     overlayDatabaseMode === OverlayDatabaseMode.Overlay ||
@@ -1131,7 +1144,7 @@ export async function initConfig(inputs: InitConfigInputs): Promise<Config> {
       logger,
     ))
   ) {
-    augmentationProperties.extraQueryExclusions.push({
+    config.extraQueryExclusions.push({
       exclude: { tags: "exclude-from-incremental" },
     });
   }
@@ -1461,17 +1474,42 @@ export function generateCodeScanningConfig(
     delete augmentedConfig.packs;
   }
 
+  return augmentedConfig;
+}
+
+/**
+ * Appends `extraQueryExclusions` to `cliConfig`'s `query-filters`.
+ *
+ * @param extraQueryExclusions The extra query exclusions to append to the `query-filters`.
+ * @param cliConfig The CodeQL CLI configuration to extend.
+ * @returns Returns `cliConfig` if there are no extra query exclusions
+ *          or a copy of `cliConfig` where the extra query exclusions
+ *          have been appended to `query-filters`.
+ */
+export function appendExtraQueryExclusions(
+  extraQueryExclusions: ExcludeQueryFilter[],
+  cliConfig: UserConfig,
+): Readonly<UserConfig> {
+  // make a copy so we can modify it and so that modifications to the input
+  // object do not affect the result that is marked as `Readonly`.
+  const augmentedConfig = cloneObject(cliConfig);
+
+  if (extraQueryExclusions.length === 0) {
+    return augmentedConfig;
+  }
+
   augmentedConfig["query-filters"] = [
     // Ordering matters. If the first filter is an inclusion, it implicitly
     // excludes all queries that are not included. If it is an exclusion,
     // it implicitly includes all queries that are not excluded. So user
     // filters (if any) should always be first to preserve intent.
     ...(augmentedConfig["query-filters"] || []),
-    ...augmentationProperties.extraQueryExclusions,
+    ...extraQueryExclusions,
   ];
   if (augmentedConfig["query-filters"]?.length === 0) {
     delete augmentedConfig["query-filters"];
   }
+
   return augmentedConfig;
 }
 
diff --git a/src/init-action.ts b/src/init-action.ts
index df22fe6a54..35bc83d2df 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -449,9 +449,8 @@ async function run() {
   let overlayBaseDatabaseStats: OverlayBaseDatabaseDownloadStats | undefined;
   try {
     if (
-      config.augmentationProperties.overlayDatabaseMode ===
-        OverlayDatabaseMode.Overlay &&
-      config.augmentationProperties.useOverlayDatabaseCaching
+      config.overlayDatabaseMode === OverlayDatabaseMode.Overlay &&
+      config.useOverlayDatabaseCaching
     ) {
       // OverlayDatabaseMode.Overlay comes in two flavors: with database
       // caching, or without. The flavor with database caching is intended to be
@@ -470,8 +469,7 @@ async function run() {
         logger,
       );
       if (!overlayBaseDatabaseStats) {
-        config.augmentationProperties.overlayDatabaseMode =
-          OverlayDatabaseMode.None;
+        config.overlayDatabaseMode = OverlayDatabaseMode.None;
         logger.info(
           "No overlay-base database found in cache, " +
             `reverting overlay database mode to ${OverlayDatabaseMode.None}.`,
@@ -479,10 +477,7 @@ async function run() {
       }
     }
 
-    if (
-      config.augmentationProperties.overlayDatabaseMode !==
-      OverlayDatabaseMode.Overlay
-    ) {
+    if (config.overlayDatabaseMode !== OverlayDatabaseMode.Overlay) {
       cleanupDatabaseClusterDirectory(config, logger);
     }
 
@@ -739,15 +734,13 @@ async function run() {
     // revert to `OverlayDatabaseMode.None`, re-initialize the database cluster
     // with the new overlay database mode.
     if (
-      config.augmentationProperties.overlayDatabaseMode !==
-        OverlayDatabaseMode.None &&
+      config.overlayDatabaseMode !== OverlayDatabaseMode.None &&
       !(await checkPacksForOverlayCompatibility(codeql, config, logger))
     ) {
       logger.info(
         "Reverting overlay database mode to None due to incompatible packs.",
       );
-      config.augmentationProperties.overlayDatabaseMode =
-        OverlayDatabaseMode.None;
+      config.overlayDatabaseMode = OverlayDatabaseMode.None;
       cleanupDatabaseClusterDirectory(config, logger, {
         disableExistingDirectoryWarning: true,
       });
diff --git a/src/overlay-database-utils.test.ts b/src/overlay-database-utils.test.ts
index fb8a48d447..61fcf48af9 100644
--- a/src/overlay-database-utils.test.ts
+++ b/src/overlay-database-utils.test.ts
@@ -120,10 +120,8 @@ const testDownloadOverlayBaseDatabaseFromCache = test.macro({
 
       const testCase = { ...defaultDownloadTestCase, ...partialTestCase };
 
-      config.augmentationProperties.overlayDatabaseMode =
-        testCase.overlayDatabaseMode;
-      config.augmentationProperties.useOverlayDatabaseCaching =
-        testCase.useOverlayDatabaseCaching;
+      config.overlayDatabaseMode = testCase.overlayDatabaseMode;
+      config.useOverlayDatabaseCaching = testCase.useOverlayDatabaseCaching;
 
       if (testCase.hasBaseDatabaseOidsFile) {
         const baseDatabaseOidsFile = path.join(
diff --git a/src/overlay-database-utils.ts b/src/overlay-database-utils.ts
index a01546f067..1df46aa785 100644
--- a/src/overlay-database-utils.ts
+++ b/src/overlay-database-utils.ts
@@ -192,7 +192,7 @@ export async function uploadOverlayBaseDatabaseToCache(
   config: Config,
   logger: Logger,
 ): Promise<boolean> {
-  const overlayDatabaseMode = config.augmentationProperties.overlayDatabaseMode;
+  const overlayDatabaseMode = config.overlayDatabaseMode;
   if (overlayDatabaseMode !== OverlayDatabaseMode.OverlayBase) {
     logger.debug(
       `Overlay database mode is ${overlayDatabaseMode}. ` +
@@ -200,7 +200,7 @@ export async function uploadOverlayBaseDatabaseToCache(
     );
     return false;
   }
-  if (!config.augmentationProperties.useOverlayDatabaseCaching) {
+  if (!config.useOverlayDatabaseCaching) {
     logger.debug(
       "Overlay database caching is disabled. " +
         "Skip uploading overlay-base database to cache.",
@@ -298,7 +298,7 @@ export async function downloadOverlayBaseDatabaseFromCache(
   config: Config,
   logger: Logger,
 ): Promise<OverlayBaseDatabaseDownloadStats | undefined> {
-  const overlayDatabaseMode = config.augmentationProperties.overlayDatabaseMode;
+  const overlayDatabaseMode = config.overlayDatabaseMode;
   if (overlayDatabaseMode !== OverlayDatabaseMode.Overlay) {
     logger.debug(
       `Overlay database mode is ${overlayDatabaseMode}. ` +
@@ -306,7 +306,7 @@ export async function downloadOverlayBaseDatabaseFromCache(
     );
     return undefined;
   }
-  if (!config.augmentationProperties.useOverlayDatabaseCaching) {
+  if (!config.useOverlayDatabaseCaching) {
     logger.debug(
       "Overlay database caching is disabled. " +
         "Skip downloading overlay-base database from cache.",
diff --git a/src/testing-utils.ts b/src/testing-utils.ts
index 624bb72cd5..6e1763b00f 100644
--- a/src/testing-utils.ts
+++ b/src/testing-utils.ts
@@ -11,7 +11,7 @@ import * as apiClient from "./api-client";
 import { GitHubApiDetails } from "./api-client";
 import { CachingKind } from "./caching-utils";
 import * as codeql from "./codeql";
-import { Config } from "./config-utils";
+import { AugmentationProperties, Config } from "./config-utils";
 import * as defaults from "./defaults.json";
 import {
   CodeQLDefaultVersionInfo,
@@ -360,6 +360,7 @@ export function createTestConfig(overrides: Partial<Config>): Config {
       languages: [],
       buildMode: undefined,
       originalUserInput: {},
+      computedConfig: {},
       tempDir: "",
       codeQLCmd: "",
       gitHubVersion: {
@@ -372,13 +373,13 @@ export function createTestConfig(overrides: Partial<Config>): Config {
       augmentationProperties: {
         packsInputCombines: false,
         queriesInputCombines: false,
-        extraQueryExclusions: [],
-        overlayDatabaseMode: OverlayDatabaseMode.None,
-        useOverlayDatabaseCaching: false,
-      },
+      } satisfies AugmentationProperties,
       trapCaches: {},
       trapCacheDownloadTime: 0,
       dependencyCachingEnabled: CachingKind.None,
+      extraQueryExclusions: [],
+      overlayDatabaseMode: OverlayDatabaseMode.None,
+      useOverlayDatabaseCaching: false,
     } satisfies Config,
     overrides,
   );