Merge pull request #3905 from github/update-v4.35.5-d4b485515

Merge main into releases/v4
Add changelog entry for #3899
2026-05-24 16:14:33 +00:00 · 2026-05-15 12:22:46 +01:00 · 2026-05-15 11:58:39 +01:00 · 2026-05-15 10:48:24 +00:00 · 2026-05-15 10:11:56 +00:00 · 2026-05-14 19:14:01 +01:00
127 changed files with 77174 additions and 1370301 deletions
@@ -1,5 +1,5 @@
 name: "CodeQL config"
-queries: 
+queries:
  - name: Run custom queries
    uses: ./queries
  # Run all extra query suites, both because we want to
@@ -13,3 +13,5 @@ queries:
 paths-ignore:
  - lib
  - tests
+  - "**/*.test.ts"
+  - "**/testing-util.ts"
@@ -59,7 +59,7 @@ jobs:
          use-all-platform-bundle: 'false'
          setup-kotlin: 'true'
      - name: Set up Ruby
-        uses: ruby/setup-ruby@4c56a21280b36d862b5fc31348f463d60bdc55d5 # v1.301.0
+        uses: ruby/setup-ruby@c4e5b1316158f92e3d49443a9d58b31d25ac0f8f # v1.306.0
        with:
          ruby-version: 2.6
      - name: Install Code Scanning integration
@@ -6,13 +6,6 @@ env:
  # Diff informed queries add an additional query filter which is not yet
  # taken into account by these tests.
  CODEQL_ACTION_DIFF_INFORMED_QUERIES: false
-  # Specify overlay enablement manually to ensure stability around the exclude-from-incremental
-  # query filter. Here we only enable for the default code scanning suite.
-  CODEQL_ACTION_OVERLAY_ANALYSIS: true
-  CODEQL_ACTION_OVERLAY_ANALYSIS_JAVASCRIPT: false
-  CODEQL_ACTION_OVERLAY_ANALYSIS_CODE_SCANNING_JAVASCRIPT: true
-  CODEQL_ACTION_OVERLAY_ANALYSIS_STATUS_CHECK: false
-  CODEQL_ACTION_OVERLAY_ANALYSIS_SKIP_RESOURCE_CHECKS: true

 on:
  push:
@@ -79,33 +72,13 @@ jobs:
      with:
        version: ${{ matrix.version }}

-    # On PRs, overlay analysis may change the config that is passed to the CLI.
-    # Therefore, we have two variants of the following test, one for PRs and one for other events.
-    - name: Empty file (non-PR)
-      if: github.event_name != 'pull_request'
+    - name: Empty file
      uses: ./../action/.github/actions/check-codescanning-config
      with:
        expected-config-file-contents: "{}"
        languages: javascript
        tools: ${{ steps.prepare-test.outputs.tools-url }}

-    - name: Empty file (PR)
-      if: github.event_name == 'pull_request'
-      uses: ./../action/.github/actions/check-codescanning-config
-      with:
-        expected-config-file-contents: |
-          {
-            "query-filters": [
-              {
-                "exclude": {
-                  "tags": "exclude-from-incremental"
-                }
-              }
-            ]
-          }
-        languages: javascript
-        tools: ${{ steps.prepare-test.outputs.tools-url }}
-
    - name: Packs from input
      if: success() || failure()
      uses: ./../action/.github/actions/check-codescanning-config
@@ -0,0 +1,106 @@
+# Workflow runs on main, on a release branch, and that were triggered as part of a merge group have
+# already passed CI before being merged. Therefore if they fail, we should make sure that there
+# wasn't a transient failure by rerunning the failed jobs once before investigating further.
+name: Deflake
+
+on:
+  workflow_run:
+    types: [completed]
+    # Exclude workflows that have significant side effects, like publishing releases. It's OK to
+    # retry CodeQL analysis.
+    workflows:
+      - Check Expected Release Files
+      - Code-Scanning config CLI tests
+      - CodeQL action
+      - Manual Check - go
+      - "PR Check - All-platform bundle"
+      - "PR Check - Analysis kinds"
+      - "PR Check - Analyze: 'ref' and 'sha' from inputs"
+      - "PR Check - autobuild-action"
+      - "PR Check - Autobuild direct tracing (custom working directory)"
+      - "PR Check - Autobuild working directory"
+      - "PR Check - Build mode autobuild"
+      - "PR Check - Build mode manual"
+      - "PR Check - Build mode none"
+      - "PR Check - Build mode rollback"
+      - "PR Check - Bundle: Caching checks"
+      - "PR Check - Bundle: From nightly"
+      - "PR Check - Bundle: From toolcache"
+      - "PR Check - Bundle: Zstandard checks"
+      - "PR Check - C/C\\+\\+: autoinstalling dependencies (Linux)"
+      - "PR Check - C/C\\+\\+: autoinstalling dependencies is skipped (macOS)"
+      - "PR Check - C/C\\+\\+: disabling autoinstalling dependencies (Linux)"
+      - "PR Check - Clean up database cluster directory"
+      - "PR Check - CodeQL Bundle All"
+      - "PR Check - Config export"
+      - "PR Check - Config input"
+      - "PR Check - Custom source root"
+      - "PR Check - Debug artifact upload"
+      - "PR Check - Debug artifacts after failure"
+      - "PR Check - Diagnostic export"
+      - "PR Check - Export file baseline information"
+      - "PR Check - Extractor ram and threads options test"
+      - "PR Check - Go: Custom queries"
+      - "PR Check - Go: diagnostic when Go is changed after init step"
+      - "PR Check - Go: diagnostic when `file` is not installed"
+      - "PR Check - Go: tracing with autobuilder step"
+      - "PR Check - Go: tracing with custom build steps"
+      - "PR Check - Go: tracing with legacy workflow"
+      - "PR Check - Go: workaround for indirect tracing"
+      - "PR Check - Job run UUID added to SARIF"
+      - "PR Check - Language aliases"
+      - "PR Check - Local CodeQL bundle"
+      - "PR Check - Multi-language repository"
+      - "PR Check - Overlay database init fallback"
+      - "PR Check - Packaging: Action input"
+      - "PR Check - Packaging: Config and input"
+      - "PR Check - Packaging: Config and input passed to the CLI"
+      - "PR Check - Packaging: Config file"
+      - "PR Check - Packaging: Download using registries"
+      - "PR Check - Proxy test"
+      - "PR Check - Remote config file"
+      - "PR Check - Resolve environment"
+      - "PR Check - RuboCop multi-language"
+      - "PR Check - Ruby analysis"
+      - "PR Check - Rust analysis"
+      - "PR Check - Split workflow"
+      - "PR Check - Start proxy"
+      - "PR Check - Submit SARIF after failure"
+      - "PR Check - Swift analysis using a custom build command"
+      - "PR Check - Swift analysis using autobuild"
+      - "PR Check - Test different uses of `upload-sarif`"
+      - "PR Check - Test unsetting environment variables"
+      - "PR Check - Upload-sarif: ref and sha from inputs"
+      - "PR Check - Use a custom `checkout_path`"
+      - PR Checks
+      - Query filters tests
+      - Test that the workaround for python 3.12 on windows works
+
+jobs:
+  rerun-on-failure:
+    name: Rerun failed jobs
+    if: >-
+      github.event.workflow_run.conclusion == 'failure' &&
+      github.event.workflow_run.run_attempt == 1 &&
+      (
+        github.event.workflow_run.head_branch == 'main' ||
+        startsWith(github.event.workflow_run.head_branch, 'releases/') ||
+        github.event.workflow_run.event == 'merge_group'
+      )
+    runs-on: ubuntu-slim
+    permissions:
+      actions: write
+    steps:
+      - name: Rerun failed jobs in ${{ github.event.workflow_run.name }}
+        env:
+          GH_TOKEN: ${{ github.token }}
+          GH_REPO: ${{ github.repository }}
+          RUN_ID: ${{ github.event.workflow_run.id }}
+          RUN_NAME: ${{ github.event.workflow_run.name }}
+          RUN_URL: ${{ github.event.workflow_run.html_url }}
+        run: |
+          echo "Rerunning failed jobs for workflow run ${RUN_ID}"
+          gh run rerun "${RUN_ID}" --failed
+          echo "### Reran failed jobs :recycle:" >> "$GITHUB_STEP_SUMMARY"
+          echo "" >> "$GITHUB_STEP_SUMMARY"
+          echo "Workflow: [${RUN_NAME}](${RUN_URL})" >> "$GITHUB_STEP_SUMMARY"
@@ -131,7 +131,7 @@ jobs:
          echo "::endgroup::"

      - name: Generate token
-        uses: actions/create-github-app-token@v3.1.1
+        uses: actions/create-github-app-token@v3.2.0
        id: app-token
        with:
          app-id: ${{ vars.AUTOMATION_APP_ID }}
@@ -136,7 +136,7 @@ jobs:

      - name: Generate token
        if: github.event_name == 'workflow_dispatch'
-        uses: actions/create-github-app-token@v3.1.1
+        uses: actions/create-github-app-token@v3.2.0
        id: app-token
        with:
          app-id: ${{ vars.AUTOMATION_APP_ID }}
@@ -63,13 +63,10 @@ jobs:
        with:
          tools: https://github.com/github/codeql-action/releases/download/${{ github.event.release.tag_name }}/codeql-bundle-linux64.tar.gz

-      - name: Update language aliases
+      - name: Update built-in languages
+        run: npx tsx pr-checks/update-builtin-languages.ts "$CODEQL_PATH"
        env:
          CODEQL_PATH: ${{ steps.setup-codeql.outputs.codeql-path }}
-        run: |
-          "$CODEQL_PATH" resolve languages --format=betterjson --extractor-include-aliases \
-            | jq -S '.aliases // {}' \
-            > src/known-language-aliases.json

      - name: Bump Action minor version if new CodeQL minor version series
        id: bump-action-version
@@ -93,7 +93,7 @@ jobs:
      pull-requests: write # needed to create pull request
    steps:
    - name: Generate token
-      uses: actions/create-github-app-token@v3.1.1
+      uses: actions/create-github-app-token@v3.2.0
      id: app-token
      with:
        app-id: ${{ vars.AUTOMATION_APP_ID }}
@@ -19,7 +19,7 @@
    "scope": "javascript, typescript",
    "prefix": "testMacro",
    "body": [
-      "const ${1:nameMacro} = test.macro({",
+      "const ${1:nameMacro} = makeMacro({",
      "  exec: async (t: ExecutionContext<unknown>) => {},",
      "",
      "  title: (providedTitle = \"\") => `${2:common title} - \\${providedTitle}`,",
@@ -2,12 +2,32 @@

 See the [releases page](https://github.com/github/codeql-action/releases) for the relevant changes to the CodeQL CLI and language packs.

-## [UNRELEASED]
+## 4.35.5 - 15 May 2026
+
+- We have improved how the JavaScript bundles for the CodeQL Action are generated to avoid duplication across bundles and reduce the size of the repository by around 70%. This should have no effect on the runtime behaviour of the CodeQL Action. [#3899](https://github.com/github/codeql-action/pull/3899)
+- For performance and accuracy reasons, [improved incremental analysis](https://github.com/github/roadmap/issues/1158) will now only be enabled on a pull request when diff-informed analysis is also enabled for that run. If diff-informed analysis is unavailable (for example, because the PR diff ranges could not be computed), the action will fall back to a full analysis. [#3791](https://github.com/github/codeql-action/pull/3791)
+- If multiple inputs are provided for the GitHub-internal `analysis-kinds` input, only `code-scanning` will be enabled. The `analysis-kinds` input is experimental, for GitHub-internal use only, and may change without notice at any time. [#3892](https://github.com/github/codeql-action/pull/3892)
+- Added an experimental change which, when running a Code Scanning analysis for a PR with [improved incremental analysis](https://github.com/github/roadmap/issues/1158) enabled, prefers CodeQL CLI versions that have a cached overlay-base database for the configured languages. This speeds up analysis for a repository when there is not yet a cached overlay-base database for the latest CLI version. We expect to roll this change out to everyone in May. [#3880](https://github.com/github/codeql-action/pull/3880)
+
+## 4.35.4 - 07 May 2026
+
+- Update default CodeQL bundle version to [2.25.4](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.25.4). [#3881](https://github.com/github/codeql-action/pull/3881)
+
+## 4.35.3 - 01 May 2026
+
+- _Upcoming breaking change_: Add a deprecation warning for customers using CodeQL version 2.19.3 and earlier. These versions of CodeQL were discontinued on 9 April 2026 alongside GitHub Enterprise Server 3.15, and will be unsupported by the next minor release of the CodeQL Action. [#3837](https://github.com/github/codeql-action/pull/3837)
+- Configurations for private registries that use Cloudsmith or GCP OIDC are now accepted. [#3850](https://github.com/github/codeql-action/pull/3850)
+- Best-effort connection tests for private registries now use `GET` requests instead of `HEAD` for better compatibility with various registry implementations. For NuGet feeds, the test is now always performed against the service index. [#3853](https://github.com/github/codeql-action/pull/3853)
+- Fixed a bug where two diagnostics produced within the same millisecond could overwrite each other on disk, causing one of them to be lost. [#3852](https://github.com/github/codeql-action/pull/3852)
+- Update default CodeQL bundle version to [2.25.3](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.25.3). [#3865](https://github.com/github/codeql-action/pull/3865)
+
+## 4.35.2 - 15 Apr 2026

 - The undocumented TRAP cache cleanup feature that could be enabled using the `CODEQL_ACTION_CLEANUP_TRAP_CACHES` environment variable is deprecated and will be removed in May 2026. If you are affected by this, we recommend disabling TRAP caching by passing the `trap-caching: false` input to the `init` Action. [#3795](https://github.com/github/codeql-action/pull/3795)
 - The Git version 2.36.0 requirement for improved incremental analysis now only applies to repositories that contain submodules. [#3789](https://github.com/github/codeql-action/pull/3789)
 - Python analysis on GHES no longer extracts the standard library, relying instead on models of the standard library. This should result in significantly faster extraction and analysis times, while the effect on alerts should be minimal. [#3794](https://github.com/github/codeql-action/pull/3794)
 - Fixed a bug in the validation of OIDC configurations for private registries that was added in CodeQL Action 4.33.0 / 3.33.0. [#3807](https://github.com/github/codeql-action/pull/3807)
+- Update default CodeQL bundle version to [2.25.2](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.25.2). [#3823](https://github.com/github/codeql-action/pull/3823)

 ## 4.35.1 - 27 Mar 2026

@@ -72,6 +72,7 @@ We typically release new minor versions of the CodeQL Action and Bundle when a n

 | Minimum CodeQL Action | Minimum CodeQL Bundle Version | GitHub Environment | Notes |
 |-----------------------|-------------------------------|--------------------|-------|
+| `v4.33.0` | `2.24.3` | Enterprise Server 3.21 | |
 | `v4.31.10` | `2.23.9` | Enterprise Server 3.20 | |
 | `v3.29.11` | `2.22.4` | Enterprise Server 3.19 | |
 | `v3.28.21` | `2.21.3` | Enterprise Server 3.18 | |
@@ -95,5 +95,5 @@ outputs:
    description: The ID of the uploaded SARIF file.
 runs:
  using: node24
-  main: "../lib/analyze-action.js"
-  post: "../lib/analyze-action-post.js"
+  main: "../lib/analyze-entry.js"
+  post: "../lib/analyze-post-entry.js"
@@ -16,4 +16,4 @@ inputs:
    required: false
 runs:
  using: node24
-  main: '../lib/autobuild-action.js'
+  main: '../lib/autobuild-entry.js'
@@ -1,5 +1,5 @@
-import { copyFile, rm, writeFile } from "node:fs/promises";
-import { dirname, join } from "node:path";
+import { copyFile, readFile, rm, writeFile } from "node:fs/promises";
+import { basename, dirname, join } from "node:path";
 import { fileURLToPath } from "node:url";

 import * as esbuild from "esbuild";
@@ -62,18 +62,123 @@ const onEndPlugin = {
  },
 };

+/** The name of the virtual `entry-points` module. */
+const SHARED_ENTRYPOINT = "entry-points";
+
+/**
+ * This plugin finds all source files that contain action entry points.
+ * It then generates the virtual `entry-points` module which imports all identifies files,
+ * and re-exports their `runWrapper` functions with suitable aliases.
+ * A tiny stub file is emitted for each Action entrypoint. Each stub imports the shared bundle
+ * and calls the respective entry point.
+ *
+ * @type {esbuild.Plugin}
+ */
+const entryPointsPlugin = {
+  name: "entry-points",
+  setup(build) {
+    const namespace = "actions";
+    const actions = [];
+
+    const toPascal = (s) =>
+      s.replace(/(^|-)([a-z0-9])/gi, (_, __, c) => c.toUpperCase());
+
+    // Find the source files containing action entry points.
+    build.onStart(() => {
+      const actionFiles = globSync("src/*-action{,-post}.ts");
+      for (const actionFile of actionFiles) {
+        const match = basename(actionFile).match(/(.*)-action(-post)?/);
+
+        if (match.length < 2) {
+          throw new Error(`'${actionFile}' didn't match expected pattern.`);
+        }
+
+        const actionName = match[1];
+        const isPost = match[2] !== undefined;
+
+        actions.push({
+          path: actionFile,
+          name: actionName,
+          isPost,
+          pascalCaseName: `${toPascal(actionName)}${isPost ? "Post" : ""}Action`,
+        });
+      }
+    });
+
+    // Resolve the virtual `entry-points` file and set the corresponding namespace.
+    // Ideally, we'd `RegExp.escape` the entrypoint here, but that API isn't supported in Node 20.
+    // Since we're dealing with a hardcoded string, this isn't too much of a problem.
+    build.onResolve({ filter: new RegExp(`^${SHARED_ENTRYPOINT}$`) }, () => {
+      return { path: SHARED_ENTRYPOINT, namespace };
+    });
+
+    // Generate the virtual `entry-points` file based on the actions we discovered.
+    // Restrict using the namespace. The path filter does not need to discriminate any further.
+    build.onLoad({ filter: /.*/, namespace }, async () => {
+      const wrapperTemplatePath = "entry-wrapper.js.tpl";
+      const wrapperTemplate = await readFile(
+        join(SRC_DIR, wrapperTemplatePath),
+        "utf-8",
+      );
+
+      const actionsSorted = actions.sort((a, b) =>
+        a.name.localeCompare(b.name),
+      );
+      const imports = actionsSorted
+        .map(
+          (action) =>
+            `import * as ${action.pascalCaseName} from "./src/${basename(action.path)}"`,
+        )
+        .join("\n");
+      const wrappers = actionsSorted
+        .map((action) =>
+          wrapperTemplate.replaceAll("__ACTION__", action.pascalCaseName),
+        )
+        .join("\n\n");
+
+      return {
+        contents: `"use strict";\n${imports}\n\n${wrappers}\n`,
+        resolveDir: ".",
+        loader: "ts",
+      };
+    });
+
+    // Emit entry point stubs for each action using the entry template.
+    build.onEnd(async (result) => {
+      // Read the entry point template.
+      const templatePath = "action-entry.js.tpl";
+      const template = await readFile(join(SRC_DIR, templatePath), "utf-8");
+
+      const makeHeader = (sourceFile) =>
+        `// Automatically generated from '${templatePath}' for 'src/${basename(sourceFile)}'.\n\n`;
+
+      // Write entry point stubs for each action.
+      for (const action of actions) {
+        await writeFile(
+          join(
+            OUT_DIR,
+            `${action.name}${action.isPost ? "-post" : ""}-entry.js`,
+          ),
+          makeHeader(action.path) +
+            template.replaceAll("__ACTION__", action.pascalCaseName),
+        );
+      }
+    });
+  },
+};
+
 const context = await esbuild.context({
  // Include upload-lib.ts as an entry point for use in testing environments.
-  entryPoints: globSync([
-    `${SRC_DIR}/*-action.ts`,
-    `${SRC_DIR}/*-action-post.ts`,
-    "src/upload-lib.ts",
-  ]),
+  entryPoints: [
+    { in: SHARED_ENTRYPOINT, out: SHARED_ENTRYPOINT },
+    join(SRC_DIR, "upload-lib.ts"),
+  ],
  bundle: true,
  format: "cjs",
  outdir: OUT_DIR,
  platform: "node",
-  plugins: [cleanPlugin, copyDefaultsPlugin, onEndPlugin],
+  external: ["./entry-points"],
+  plugins: [cleanPlugin, copyDefaultsPlugin, entryPointsPlugin, onEndPlugin],
  target: ["node20"],
  define: {
    __CODEQL_ACTION_VERSION__: JSON.stringify(pkg.version),
@@ -171,5 +171,5 @@ outputs:
    description: The version of the CodeQL binary used for analysis
 runs:
  using: node24
-  main: '../lib/init-action.js'
-  post: '../lib/init-action-post.js'
+  main: '../lib/init-entry.js'
+  post: '../lib/init-post-entry.js'
@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/analyze-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runAnalyzeAction)();
@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/analyze-action-post.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runAnalyzePostAction)();
@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/autobuild-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runAutobuildAction)();
@@ -1,6 +1,6 @@
 {
-  "bundleVersion": "codeql-bundle-v2.25.1",
-  "cliVersion": "2.25.1",
-  "priorBundleVersion": "codeql-bundle-v2.24.3",
-  "priorCliVersion": "2.24.3"
+  "bundleVersion": "codeql-bundle-v2.25.4",
+  "cliVersion": "2.25.4",
+  "priorBundleVersion": "codeql-bundle-v2.25.3",
+  "priorCliVersion": "2.25.3"
 }
@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/init-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runInitAction)();
@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/init-action-post.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runInitPostAction)();
@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/resolve-environment-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runResolveEnvironmentAction)();
@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/setup-codeql-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runSetupCodeqlAction)();
@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/start-proxy-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runStartProxyAction)();
@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/start-proxy-action-post.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runStartProxyPostAction)();
@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/upload-sarif-action.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runUploadSarifAction)();
@@ -0,0 +1,6 @@
+// Automatically generated from 'action-entry.js.tpl' for 'src/upload-sarif-action-post.ts'.
+
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.runUploadSarifPostAction)();
@@ -1,18 +1,18 @@
 {
  "name": "codeql",
-  "version": "4.35.2",
+  "version": "4.35.5",
  "private": true,
  "description": "CodeQL action",
  "scripts": {
    "_build_comment": "echo 'Run the full build so we typecheck the project and can reuse the transpiled files in npm test'",
-    "build": "./scripts/check-node-modules.sh && npm run transpile && node build.mjs && npx tsx ./pr-checks/bundle-metadata.ts",
+    "build": "./scripts/check-node-modules.sh && npm run transpile && node build.mjs",
    "lint": "eslint --report-unused-disable-directives --max-warnings=0 .",
    "lint-ci": "SARIF_ESLINT_IGNORE_SUPPRESSED=true eslint --report-unused-disable-directives --max-warnings=0 . --format @microsoft/eslint-formatter-sarif --output-file=eslint.sarif",
    "lint-fix": "eslint --report-unused-disable-directives --max-warnings=0 . --fix",
    "ava": "npm run transpile && ava --verbose",
    "test": "npm run ava -- src/",
    "test-debug": "npm run test -- --timeout=20m",
-    "transpile": "tsc --build --verbose"
+    "transpile": "tsc --build --verbose tsconfig.json"
  },
  "license": "MIT",
  "workspaces": [
@@ -32,7 +32,7 @@
    "@octokit/plugin-retry": "^8.1.0",
    "archiver": "^7.0.1",
    "fast-deep-equal": "^3.1.3",
-    "follow-redirects": "^1.15.11",
+    "follow-redirects": "^1.16.0",
    "get-folder-size": "^5.0.0",
    "https-proxy-agent": "^7.0.6",
    "js-yaml": "^4.1.1",
@@ -40,35 +40,35 @@
    "long": "^5.3.2",
    "node-forge": "^1.4.0",
    "semver": "^7.7.4",
-    "uuid": "^13.0.0"
+    "uuid": "^14.0.0"
  },
  "devDependencies": {
-    "@ava/typescript": "6.0.0",
-    "@eslint/compat": "^2.0.4",
+    "@ava/typescript": "7.0.0",
+    "@eslint/compat": "^2.0.5",
    "@microsoft/eslint-formatter-sarif": "^3.1.0",
    "@octokit/types": "^16.0.0",
    "@types/archiver": "^7.0.0",
    "@types/follow-redirects": "^1.14.4",
    "@types/js-yaml": "^4.0.9",
-    "@types/node": "^20.19.9",
+    "@types/node": "^20.19.39",
    "@types/node-forge": "^1.3.14",
    "@types/sarif": "^2.1.7",
    "@types/semver": "^7.7.1",
    "@types/sinon": "^21.0.1",
    "ava": "^7.0.0",
    "esbuild": "^0.28.0",
-    "eslint": "^9.39.2",
-    "eslint-import-resolver-typescript": "^3.8.7",
+    "eslint": "^9.39.4",
+    "eslint-import-resolver-typescript": "^4.4.4",
    "eslint-plugin-github": "^6.0.0",
    "eslint-plugin-import-x": "^4.16.2",
    "eslint-plugin-jsdoc": "^62.9.0",
    "eslint-plugin-no-async-foreach": "^0.1.1",
    "glob": "^11.1.0",
-    "globals": "^17.4.0",
+    "globals": "^17.6.0",
    "nock": "^14.0.12",
-    "sinon": "^21.0.3",
-    "typescript": "^6.0.2",
-    "typescript-eslint": "^8.58.0"
+    "sinon": "^21.1.2",
+    "typescript": "^6.0.3",
+    "typescript-eslint": "^8.59.2"
  },
  "overrides": {
    "@actions/tool-cache": {
@@ -89,7 +89,7 @@
    "eslint-plugin-jsx-a11y": {
      "semver": ">=6.3.1"
    },
-    "brace-expansion@2.0.1": "2.0.2",
-    "glob": "^11.1.0"
+    "glob": "^11.1.0",
+    "undici": "^6.24.0"
  }
 }
@@ -5,7 +5,7 @@ versions:
  - default
 steps:
  - name: Set up Ruby
-    uses: ruby/setup-ruby@4c56a21280b36d862b5fc31348f463d60bdc55d5 # v1.301.0
+    uses: ruby/setup-ruby@c4e5b1316158f92e3d49443a9d58b31d25ac0f8f # v1.306.0
    with:
      ruby-version: 2.6
  - name: Install Code Scanning integration
@@ -11,3 +11,13 @@ export const PR_CHECK_EXCLUDED_FILE = path.join(PR_CHECKS_DIR, "excluded.yml");

 /** The path to the esbuild metadata file. */
 export const BUNDLE_METADATA_FILE = path.join(PR_CHECKS_DIR, "..", "meta.json");
+
+/** The `src` directory. */
+const SOURCE_ROOT = path.join(PR_CHECKS_DIR, "..", "src");
+
+/** The path to the built-in languages file. */
+export const BUILTIN_LANGUAGES_FILE = path.join(
+  SOURCE_ROOT,
+  "languages",
+  "builtin.json",
+);
@@ -7,10 +7,10 @@
    "@octokit/core": "^7.0.6",
    "@octokit/plugin-paginate-rest": ">=9.2.2",
    "@octokit/plugin-rest-endpoint-methods": "^17.0.0",
-    "yaml": "^2.8.3"
+    "yaml": "^2.8.4"
  },
  "devDependencies": {
-    "@types/node": "^20.19.9",
+    "@types/node": "^20.19.39",
    "tsx": "^4.21.0"
  }
 }
@@ -5,7 +5,7 @@ import * as path from "path";

 import * as yaml from "yaml";

-import { KnownLanguage } from "../src/languages";
+import { BuiltInLanguage } from "../src/languages";

 /** Known workflow input names. */
 enum KnownInputName {
@@ -91,8 +91,8 @@ interface LanguageSetup {
  steps: Step[];
 }

-/** Describes partial mappings from known languages to their specific setup information. */
-type LanguageSetups = Partial<Record<KnownLanguage, LanguageSetup>>;
+/** Describes partial mappings from built-in languages to their specific setup information. */
+type LanguageSetups = Partial<Record<BuiltInLanguage, LanguageSetup>>;

 // The default set of CodeQL Bundle versions to use for the PR checks.
 const defaultTestVersions = [
@@ -125,7 +125,7 @@ const defaultLanguageVersions = {
  java: "17",
  python: "3.13",
  csharp: "9.x",
-} as const satisfies Partial<Record<KnownLanguage, string>>;
+} as const satisfies Partial<Record<BuiltInLanguage, string>>;

 /** A mapping from known input names to their specifications. */
 const inputSpecs: WorkflowInputs = {
@@ -364,7 +364,7 @@ function getSetupSteps(checkSpecification: JobSpecification): {
  const inputs: Array<Set<KnownInputName>> = [];
  const steps: Step[] = [];

-  for (const language of Object.values(KnownLanguage).sort()) {
+  for (const language of Object.values(BuiltInLanguage).sort()) {
    const setupSpec = languageSetups[language];

    if (
@@ -0,0 +1,131 @@
+#!/usr/bin/env npx tsx
+
+/*
+ * Updates src/languages/builtin.json by querying the CodeQL CLI for:
+ * - Languages that have default queries (via codeql-extractor.yml)
+ * - Language aliases (via `codeql resolve languages --format=betterjson --extractor-include-aliases`)
+ *
+ * Usage:
+ *   npx tsx pr-checks/update-builtin-languages.ts [path-to-codeql]
+ *
+ * If no path is given, falls back to "codeql".
+ */
+
+import { execFileSync } from "node:child_process";
+import * as fs from "node:fs";
+import * as path from "node:path";
+
+import * as yaml from "yaml";
+
+import { EnvVar } from "../src/environment";
+
+import { BUILTIN_LANGUAGES_FILE } from "./config";
+
+/** Resolve all known language extractor directories. */
+function resolveLanguages(codeqlPath: string): Record<string, string[]> {
+  return JSON.parse(
+    execFileSync(codeqlPath, ["resolve", "languages", "--format=json"], {
+      encoding: "utf8",
+      env: {
+        ...process.env,
+        [EnvVar.EXPERIMENTAL_FEATURES]: "true", // include experimental languages
+      },
+    }),
+  ) as Record<string, string[]>;
+}
+
+/**
+ * Return the sorted list of languages whose extractors ship default queries.
+ *
+ * @param extractorDirs - Map from language to list of extractor directories
+ */
+function findLanguagesWithDefaultQueries(
+  extractorDirs: Record<string, string[]>,
+): string[] {
+  const languages: string[] = [];
+
+  for (const [language, dirs] of Object.entries(extractorDirs)) {
+    if (dirs.length !== 1) {
+      throw new Error(
+        `Expected exactly one extractor directory for language '${language}', but found ${dirs.length}: ${dirs.join(
+          ", ",
+        )}`,
+      );
+    }
+
+    const extractorYmlPath = path.join(dirs[0], "codeql-extractor.yml");
+
+    if (!fs.existsSync(extractorYmlPath)) {
+      throw new Error(
+        `Extractor YAML not found for language '${language}' at expected path: ${extractorYmlPath}`,
+      );
+    }
+
+    const extractorYml = yaml.parse(fs.readFileSync(extractorYmlPath, "utf8"));
+    const defaultQueries: unknown[] | undefined = extractorYml.default_queries;
+
+    if (Array.isArray(defaultQueries) && defaultQueries.length > 0) {
+      console.log(
+        `  ✅ ${language}: included (default queries: ${JSON.stringify(defaultQueries)})`,
+      );
+      languages.push(language);
+    } else {
+      console.log(`  ❌ ${language}: excluded (no default queries)`);
+    }
+  }
+
+  return languages.sort();
+}
+
+/**
+ * Resolve language aliases from the CodeQL CLI, keeping only those whose
+ * target is in the given set of included languages.
+ */
+function resolveAliases(
+  codeqlPath: string,
+  includedLanguages: Set<string>,
+): Record<string, string> {
+  const betterjsonOutput = JSON.parse(
+    execFileSync(
+      codeqlPath,
+      [
+        "resolve",
+        "languages",
+        "--format=betterjson",
+        "--extractor-include-aliases",
+      ],
+      { encoding: "utf8" },
+    ),
+  );
+
+  return Object.fromEntries(
+    Object.entries((betterjsonOutput.aliases ?? {}) as Record<string, string>)
+      .filter(([, target]) => includedLanguages.has(target))
+      .sort(([a], [b]) => a.localeCompare(b)),
+  );
+}
+
+/** Write the built-in languages data to disk. */
+function writeBuiltinLanguages(
+  languages: string[],
+  aliases: Record<string, string>,
+): void {
+  const content = `${JSON.stringify({ languages, aliases }, null, 2)}\n`;
+  fs.mkdirSync(path.dirname(BUILTIN_LANGUAGES_FILE), { recursive: true });
+  fs.writeFileSync(BUILTIN_LANGUAGES_FILE, content);
+
+  console.log(`\nWrote ${BUILTIN_LANGUAGES_FILE}`);
+  console.log(`  Languages: ${languages.join(", ")}`);
+  console.log(`  Aliases: ${Object.keys(aliases).join(", ")}`);
+}
+
+function main(): void {
+  const codeqlPath = process.argv[2] || "codeql";
+
+  const extractorDirs = resolveLanguages(codeqlPath);
+  const languages = findLanguagesWithDefaultQueries(extractorDirs);
+  const aliases = resolveAliases(codeqlPath, new Set(languages));
+  writeBuiltinLanguages(languages, aliases);
+}
+
+main();
@@ -22,4 +22,4 @@ outputs:
    description: The inferred build environment configuration.
 runs:
  using: node24
-  main: '../lib/resolve-environment-action.js'
+  main: '../lib/resolve-environment-entry.js'
@@ -19,6 +19,25 @@ inputs:
      If not specified, the Action will check in several places until it finds
      the CodeQL tools.
    required: false
+  languages:
+    description: >-
+      A comma-separated list of CodeQL languages that will be analyzed in subsequent
+      `github/codeql-action/init` and `github/codeql-action/analyze` invocations. If specified, the
+      Action may use this list to select a CodeQL CLI version that is best suited to analyzing those
+      languages, for example by preferring a version that has a cached overlay-base database for the
+      specified languages. This input is not remembered and must also be passed to
+      `github/codeql-action/init`.
+    required: false
+  analysis-kinds:
+    description: >-
+      [Internal] A comma-separated list of analysis kinds that subsequent
+      `github/codeql-action/init` invocations will enable. If specified, the Action may use this
+      list to select a CodeQL CLI version that is best suited to those analysis kinds. This input is
+      not remembered and must also be passed to `github/codeql-action/init`.
+
+      Available options are the same as for the `analysis-kinds` input on the `init` Action.
+    default: 'code-scanning'
+    required: true
  token:
    description: GitHub token to use for authenticating with this instance of GitHub.
    default: ${{ github.token }}
@@ -36,4 +55,4 @@ outputs:
    description: The version of the CodeQL binary that was installed.
 runs:
  using: node24
-  main: '../lib/setup-codeql-action.js'
+  main: '../lib/setup-codeql-entry.js'
@@ -0,0 +1,4 @@
+"use strict";
+
+const import_entry_points = require("./entry-points");
+void (0, import_entry_points.run__ACTION__)();
@@ -16,7 +16,7 @@ import {
 } from "./analyses";
 import { EnvVar } from "./environment";
 import { getRunnerLogger } from "./logging";
-import { setupTests } from "./testing-utils";
+import { createFeatures, RecordingLogger, setupTests } from "./testing-utils";
 import { AssessmentPayload } from "./upload-lib/types";
 import { ConfigurationError } from "./util";

@@ -53,24 +53,56 @@ test("Parsing analysis kinds requires at least one analysis kind", async (t) =>
 test.serial(
  "getAnalysisKinds - returns expected analysis kinds for `analysis-kinds` input",
  async (t) => {
+    process.env[EnvVar.TEST_MODE] = "true";
+    const features = createFeatures([]);
    const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
    requiredInputStub
      .withArgs("analysis-kinds")
      .returns("code-scanning,code-quality");
-    const result = await getAnalysisKinds(getRunnerLogger(true), true);
+    const result = await getAnalysisKinds(
+      getRunnerLogger(true),
+      features,
+      true,
+    );
    t.assert(result.includes(AnalysisKind.CodeScanning));
    t.assert(result.includes(AnalysisKind.CodeQuality));
  },
 );

+test.serial(
+  "getAnalysisKinds - only use `code-scanning` for multiple analysis kinds outside of test mode",
+  async (t) => {
+    process.env[EnvVar.TEST_MODE] = "false";
+    const features = createFeatures([]);
+    const logger = new RecordingLogger();
+    const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
+    requiredInputStub
+      .withArgs("analysis-kinds")
+      .returns("code-scanning,code-quality");
+    const result = await getAnalysisKinds(logger, features, true);
+    t.deepEqual(result, [AnalysisKind.CodeScanning]);
+    t.assert(
+      logger.hasMessage(
+        "Continuing with only `analysis-kinds: code-scanning`.",
+      ),
+    );
+  },
+);
+
 test.serial(
  "getAnalysisKinds - includes `code-quality` when deprecated `quality-queries` input is used",
  async (t) => {
+    process.env[EnvVar.TEST_MODE] = "true";
+    const features = createFeatures([]);
    const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
    requiredInputStub.withArgs("analysis-kinds").returns("code-scanning");
    const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
    optionalInputStub.withArgs("quality-queries").returns("code-quality");
-    const result = await getAnalysisKinds(getRunnerLogger(true), true);
+    const result = await getAnalysisKinds(
+      getRunnerLogger(true),
+      features,
+      true,
+    );
    t.assert(result.includes(AnalysisKind.CodeScanning));
    t.assert(result.includes(AnalysisKind.CodeQuality));
  },
@@ -79,9 +111,12 @@ test.serial(
 test.serial(
  "getAnalysisKinds - throws if `analysis-kinds` input is invalid",
  async (t) => {
+    const features = createFeatures([]);
    const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
    requiredInputStub.withArgs("analysis-kinds").returns("no-such-thing");
-    await t.throwsAsync(getAnalysisKinds(getRunnerLogger(true), true));
+    await t.throwsAsync(
+      getAnalysisKinds(getRunnerLogger(true), features, true),
+    );
  },
 );

@@ -98,11 +133,17 @@ for (let i = 0; i < analysisKinds.length; i++) {
      test.serial(
        `getAnalysisKinds - allows ${analysisKind} with ${otherAnalysis}`,
        async (t) => {
+          process.env[EnvVar.TEST_MODE] = "true";
+          const features = createFeatures([]);
          const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
          requiredInputStub
            .withArgs("analysis-kinds")
            .returns([analysisKind, otherAnalysis].join(","));
-          const result = await getAnalysisKinds(getRunnerLogger(true), true);
+          const result = await getAnalysisKinds(
+            getRunnerLogger(true),
+            features,
+            true,
+          );
          t.is(result.length, 2);
        },
      );
@@ -110,14 +151,18 @@ for (let i = 0; i < analysisKinds.length; i++) {
      test.serial(
        `getAnalysisKinds - throws if ${analysisKind} is enabled with ${otherAnalysis}`,
        async (t) => {
+          const features = createFeatures([]);
          const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
          requiredInputStub
            .withArgs("analysis-kinds")
            .returns([analysisKind, otherAnalysis].join(","));
-          await t.throwsAsync(getAnalysisKinds(getRunnerLogger(true), true), {
-            instanceOf: ConfigurationError,
-            message: `${analysisKind} and ${otherAnalysis} cannot be enabled at the same time`,
-          });
+          await t.throwsAsync(
+            getAnalysisKinds(getRunnerLogger(true), features, true),
+            {
+              instanceOf: ConfigurationError,
+              message: `${analysisKind} and ${otherAnalysis} cannot be enabled at the same time`,
+            },
+          );
        },
      );
    }
@@ -4,13 +4,14 @@ import {
  getRequiredInput,
 } from "./actions-util";
 import { EnvVar } from "./environment";
+import { Feature, FeatureEnablement } from "./feature-flags";
 import { Logger } from "./logging";
 import {
  AssessmentPayload,
  BasePayload,
  UploadPayload,
 } from "./upload-lib/types";
-import { ConfigurationError, getRequiredEnvParam } from "./util";
+import { ConfigurationError, getRequiredEnvParam, isInTestMode } from "./util";

 export enum AnalysisKind {
  CodeScanning = "code-scanning",
@@ -77,6 +78,7 @@ let cachedAnalysisKinds: AnalysisKind[] | undefined;
 */
 export async function getAnalysisKinds(
  logger: Logger,
+  features: FeatureEnablement,
  skipCache: boolean = false,
 ): Promise<AnalysisKind[]> {
  if (!skipCache && cachedAnalysisKinds !== undefined) {
@@ -120,6 +122,25 @@ export async function getAnalysisKinds(
    }
  }

+  // Log an error if we have multiple inputs for `analysis-kinds` outside of test mode,
+  // and enable only `code-scanning`.
+  if (
+    !isInTestMode() &&
+    analysisKinds.length > 1 &&
+    !(await features.getValue(Feature.AllowMultipleAnalysisKinds))
+  ) {
+    logger.error(
+      "The `analysis-kinds` input is experimental and for GitHub-internal use only. " +
+        "Its behaviour may change at any time or be removed entirely. " +
+        "Specifying multiple values as input is no longer supported. " +
+        "Continuing with only `analysis-kinds: code-scanning`.",
+    );
+
+    // Only enable Code Scanning.
+    cachedAnalysisKinds = [AnalysisKind.CodeScanning];
+    return cachedAnalysisKinds;
+  }
+
  // Cache the analysis kinds and return them.
  cachedAnalysisKinds = analysisKinds;
  return cachedAnalysisKinds;
@@ -3,6 +3,7 @@ import * as sinon from "sinon";

 import * as actionsUtil from "./actions-util";
 import * as analyze from "./analyze";
+import { runWrapper } from "./analyze-action";
 import * as api from "./api-client";
 import * as configUtils from "./config-utils";
 import * as gitUtils from "./git-utils";
@@ -62,14 +63,8 @@ test("analyze action with RAM & threads from environment variables", async (t) =

    const runFinalizeStub = sinon.stub(analyze, "runFinalize");
    const runQueriesStub = sinon.stub(analyze, "runQueries");
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    const analyzeAction = require("./analyze-action");

-    // When analyze-action.ts loads, it runs an async function from the top
-    // level but does not wait for it to finish. To ensure that calls to
-    // runFinalize and runQueries are correctly captured by spies, we explicitly
-    // wait for the action promise to complete before starting verification.
-    await analyzeAction.runPromise;
+    await runWrapper();

    t.assert(
      runFinalizeStub.calledOnceWith(
@@ -3,6 +3,7 @@ import * as sinon from "sinon";

 import * as actionsUtil from "./actions-util";
 import * as analyze from "./analyze";
+import { runWrapper } from "./analyze-action";
 import * as api from "./api-client";
 import * as configUtils from "./config-utils";
 import * as gitUtils from "./git-utils";
@@ -60,14 +61,8 @@ test("analyze action with RAM & threads from action inputs", async (t) => {

    const runFinalizeStub = sinon.stub(analyze, "runFinalize");
    const runQueriesStub = sinon.stub(analyze, "runQueries");
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    const analyzeAction = require("./analyze-action");

-    // When analyze-action.ts loads, it runs an async function from the top
-    // level but does not wait for it to finish. To ensure that calls to
-    // runFinalize and runQueries are correctly captured by spies, we explicitly
-    // wait for the action promise to complete before starting verification.
-    await analyzeAction.runPromise;
+    await runWrapper();

    t.assert(
      runFinalizeStub.calledOnceWith(
@@ -20,7 +20,7 @@ import { EnvVar } from "./environment";
 import { getActionsLogger } from "./logging";
 import { checkGitHubVersionInRange, getErrorMessage } from "./util";

-async function runWrapper() {
+export async function runWrapper() {
  // To capture errors appropriately, keep as much code within the try-catch as
  // possible, and only use safe functions outside.

@@ -72,5 +72,3 @@ async function runWrapper() {
    );
  }
 }
-
-void runWrapper();
@@ -30,7 +30,7 @@ import {
 } from "./dependency-caching";
 import { EnvVar } from "./environment";
 import { initFeatures } from "./feature-flags";
-import { KnownLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages";
 import { getActionsLogger, Logger } from "./logging";
 import { cleanupAndUploadOverlayBaseDatabaseToCache } from "./overlay/caching";
 import { getRepositoryNwo } from "./repository";
@@ -135,9 +135,13 @@ function hasBadExpectErrorInput(): boolean {
 function doesGoExtractionOutputExist(config: Config): boolean {
  const golangDbDirectory = util.getCodeQLDatabasePath(
    config,
-    KnownLanguage.go,
+    BuiltInLanguage.go,
+  );
+  const trapDirectory = path.join(
+    golangDbDirectory,
+    "trap",
+    BuiltInLanguage.go,
  );
-  const trapDirectory = path.join(golangDbDirectory, "trap", KnownLanguage.go);
  return (
    fs.existsSync(trapDirectory) &&
    fs
@@ -169,7 +173,7 @@ function doesGoExtractionOutputExist(config: Config): boolean {
 * whether any extraction output already exists for Go.
 */
 async function runAutobuildIfLegacyGoWorkflow(config: Config, logger: Logger) {
-  if (!config.languages.includes(KnownLanguage.go)) {
+  if (!config.languages.includes(BuiltInLanguage.go)) {
    return;
  }
  if (config.buildMode) {
@@ -182,7 +186,7 @@ async function runAutobuildIfLegacyGoWorkflow(config: Config, logger: Logger) {
    logger.debug("Won't run Go autobuild since it has already been run.");
    return;
  }
-  if (dbIsFinalized(config, KnownLanguage.go, logger)) {
+  if (dbIsFinalized(config, BuiltInLanguage.go, logger)) {
    logger.debug(
      "Won't run Go autobuild since there is already a finalized database for Go.",
    );
@@ -205,7 +209,7 @@ async function runAutobuildIfLegacyGoWorkflow(config: Config, logger: Logger) {
  logger.debug(
    "Running Go autobuild because extraction output (TRAP files) for Go code has not been found.",
  );
-  await runAutobuild(config, KnownLanguage.go, logger);
+  await runAutobuild(config, BuiltInLanguage.go, logger);
 }

 async function run(startedAt: Date) {
@@ -519,14 +523,11 @@ async function run(startedAt: Date) {
  }
 }

-// Module-level startedAt so it can be accessed by runWrapper for error reporting
-const startedAt = new Date();
-export const runPromise = run(startedAt);
-
-async function runWrapper() {
+export async function runWrapper() {
+  const startedAt = new Date();
  const logger = getActionsLogger();
  try {
-    await runPromise;
+    await run(startedAt);
  } catch (error) {
    core.setFailed(`analyze action failed: ${util.getErrorMessage(error)}`);
    await sendUnhandledErrorStatusReport(
@@ -538,5 +539,3 @@ async function runWrapper() {
  }
  await util.checkForTimeout();
 }
-
-void runWrapper();
@@ -14,7 +14,7 @@ import {
 } from "./analyze";
 import { createStubCodeQL } from "./codeql";
 import { Feature } from "./feature-flags";
-import { KnownLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages";
 import { getRunnerLogger } from "./logging";
 import {
  setupTests,
@@ -41,7 +41,7 @@ test.serial("status report fields", async (t) => {
    const threadsFlag = "";
    sinon.stub(uploadLib, "validateSarifFileSchema");

-    for (const language of Object.values(KnownLanguage)) {
+    for (const language of Object.values(BuiltInLanguage)) {
      const codeql = createStubCodeQL({
        databaseRunQueries: async () => {},
        databaseInterpretResults: async (
@@ -130,13 +130,13 @@ test.serial("status report fields", async (t) => {
 test("resolveQuerySuiteAlias", (t) => {
  // default query suite names should resolve to something language-specific ending in `.qls`.
  for (const suite of defaultSuites) {
-    const resolved = resolveQuerySuiteAlias(KnownLanguage.go, suite);
+    const resolved = resolveQuerySuiteAlias(BuiltInLanguage.go, suite);
    t.assert(
      path.extname(resolved) === ".qls",
      "Resolved default suite doesn't end in .qls",
    );
    t.assert(
-      resolved.indexOf(KnownLanguage.go) >= 0,
+      resolved.indexOf(BuiltInLanguage.go) >= 0,
      "Resolved default suite doesn't contain language name",
    );
  }
@@ -145,12 +145,12 @@ test("resolveQuerySuiteAlias", (t) => {
  const names = ["foo", "bar", "codeql/go-queries@1.0"];

  for (const name of names) {
-    t.deepEqual(resolveQuerySuiteAlias(KnownLanguage.go, name), name);
+    t.deepEqual(resolveQuerySuiteAlias(BuiltInLanguage.go, name), name);
  }
 });

 test("addSarifExtension", (t) => {
-  for (const language of Object.values(KnownLanguage)) {
+  for (const language of Object.values(BuiltInLanguage)) {
    t.deepEqual(addSarifExtension(CodeScanning, language), `${language}.sarif`);
    t.deepEqual(
      addSarifExtension(CodeQuality, language),
@@ -21,7 +21,7 @@ import {
 } from "./diff-informed-analysis-utils";
 import { EnvVar } from "./environment";
 import { FeatureEnablement, Feature } from "./feature-flags";
-import { KnownLanguage, Language } from "./languages";
+import { BuiltInLanguage, Language } from "./languages";
 import { Logger, withGroupAsync } from "./logging";
 import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import type * as sarif from "./sarif";
@@ -41,7 +41,7 @@ export class CodeQLAnalysisError extends Error {
  }
 }

-type KnownLanguageKey = keyof typeof KnownLanguage;
+type BuiltInLanguageKey = keyof typeof BuiltInLanguage;

 type RunQueriesDurationStatusReport = {
  /**
@@ -50,12 +50,12 @@ type RunQueriesDurationStatusReport = {
   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
   * taken to run _all_ the queries.
   */
-  [L in KnownLanguageKey as `analyze_builtin_queries_${L}_duration_ms`]?: number;
+  [L in BuiltInLanguageKey as `analyze_builtin_queries_${L}_duration_ms`]?: number;
 };

 type InterpretResultsDurationStatusReport = {
  /** Time taken in ms to interpret results for the language (or undefined if this language was not analyzed). */
-  [L in KnownLanguageKey as `interpret_results_${L}_duration_ms`]?: number;
+  [L in BuiltInLanguageKey as `interpret_results_${L}_duration_ms`]?: number;
 };

 export interface QueriesStatusReport
@@ -115,12 +115,12 @@ export async function runExtraction(

    if (await shouldExtractLanguage(codeql, config, language)) {
      logger.startGroup(`Extracting ${language}`);
-      if (language === KnownLanguage.python) {
+      if (language === BuiltInLanguage.python) {
        await setupPythonExtractor(logger);
      }
      if (config.buildMode) {
        if (
-          language === KnownLanguage.cpp &&
+          language === BuiltInLanguage.cpp &&
          config.buildMode === BuildMode.Autobuild
        ) {
          await setupCppAutobuild(codeql, logger);
@@ -131,14 +131,14 @@ export async function runExtraction(
        // a stable path that caches can be restored into and that we can cache at the
        // end of the workflow (i.e. that does not get removed when the scratch directory is).
        if (
-          language === KnownLanguage.java &&
+          language === BuiltInLanguage.java &&
          config.buildMode === BuildMode.None
        ) {
          process.env["CODEQL_EXTRACTOR_JAVA_OPTION_BUILDLESS_DEPENDENCY_DIR"] =
            getJavaTempDependencyDir();
        }
        if (
-          language === KnownLanguage.csharp &&
+          language === BuiltInLanguage.csharp &&
          config.buildMode === BuildMode.None &&
          (await features.getValue(Feature.CsharpCacheBuildModeNone))
        ) {
@@ -251,16 +251,9 @@ export async function setupDiffInformedQueryRun(
        diffRanges,
        checkoutPath,
      );
-      if (packDir === undefined) {
-        logger.warning(
-          "Cannot create diff range extension pack for diff-informed queries; " +
-            "reverting to performing full analysis.",
-        );
-      } else {
-        logger.info(
-          `Successfully created diff range extension pack at ${packDir}.`,
-        );
-      }
+      logger.info(
+        `Successfully created diff range extension pack at ${packDir}.`,
+      );
      return packDir;
    },
  );
@@ -314,18 +307,13 @@ extensions:
 * @param ranges The file line ranges, as returned by
 * `getPullRequestEditedDiffRanges`.
 * @param checkoutPath The path at which the repository was checked out.
- * @returns The absolute path of the directory containing the extension pack, or
- * `undefined` if no extension pack was created.
+ * @returns The absolute path of the directory containing the extension pack.
 */
 function writeDiffRangeDataExtensionPack(
  logger: Logger,
-  ranges: DiffThunkRange[] | undefined,
+  ranges: DiffThunkRange[],
  checkoutPath: string,
-): string | undefined {
-  if (ranges === undefined) {
-    return undefined;
-  }
-
+): string {
  if (ranges.length === 0) {
    // An empty diff range means that there are no added or modified lines in
    // the pull request. But the `restrictAlertsTo` extensible predicate
@@ -698,7 +686,7 @@ export async function warnIfGoInstalledAfterInit(

      addDiagnostic(
        config,
-        KnownLanguage.go,
+        BuiltInLanguage.go,
        makeDiagnostic(
          "go/workflow/go-installed-after-codeql-init",
          "Go was installed after the `codeql-action/init` Action was run",
@@ -128,6 +128,8 @@ export async function getGitHubVersionFromApi(

  // Doesn't strictly have to be the meta endpoint as we're only
  // using the response headers which are available on every request.
+  //
+  // See https://docs.github.com/en/rest/meta/meta#get-github-meta-information.
  // eslint-disable-next-line @typescript-eslint/no-unsafe-call
  const response = await apiClient.rest.meta.get();

@@ -164,6 +166,9 @@ export async function getGitHubVersion(): Promise<GitHubVersion> {

 /**
 * Get the path of the currently executing workflow relative to the repository root.
+ *
+ * See https://docs.github.com/en/rest/actions/workflow-runs#get-a-workflow-run
+ * and https://docs.github.com/en/rest/actions/workflows#get-a-workflow.
 */
 export async function getWorkflowRelativePath(): Promise<string> {
  const repo_nwo = getRepositoryNwo();
@@ -252,9 +257,13 @@ export interface ActionsCacheItem {
  size_in_bytes?: number;
 }

-/** List all Actions cache entries matching the provided key and ref. */
+/**
+ * List all Actions cache entries starting with the provided key prefix and matching the provided ref.
+ *
+ * See https://docs.github.com/en/rest/actions/cache#list-github-actions-caches-for-a-repository.
+ */
 export async function listActionsCaches(
-  key: string,
+  keyPrefix: string,
  ref?: string,
 ): Promise<ActionsCacheItem[]> {
  const repositoryNwo = getRepositoryNwo();
@@ -264,13 +273,17 @@ export async function listActionsCaches(
    {
      owner: repositoryNwo.owner,
      repo: repositoryNwo.repo,
-      key,
+      key: keyPrefix,
      ref,
    },
  );
 }

-/** Delete an Actions cache item by its ID. */
+/**
+ * Delete an Actions cache item by its ID.
+ *
+ * See https://docs.github.com/en/rest/actions/cache#delete-a-github-actions-cache-for-a-repository-using-a-cache-id.
+ */
 export async function deleteActionsCache(id: number) {
  const repositoryNwo = getRepositoryNwo();

@@ -281,7 +294,11 @@ export async function deleteActionsCache(id: number) {
  });
 }

-/** Retrieve all custom repository properties. */
+/**
+ * Retrieve all custom repository properties.
+ *
+ * See https://docs.github.com/en/rest/repos/custom-properties#get-all-custom-property-values-for-a-repository.
+ */
 export async function getRepositoryProperties(repositoryNwo: RepositoryNwo) {
  return getApiClient().request("GET /repos/:owner/:repo/properties/values", {
    owner: repositoryNwo.owner,
@@ -1 +1 @@
-{"maximumVersion": "3.21", "minimumVersion": "3.14"}
+{"maximumVersion": "3.21", "minimumVersion": "3.16"}
@@ -141,9 +141,9 @@ test("scanArtifactsForTokens handles files without tokens", async (t) => {
  }
 });

+// `scanArchiveFile` does not support Windows, so we skip this test there.
 if (os.platform() !== "win32") {
  test("scanArtifactsForTokens finds token in debug artifacts", async (t) => {
-    t.timeout(15000); // 15 seconds
    const messages: LoggedMessage[] = [];
    const logger = getRecordingLogger(messages, { logToConsole: false });
    // The zip here is a regression test based on
@@ -156,6 +156,10 @@ async function scanArchiveFile(
    );
  }

+  if (process.platform === "win32") {
+    throw new Error("Scanning archives is not supported on Windows.");
+  }
+
  const result: ScanResult = {
    scannedFiles: 0,
    findings: [],
@@ -142,7 +142,7 @@ async function run(startedAt: Date) {
  await sendCompletedStatusReport(config, logger, startedAt, languages ?? []);
 }

-async function runWrapper() {
+export async function runWrapper() {
  const startedAt = new Date();
  const logger = getActionsLogger();
  try {
@@ -157,5 +157,3 @@ async function runWrapper() {
    );
  }
 }
-
-void runWrapper();
@@ -7,7 +7,7 @@ import * as configUtils from "./config-utils";
 import { DocUrl } from "./doc-url";
 import { EnvVar } from "./environment";
 import { Feature, featureConfig, initFeatures } from "./feature-flags";
-import { KnownLanguage, Language } from "./languages";
+import { BuiltInLanguage, Language } from "./languages";
 import { Logger } from "./logging";
 import { getRepositoryNwo } from "./repository";
 import { asyncFilter, BuildMode } from "./util";
@@ -72,7 +72,7 @@ export async function determineAutobuildLanguages(
   * version of the CodeQL Action.
   */
  const autobuildLanguagesWithoutGo = autobuildLanguages.filter(
-    (l) => l !== KnownLanguage.go,
+    (l) => l !== BuiltInLanguage.go,
  );

  const languages: Language[] = [];
@@ -84,7 +84,7 @@ export async function determineAutobuildLanguages(
  // If Go is requested, run the Go autobuilder last to ensure it doesn't
  // interfere with the other autobuilder.
  if (autobuildLanguages.length !== autobuildLanguagesWithoutGo.length) {
-    languages.push(KnownLanguage.go);
+    languages.push(BuiltInLanguage.go);
  }

  logger.debug(`Will autobuild ${languages.join(" and ")}.`);
@@ -156,7 +156,7 @@ export async function runAutobuild(
 ) {
  logger.startGroup(`Attempting to automatically build ${language} code`);
  const codeQL = await getCodeQL(config.codeQLCmd);
-  if (language === KnownLanguage.cpp) {
+  if (language === BuiltInLanguage.cpp) {
    await setupCppAutobuild(codeQL, logger);
  }
  if (config.buildMode) {
@@ -164,7 +164,7 @@ export async function runAutobuild(
  } else {
    await codeQL.runAutobuild(config, language);
  }
-  if (language === KnownLanguage.go) {
+  if (language === BuiltInLanguage.go) {
    core.exportVariable(EnvVar.DID_AUTOBUILD_GOLANG, "true");
  }
  logger.endGroup();
@@ -21,7 +21,7 @@ import {
 import type { Config } from "./config-utils";
 import * as defaults from "./defaults.json";
 import { DocUrl } from "./doc-url";
-import { KnownLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages";
 import { getRunnerLogger } from "./logging";
 import { ToolsSource } from "./setup-codeql";
 import {
@@ -33,6 +33,7 @@ import {
  mockBundleDownloadApi,
  makeVersionInfo,
  createTestConfig,
+  makeMacro,
 } from "./testing-utils";
 import { ToolsDownloadStatusReport } from "./tools-download";
 import * as util from "./util";
@@ -46,7 +47,7 @@ test.beforeEach(() => {
  initializeEnvironment("1.2.3");

  stubConfig = createTestConfig({
-    languages: [KnownLanguage.cpp],
+    languages: [BuiltInLanguage.cpp],
  });
 });

@@ -70,8 +71,10 @@ async function installIntoToolcache({
    tmpDir,
    util.GitHubVariant.GHES,
    cliVersion !== undefined
-      ? { cliVersion, tagName }
+      ? { enabledVersions: [{ cliVersion, tagName }] }
      : SAMPLE_DEFAULT_CLI_VERSION,
+    undefined, // rawLanguages
+    false, // useOverlayAwareDefaultCliVersion
    createFeatures([]),
    getRunnerLogger(true),
    false,
@@ -115,7 +118,7 @@ async function stubCodeql(): Promise<codeql.CodeQL> {
  sinon.stub(codeqlObject, "getVersion").resolves(makeVersionInfo("2.17.6"));
  sinon
    .stub(codeqlObject, "isTracedLanguage")
-    .withArgs(KnownLanguage.cpp)
+    .withArgs(BuiltInLanguage.cpp)
    .resolves(true);
  return codeqlObject;
 }
@@ -143,6 +146,8 @@ test.serial(
          tmpDir,
          util.GitHubVariant.DOTCOM,
          SAMPLE_DEFAULT_CLI_VERSION,
+          undefined, // rawLanguages
+          false, // useOverlayAwareDefaultCliVersion
          features,
          getRunnerLogger(true),
          false,
@@ -175,6 +180,8 @@ test.serial(
        tmpDir,
        util.GitHubVariant.DOTCOM,
        SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        features,
        getRunnerLogger(true),
        false,
@@ -214,6 +221,8 @@ test.serial(
        tmpDir,
        util.GitHubVariant.DOTCOM,
        SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        features,
        getRunnerLogger(true),
        false,
@@ -264,6 +273,8 @@ for (const {
          tmpDir,
          util.GitHubVariant.DOTCOM,
          SAMPLE_DEFAULT_CLI_VERSION,
+          undefined, // rawLanguages
+          false, // useOverlayAwareDefaultCliVersion
          features,
          getRunnerLogger(true),
          false,
@@ -284,11 +295,11 @@ for (const {
 for (const toolcacheVersion of [
  // Test that we use the tools from the toolcache when `SAMPLE_DEFAULT_CLI_VERSION` is requested
  // and `SAMPLE_DEFAULT_CLI_VERSION-` is in the toolcache.
-  SAMPLE_DEFAULT_CLI_VERSION.cliVersion,
-  `${SAMPLE_DEFAULT_CLI_VERSION.cliVersion}-20230101`,
+  SAMPLE_DEFAULT_CLI_VERSION.enabledVersions[0].cliVersion,
+  `${SAMPLE_DEFAULT_CLI_VERSION.enabledVersions[0].cliVersion}-20230101`,
 ]) {
  test.serial(
-    `uses tools from toolcache when ${SAMPLE_DEFAULT_CLI_VERSION.cliVersion} is requested and ` +
+    `uses tools from toolcache when ${SAMPLE_DEFAULT_CLI_VERSION.enabledVersions[0].cliVersion} is requested and ` +
      `${toolcacheVersion} is installed`,
    async (t) => {
      const features = createFeatures([]);
@@ -308,11 +319,16 @@ for (const toolcacheVersion of [
          tmpDir,
          util.GitHubVariant.DOTCOM,
          SAMPLE_DEFAULT_CLI_VERSION,
+          undefined, // rawLanguages
+          false, // useOverlayAwareDefaultCliVersion
          features,
          getRunnerLogger(true),
          false,
        );
-        t.is(result.toolsVersion, SAMPLE_DEFAULT_CLI_VERSION.cliVersion);
+        t.is(
+          result.toolsVersion,
+          SAMPLE_DEFAULT_CLI_VERSION.enabledVersions[0].cliVersion,
+        );
        t.is(result.toolsSource, ToolsSource.Toolcache);
        t.is(result.toolsDownloadStatusReport?.combinedDurationMs, undefined);
        t.is(result.toolsDownloadStatusReport?.downloadDurationMs, undefined);
@@ -342,9 +358,15 @@ test.serial(
        tmpDir,
        util.GitHubVariant.GHES,
        {
-          cliVersion: defaults.cliVersion,
-          tagName: defaults.bundleVersion,
+          enabledVersions: [
+            {
+              cliVersion: defaults.cliVersion,
+              tagName: defaults.bundleVersion,
+            },
+          ],
        },
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        features,
        getRunnerLogger(true),
        false,
@@ -384,9 +406,15 @@ test.serial(
        tmpDir,
        util.GitHubVariant.GHES,
        {
-          cliVersion: defaults.cliVersion,
-          tagName: defaults.bundleVersion,
+          enabledVersions: [
+            {
+              cliVersion: defaults.cliVersion,
+              tagName: defaults.bundleVersion,
+            },
+          ],
        },
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        features,
        getRunnerLogger(true),
        false,
@@ -426,6 +454,8 @@ test.serial(
        tmpDir,
        util.GitHubVariant.DOTCOM,
        SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        features,
        getRunnerLogger(true),
        false,
@@ -467,6 +497,8 @@ test.serial(
        tmpDir,
        util.GitHubVariant.DOTCOM,
        SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        features,
        getRunnerLogger(true),
        false,
@@ -540,7 +572,7 @@ test.serial("getExtraOptions throws for bad content", (t) => {
 });

 // Test macro for ensuring different variants of injected augmented configurations
-const injectedConfigMacro = test.macro({
+const injectedConfigMacro = makeMacro({
  exec: async (
    t: ExecutionContext<unknown>,
    augmentationProperties: AugmentationProperties,
@@ -590,9 +622,8 @@ const injectedConfigMacro = test.macro({
    `databaseInitCluster() injected config: ${providedTitle}`,
 });

-test.serial(
+injectedConfigMacro.serial(
  "basic",
-  injectedConfigMacro,
  {
    ...defaultAugmentationProperties,
  },
@@ -600,9 +631,8 @@ test.serial(
  {},
 );

-test.serial(
+injectedConfigMacro.serial(
  "injected packs from input",
-  injectedConfigMacro,
  {
    ...defaultAugmentationProperties,
    packsInput: ["xxx", "yyy"],
@@ -613,9 +643,8 @@ test.serial(
  },
 );

-test.serial(
+injectedConfigMacro.serial(
  "injected packs from input with existing packs combines",
-  injectedConfigMacro,
  {
    ...defaultAugmentationProperties,
    packsInputCombines: true,
@@ -635,9 +664,8 @@ test.serial(
  },
 );

-test.serial(
+injectedConfigMacro.serial(
  "injected packs from input with existing packs overrides",
-  injectedConfigMacro,
  {
    ...defaultAugmentationProperties,
    packsInput: ["xxx", "yyy"],
@@ -655,9 +683,8 @@ test.serial(
 );

 // similar, but with queries
-test.serial(
+injectedConfigMacro.serial(
  "injected queries from input",
-  injectedConfigMacro,
  {
    ...defaultAugmentationProperties,
    queriesInput: [{ uses: "xxx" }, { uses: "yyy" }],
@@ -675,9 +702,8 @@ test.serial(
  },
 );

-test.serial(
+injectedConfigMacro.serial(
  "injected queries from input overrides",
-  injectedConfigMacro,
  {
    ...defaultAugmentationProperties,
    queriesInput: [{ uses: "xxx" }, { uses: "yyy" }],
@@ -699,9 +725,8 @@ test.serial(
  },
 );

-test.serial(
+injectedConfigMacro.serial(
  "injected queries from input combines",
-  injectedConfigMacro,
  {
    ...defaultAugmentationProperties,
    queriesInputCombines: true,
@@ -727,9 +752,8 @@ test.serial(
  },
 );

-test.serial(
+injectedConfigMacro.serial(
  "injected queries from input combines 2",
-  injectedConfigMacro,
  {
    ...defaultAugmentationProperties,
    queriesInputCombines: true,
@@ -749,9 +773,8 @@ test.serial(
  },
 );

-test.serial(
+injectedConfigMacro.serial(
  "injected queries and packs, but empty",
-  injectedConfigMacro,
  {
    ...defaultAugmentationProperties,
    queriesInputCombines: true,
@@ -768,9 +791,8 @@ test.serial(
  {},
 );

-test.serial(
+injectedConfigMacro.serial(
  "repo property queries have the highest precedence",
-  injectedConfigMacro,
  {
    ...defaultAugmentationProperties,
    queriesInputCombines: true,
@@ -790,9 +812,8 @@ test.serial(
  },
 );

-test.serial(
+injectedConfigMacro.serial(
  "repo property queries combines with queries input",
-  injectedConfigMacro,
  {
    ...defaultAugmentationProperties,
    queriesInputCombines: false,
@@ -817,9 +838,8 @@ test.serial(
  },
 );

-test.serial(
+injectedConfigMacro.serial(
  "repo property queries combines everything else",
-  injectedConfigMacro,
  {
    ...defaultAugmentationProperties,
    queriesInputCombines: true,
@@ -956,7 +976,8 @@ test.serial("runTool summarizes autobuilder errors", async (t) => {
  sinon.stub(io, "which").resolves("");

  await t.throwsAsync(
-    async () => await codeqlObject.runAutobuild(stubConfig, KnownLanguage.java),
+    async () =>
+      await codeqlObject.runAutobuild(stubConfig, BuiltInLanguage.java),
    {
      instanceOf: util.ConfigurationError,
      message:
@@ -982,7 +1003,8 @@ test.serial("runTool truncates long autobuilder errors", async (t) => {
  sinon.stub(io, "which").resolves("");

  await t.throwsAsync(
-    async () => await codeqlObject.runAutobuild(stubConfig, KnownLanguage.java),
+    async () =>
+      await codeqlObject.runAutobuild(stubConfig, BuiltInLanguage.java),
    {
      instanceOf: util.ConfigurationError,
      message:
@@ -282,17 +282,17 @@ const CODEQL_MINIMUM_VERSION = "2.17.6";
 /**
 * This version will shortly become the oldest version of CodeQL that the Action will run with.
 */
-const CODEQL_NEXT_MINIMUM_VERSION = "2.17.6";
+const CODEQL_NEXT_MINIMUM_VERSION = "2.19.4";

 /**
 * This is the version of GHES that was most recently deprecated.
 */
-const GHES_VERSION_MOST_RECENTLY_DEPRECATED = "3.13";
+const GHES_VERSION_MOST_RECENTLY_DEPRECATED = "3.15";

 /**
 * This is the deprecation date for the version of GHES that was most recently deprecated.
 */
-const GHES_MOST_RECENT_DEPRECATION_DATE = "2025-06-19";
+const GHES_MOST_RECENT_DEPRECATION_DATE = "2026-04-09";

 /** The CLI verbosity level to use for extraction in debug mode. */
 const EXTRACTION_DEBUG_MODE_VERBOSITY = "progress++";
@@ -305,6 +305,8 @@ const EXTRACTION_DEBUG_MODE_VERBOSITY = "progress++";
 * @param tempDir
 * @param variant
 * @param defaultCliVersion
+ * @param rawLanguages Raw set of languages.
+ * @param useOverlayAwareDefaultCliVersion Whether to select an overlay-aware default CLI version.
 * @param features Information about the features that are enabled.
 * @param logger
 * @param checkVersion Whether to check that CodeQL CLI meets the minimum
@@ -317,6 +319,8 @@ export async function setupCodeQL(
  tempDir: string,
  variant: util.GitHubVariant,
  defaultCliVersion: CodeQLDefaultVersionInfo,
+  rawLanguages: string[] | undefined,
+  useOverlayAwareDefaultCliVersion: boolean,
  features: FeatureEnablement,
  logger: Logger,
  checkVersion: boolean,
@@ -340,6 +344,8 @@ export async function setupCodeQL(
      tempDir,
      variant,
      defaultCliVersion,
+      rawLanguages,
+      useOverlayAwareDefaultCliVersion,
      features,
      logger,
    );
@@ -18,9 +18,10 @@ import { Feature } from "./feature-flags";
 import { RepositoryProperties } from "./feature-flags/properties";
 import * as gitUtils from "./git-utils";
 import { GitVersionInfo } from "./git-utils";
-import { KnownLanguage, Language } from "./languages";
+import { BuiltInLanguage, Language } from "./languages";
 import { getRunnerLogger } from "./logging";
 import { CODEQL_OVERLAY_MINIMUM_VERSION } from "./overlay";
+import * as overlayDiagnostics from "./overlay/diagnostics";
 import { OverlayDisabledReason } from "./overlay/diagnostics";
 import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import * as overlayStatus from "./overlay/status";
@@ -34,6 +35,7 @@ import {
  LoggedMessage,
  mockCodeQLVersion,
  createTestConfig,
+  makeMacro,
 } from "./testing-utils";
 import {
  GitHubVariant,
@@ -215,7 +217,7 @@ test.serial("load code quality config", async (t) => {
    // And the config we expect it to result in
    const expectedConfig = createTestConfig({
      analysisKinds: [AnalysisKind.CodeQuality],
-      languages: [KnownLanguage.actions],
+      languages: [BuiltInLanguage.actions],
      // This gets set because we only have `AnalysisKind.CodeQuality`
      computedConfig: {
        "disable-default-queries": true,
@@ -268,7 +270,7 @@ test.serial(

      const expectedConfig = createTestConfig({
        analysisKinds: [AnalysisKind.CodeQuality],
-        languages: [KnownLanguage.javascript],
+        languages: [BuiltInLanguage.javascript],
        codeQLCmd: codeql.getPath(),
        computedConfig,
        dbLocation: path.resolve(tempDir, "codeql_databases"),
@@ -518,7 +520,7 @@ test.serial("load non-empty input", async (t) => {

    // And the config we expect it to parse to
    const expectedConfig = createTestConfig({
-      languages: [KnownLanguage.javascript],
+      languages: [BuiltInLanguage.javascript],
      buildMode: BuildMode.None,
      originalUserInput: userConfig,
      computedConfig: userConfig,
@@ -892,10 +894,10 @@ const mockRepositoryNwo = parseRepositoryNwo("owner/repo");
      betterResolveLanguages: (options) =>
        Promise.resolve({
          aliases: {
-            "c#": KnownLanguage.csharp,
-            c: KnownLanguage.cpp,
-            kotlin: KnownLanguage.java,
-            typescript: KnownLanguage.javascript,
+            "c#": BuiltInLanguage.csharp,
+            c: BuiltInLanguage.cpp,
+            kotlin: BuiltInLanguage.java,
+            typescript: BuiltInLanguage.javascript,
          },
          extractors: {
            cpp: [stubExtractorEntry],
@@ -944,12 +946,12 @@ const mockRepositoryNwo = parseRepositoryNwo("owner/repo");
 for (const { displayName, language, feature } of [
  {
    displayName: "Java",
-    language: KnownLanguage.java,
+    language: BuiltInLanguage.java,
    feature: Feature.DisableJavaBuildlessEnabled,
  },
  {
    displayName: "C#",
-    language: KnownLanguage.csharp,
+    language: BuiltInLanguage.csharp,
    feature: Feature.DisableCsharpBuildless,
  },
 ]) {
@@ -969,7 +971,7 @@ for (const { displayName, language, feature } of [
    const messages: LoggedMessage[] = [];
    const buildMode = await configUtils.parseBuildModeInput(
      "none",
-      [KnownLanguage.python],
+      [BuiltInLanguage.python],
      createFeatures([feature]),
      getRecordingLogger(messages),
    );
@@ -1019,7 +1021,7 @@ const defaultOverlayDatabaseModeTestSetup: OverlayDatabaseModeTestSetup = {
  isPullRequest: false,
  isDefaultBranch: false,
  buildMode: BuildMode.None,
-  languages: [KnownLanguage.javascript],
+  languages: [BuiltInLanguage.javascript],
  codeqlVersion: CODEQL_OVERLAY_MINIMUM_VERSION,
  gitRoot: "/some/git/root",
  gitVersion: new GitVersionInfo("2.39.0", "2.39.0"),
@@ -1034,10 +1036,9 @@ const defaultOverlayDatabaseModeTestSetup: OverlayDatabaseModeTestSetup = {
  repositoryProperties: {},
 };

-const checkOverlayEnablementMacro = test.macro({
+const checkOverlayEnablementMacro = makeMacro({
  exec: async (
    t: ExecutionContext,
-    _title: string,
    setupOverrides: Partial<OverlayDatabaseModeTestSetup>,
    expected:
      | {
@@ -1091,7 +1092,7 @@ const checkOverlayEnablementMacro = test.macro({
        sinon
          .stub(codeql, "isTracedLanguage")
          .callsFake(async (lang: Language) => {
-            return [KnownLanguage.java].includes(lang as KnownLanguage);
+            return lang === BuiltInLanguage.java;
          });

        // Mock git root detection
@@ -1131,11 +1132,10 @@ const checkOverlayEnablementMacro = test.macro({
      }
    });
  },
-  title: (_, title) => `checkOverlayEnablement: ${title}`,
+  title: (title) => `checkOverlayEnablement: ${title}`,
 });

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Environment variable override - Overlay",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -1146,8 +1146,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Environment variable override - OverlayBase",
  {
    overlayDatabaseEnvVar: "overlay-base",
@@ -1158,8 +1157,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Environment variable override - None",
  {
    overlayDatabaseEnvVar: "none",
@@ -1169,8 +1167,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Ignore invalid environment variable",
  {
    overlayDatabaseEnvVar: "invalid-mode",
@@ -1180,11 +1177,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Ignore feature flag when analyzing non-default branch",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
  },
  {
@@ -1192,11 +1188,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay-base database on default branch when feature enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
    isDefaultBranch: true,
  },
@@ -1206,15 +1201,14 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay-base database on default branch when feature enabled with custom analysis",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
    codeScanningConfig: {
      packs: ["some-custom-pack@1.0.0"],
-    } as UserConfig,
+    },
    isDefaultBranch: true,
  },
  {
@@ -1223,11 +1217,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay-base database on default branch when code-scanning feature enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1240,11 +1233,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay-base database on default branch if runner disk space is too low",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1260,11 +1252,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay-base database on default branch if we can't determine runner disk space",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1277,11 +1268,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay-base database on default branch if runner disk space is too low and skip resource checks flag is enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1299,11 +1289,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay-base database on default branch if runner disk space is below v2 limit and v2 resource checks enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1320,11 +1309,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay-base database on default branch if runner disk space is between v2 and v1 limits and v2 resource checks enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1342,11 +1330,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay-base database on default branch if runner disk space is between v2 and v1 limits and v2 resource checks not enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1362,11 +1349,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay-base database on default branch if memory flag is too low",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1379,11 +1365,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay-base database on default branch if memory flag is too low but CodeQL >= 2.24.3",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1398,11 +1383,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay-base database on default branch if memory flag is too low and skip resource checks flag is enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1417,11 +1401,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay-base database on default branch when cached status indicates previous failure",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisJavascript,
@@ -1435,11 +1418,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay analysis on PR when cached status indicates previous failure",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisJavascript,
@@ -1453,18 +1435,17 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay-base database on default branch when code-scanning feature enabled with disable-default-queries",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
    ],
    codeScanningConfig: {
      "disable-default-queries": true,
-    } as UserConfig,
+    },
    isDefaultBranch: true,
  },
  {
@@ -1472,18 +1453,17 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay-base database on default branch when code-scanning feature enabled with packs",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
    ],
    codeScanningConfig: {
      packs: ["some-custom-pack@1.0.0"],
-    } as UserConfig,
+    },
    isDefaultBranch: true,
  },
  {
@@ -1491,18 +1471,17 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay-base database on default branch when code-scanning feature enabled with queries",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
    ],
    codeScanningConfig: {
      queries: [{ uses: "some-query.ql" }],
-    } as UserConfig,
+    },
    isDefaultBranch: true,
  },
  {
@@ -1510,18 +1489,17 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay-base database on default branch when code-scanning feature enabled with query-filters",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
    ],
    codeScanningConfig: {
      "query-filters": [{ include: { "security-severity": "high" } }],
-    } as UserConfig,
+    },
    isDefaultBranch: true,
  },
  {
@@ -1529,11 +1507,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay-base database on default branch when only language-specific feature enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysisJavascript],
    isDefaultBranch: true,
  },
@@ -1542,11 +1519,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay-base database on default branch when only code-scanning feature enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysisCodeScanningJavascript],
    isDefaultBranch: true,
  },
@@ -1555,11 +1531,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay-base database on default branch when language-specific feature disabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysis],
    isDefaultBranch: true,
  },
@@ -1568,11 +1543,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay analysis on PR when feature enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
    isPullRequest: true,
  },
@@ -1582,15 +1556,14 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay analysis on PR when feature enabled with custom analysis",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
    codeScanningConfig: {
      packs: ["some-custom-pack@1.0.0"],
-    } as UserConfig,
+    },
    isPullRequest: true,
  },
  {
@@ -1599,11 +1572,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay analysis on PR when code-scanning feature enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1616,11 +1588,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay analysis on PR if runner disk space is too low",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1636,11 +1607,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay analysis on PR if runner disk space is too low and skip resource checks flag is enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1658,11 +1628,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay analysis on PR if we can't determine runner disk space",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1675,11 +1644,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay analysis on PR if memory flag is too low",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1692,11 +1660,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay analysis on PR if memory flag is too low but CodeQL >= 2.24.3",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1711,11 +1678,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay analysis on PR if memory flag is too low and skip resource checks flag is enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
@@ -1730,18 +1696,17 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay analysis on PR when code-scanning feature enabled with disable-default-queries",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
    ],
    codeScanningConfig: {
      "disable-default-queries": true,
-    } as UserConfig,
+    },
    isPullRequest: true,
  },
  {
@@ -1749,18 +1714,17 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay analysis on PR when code-scanning feature enabled with packs",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
    ],
    codeScanningConfig: {
      packs: ["some-custom-pack@1.0.0"],
-    } as UserConfig,
+    },
    isPullRequest: true,
  },
  {
@@ -1768,18 +1732,17 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay analysis on PR when code-scanning feature enabled with queries",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
    ],
    codeScanningConfig: {
      queries: [{ uses: "some-query.ql" }],
-    } as UserConfig,
+    },
    isPullRequest: true,
  },
  {
@@ -1787,18 +1750,17 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay analysis on PR when code-scanning feature enabled with query-filters",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [
      Feature.OverlayAnalysis,
      Feature.OverlayAnalysisCodeScanningJavascript,
    ],
    codeScanningConfig: {
      "query-filters": [{ include: { "security-severity": "high" } }],
-    } as UserConfig,
+    },
    isPullRequest: true,
  },
  {
@@ -1806,11 +1768,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay analysis on PR when only language-specific feature enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysisJavascript],
    isPullRequest: true,
  },
@@ -1819,11 +1780,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay analysis on PR when only code-scanning feature enabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysisCodeScanningJavascript],
    isPullRequest: true,
  },
@@ -1832,11 +1792,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay analysis on PR when language-specific feature disabled",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysis],
    isPullRequest: true,
  },
@@ -1845,8 +1804,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay PR analysis by env",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -1857,8 +1815,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay PR analysis by env on a runner with low disk space",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -1870,11 +1827,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay PR analysis by feature flag",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
    isPullRequest: true,
  },
@@ -1884,34 +1840,31 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Fallback due to autobuild with traced language",
  {
    overlayDatabaseEnvVar: "overlay",
    buildMode: BuildMode.Autobuild,
-    languages: [KnownLanguage.java],
+    languages: [BuiltInLanguage.java],
  },
  {
    disabledReason: OverlayDisabledReason.IncompatibleBuildMode,
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Fallback due to no build mode with traced language",
  {
    overlayDatabaseEnvVar: "overlay",
    buildMode: undefined,
-    languages: [KnownLanguage.java],
+    languages: [BuiltInLanguage.java],
  },
  {
    disabledReason: OverlayDisabledReason.IncompatibleBuildMode,
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Fallback due to old CodeQL version",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -1922,8 +1875,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Fallback due to missing git root",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -1934,8 +1886,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Fallback due to old git version with submodules",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -1947,8 +1898,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Fallback when git version cannot be determined and repo has submodules",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -1960,8 +1910,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay enabled when git version cannot be determined and repo has no submodules",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -1974,11 +1923,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay when disabled via repository property",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
    isPullRequest: true,
    repositoryProperties: {
@@ -1990,11 +1938,10 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay not disabled when repository property is false",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
    isPullRequest: true,
    repositoryProperties: {
@@ -2007,8 +1954,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Environment variable override takes precedence over repository property",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -2023,9 +1969,8 @@ test.serial(
 );

 // Exercise language-specific overlay analysis features code paths
-for (const language in KnownLanguage) {
-  test.serial(
-    checkOverlayEnablementMacro,
+for (const language in BuiltInLanguage) {
+  checkOverlayEnablementMacro.serial(
    `Check default overlay analysis feature for ${language}`,
    {
      languages: [language],
@@ -2042,11 +1987,10 @@ for (const language in KnownLanguage) {
 // overlay analysis enabled, even when the base overlay feature flag is on.
 // Using swift here as it doesn't currently have overlay support — update this if
 // swift gains overlay support.
-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "No overlay analysis for language without per-language overlay feature flag",
  {
-    languages: [KnownLanguage.swift],
+    languages: [BuiltInLanguage.swift],
    features: [Feature.OverlayAnalysis],
    isPullRequest: true,
  },
@@ -2200,3 +2144,87 @@ test.serial(
    });
  },
 );
+
+test("applyIncrementalAnalysisSettings: no-op when mode is not Overlay and diff ranges are unavailable", async (t) => {
+  const config = createTestConfig({});
+  config.overlayDatabaseMode = OverlayDatabaseMode.None;
+  const codeql = createStubCodeQL({});
+  const logger = getRunnerLogger(true);
+
+  await configUtils.applyIncrementalAnalysisSettings(
+    config,
+    false,
+    codeql,
+    logger,
+  );
+
+  t.is(config.overlayDatabaseMode, OverlayDatabaseMode.None);
+  t.deepEqual(config.extraQueryExclusions, []);
+});
+
+test("applyIncrementalAnalysisSettings: keeps overlay mode and adds exclusions when diff ranges are available", async (t) => {
+  const config = createTestConfig({
+    overlayDatabaseMode: OverlayDatabaseMode.Overlay,
+  });
+  const codeql = createStubCodeQL({});
+  const logger = getRunnerLogger(true);
+
+  await configUtils.applyIncrementalAnalysisSettings(
+    config,
+    true,
+    codeql,
+    logger,
+  );
+
+  t.is(config.overlayDatabaseMode, OverlayDatabaseMode.Overlay);
+  t.deepEqual(config.extraQueryExclusions, [
+    { exclude: { tags: "exclude-from-incremental" } },
+  ]);
+});
+
+test("applyIncrementalAnalysisSettings: disables overlay analysis when diff ranges are unavailable", async (t) => {
+  const config = createTestConfig({
+    overlayDatabaseMode: OverlayDatabaseMode.Overlay,
+  });
+  config.useOverlayDatabaseCaching = true;
+  const codeql = createStubCodeQL({});
+  const logger = getRunnerLogger(true);
+  const addDiagnosticsStub = sinon
+    .stub(overlayDiagnostics, "addOverlayDisablementDiagnostics")
+    .resolves();
+
+  await configUtils.applyIncrementalAnalysisSettings(
+    config,
+    false,
+    codeql,
+    logger,
+  );
+
+  t.is(config.overlayDatabaseMode, OverlayDatabaseMode.None);
+  t.is(config.useOverlayDatabaseCaching, false);
+  t.deepEqual(config.extraQueryExclusions, []);
+  t.true(addDiagnosticsStub.calledOnce);
+  t.is(
+    addDiagnosticsStub.firstCall.args[2],
+    OverlayDisabledReason.DiffInformedAnalysisNotEnabled,
+  );
+});
+
+test("applyIncrementalAnalysisSettings: adds exclusions for diff-informed-only runs", async (t) => {
+  const config = createTestConfig({});
+  config.overlayDatabaseMode = OverlayDatabaseMode.None;
+  const codeql = createStubCodeQL({});
+  const logger = getRunnerLogger(true);
+
+  await configUtils.applyIncrementalAnalysisSettings(
+    config,
+    true,
+    codeql,
+    logger,
+  );
+
+  t.is(config.overlayDatabaseMode, OverlayDatabaseMode.None);
+  t.deepEqual(config.extraQueryExclusions, [
+    { exclude: { tags: "exclude-from-incremental" } },
+  ]);
+});
@@ -31,7 +31,7 @@ import {
  addNoLanguageDiagnostic,
  makeTelemetryDiagnostic,
 } from "./diagnostics";
-import { shouldPerformDiffInformedAnalysis } from "./diff-informed-analysis-utils";
+import { prepareDiffInformedAnalysis } from "./diff-informed-analysis-utils";
 import { EnvVar } from "./environment";
 import * as errorMessages from "./error-messages";
 import { Feature, FeatureEnablement } from "./feature-flags";
@@ -48,7 +48,7 @@ import {
  hasSubmodules,
  isAnalyzingDefaultBranch,
 } from "./git-utils";
-import { KnownLanguage, Language } from "./languages";
+import { BuiltInLanguage, Language } from "./languages";
 import { Logger } from "./logging";
 import { CODEQL_OVERLAY_MINIMUM_VERSION } from "./overlay";
 import {
@@ -274,10 +274,10 @@ async function getSupportedLanguageMap(
  for (const extractor of Object.keys(resolveResult.extractors)) {
    // If the CLI supports resolving languages with default queries, use these
    // as the set of supported languages. Otherwise, require the language to be
-    // a known language.
+    // a built-in language.
    if (
      resolveSupportedLanguagesUsingCli ||
-      KnownLanguage[extractor] !== undefined
+      BuiltInLanguage[extractor] !== undefined
    ) {
      supportedLanguages[extractor] = extractor;
    }
@@ -407,6 +407,7 @@ export async function getLanguages(
  return languages;
 }

+/** Splits the `languages` input into a list of raw languages without checking if they are supported by CodeQL. */
 export function getRawLanguagesNoAutodetect(
  languagesInput: string | undefined,
 ): string[] {
@@ -947,7 +948,7 @@ async function validateOverlayDatabaseMode(
      await Promise.all(
        languages.map(
          async (l) =>
-            l !== KnownLanguage.go && // Workaround to allow overlay analysis for Go with any build
+            l !== BuiltInLanguage.go && // Workaround to allow overlay analysis for Go with any build
            // mode, since it does not yet support BMN. The Go autobuilder and/or extractor will
            // ensure that overlay-base databases are only created for supported Go build setups,
            // and that we'll fall back to full databases in other cases.
@@ -1036,13 +1037,13 @@ async function setCppTrapCachingEnvironmentVariables(
  config: Config,
  logger: Logger,
 ): Promise<void> {
-  if (config.languages.includes(KnownLanguage.cpp)) {
+  if (config.languages.includes(BuiltInLanguage.cpp)) {
    const envVar = "CODEQL_EXTRACTOR_CPP_TRAP_CACHING";
    if (process.env[envVar]) {
      logger.info(
        `Environment variable ${envVar} already set, leaving it unchanged.`,
      );
-    } else if (config.trapCaches[KnownLanguage.cpp]) {
+    } else if (config.trapCaches[BuiltInLanguage.cpp]) {
      logger.info("Enabling TRAP caching for C/C++.");
      core.exportVariable(envVar, "true");
    } else {
@@ -1076,6 +1077,48 @@ function hasQueryCustomisation(userConfig: UserConfig): boolean {
  );
 }

+/**
+ * Finalize the incremental-analysis configuration for this run.
+ *
+ * Overlay analysis has only been validated in combination with diff-informed
+ * analysis, so if `Overlay` mode was selected for a pull request but the diff
+ * ranges could not be computed, fall back to a full non-overlay analysis.
+ *
+ * Query exclusions for incremental-only queries are then applied whenever the
+ * diff ranges are available — which, after the fallback above, is exactly the
+ * set of runs where any kind of incremental analysis (overlay or
+ * diff-informed) is in effect.
+ */
+export async function applyIncrementalAnalysisSettings(
+  config: Config,
+  hasDiffRanges: boolean,
+  codeql: CodeQL,
+  logger: Logger,
+): Promise<void> {
+  if (
+    config.overlayDatabaseMode === OverlayDatabaseMode.Overlay &&
+    !hasDiffRanges
+  ) {
+    logger.info(
+      `Reverting overlay database mode to ${OverlayDatabaseMode.None} ` +
+        "because the PR diff ranges could not be computed.",
+    );
+    config.overlayDatabaseMode = OverlayDatabaseMode.None;
+    config.useOverlayDatabaseCaching = false;
+    await addOverlayDisablementDiagnostics(
+      config,
+      codeql,
+      OverlayDisabledReason.DiffInformedAnalysisNotEnabled,
+    );
+  }
+
+  if (hasDiffRanges) {
+    config.extraQueryExclusions.push({
+      exclude: { tags: "exclude-from-incremental" },
+    });
+  }
+}
+
 /**
 * Load and return the config.
 *
@@ -1230,18 +1273,18 @@ export async function initConfig(
    );
  }

-  if (
-    config.overlayDatabaseMode === OverlayDatabaseMode.Overlay ||
-    (await shouldPerformDiffInformedAnalysis(
-      inputs.codeql,
-      inputs.features,
-      logger,
-    ))
-  ) {
-    config.extraQueryExclusions.push({
-      exclude: { tags: "exclude-from-incremental" },
-    });
-  }
+  const hasDiffRanges = await prepareDiffInformedAnalysis(
+    inputs.codeql,
+    inputs.features,
+    logger,
+  );
+
+  await applyIncrementalAnalysisSettings(
+    config,
+    hasDiffRanges,
+    inputs.codeql,
+    logger,
+  );

  if (await isTrapCachingEnabled(features, config.overlayDatabaseMode)) {
    const { trapCaches, trapCacheDownloadTime } = await downloadCacheWithTime(
@@ -1539,7 +1582,7 @@ export async function parseBuildModeInput(
  }

  if (
-    languages.includes(KnownLanguage.csharp) &&
+    languages.includes(BuiltInLanguage.csharp) &&
    (await features.getValue(Feature.DisableCsharpBuildless))
  ) {
    logger.warning(
@@ -1549,7 +1592,7 @@ export async function parseBuildModeInput(
  }

  if (
-    languages.includes(KnownLanguage.java) &&
+    languages.includes(BuiltInLanguage.java) &&
    (await features.getValue(Feature.DisableJavaBuildlessEnabled))
  ) {
    logger.warning(
@@ -1,12 +1,13 @@
 import test, { ExecutionContext } from "ava";

 import { RepositoryProperties } from "../feature-flags/properties";
-import { KnownLanguage, Language } from "../languages";
+import { BuiltInLanguage, Language } from "../languages";
 import { getRunnerLogger } from "../logging";
 import {
  checkExpectedLogMessages,
  getRecordingLogger,
  LoggedMessage,
+  makeMacro,
 } from "../testing-utils";
 import { ConfigurationError, prettyPrintPack } from "../util";

@@ -15,7 +16,7 @@ import * as dbConfig from "./db-config";
 /**
 * Test macro for ensuring the packs block is valid
 */
-const parsePacksMacro = test.macro({
+const parsePacksMacro = makeMacro({
  exec: (
    t: ExecutionContext<unknown>,
    packsInput: string,
@@ -33,7 +34,7 @@ const parsePacksMacro = test.macro({
 /**
 * Test macro for testing when the packs block is invalid
 */
-const parsePacksErrorMacro = test.macro({
+const parsePacksErrorMacro = makeMacro({
  exec: (
    t: ExecutionContext<unknown>,
    packsInput: string,
@@ -49,45 +50,42 @@ const parsePacksErrorMacro = test.macro({
 /**
 * Test macro for testing when the packs block is invalid
 */
-const invalidPackNameMacro = test.macro({
-  exec: (t: ExecutionContext, name: string) =>
-    parsePacksErrorMacro.exec(
+const invalidPackNameMacro = makeMacro({
+  exec: (t: ExecutionContext, arg: string) =>
+    parsePacksErrorMacro.fn(
      t,
-      name,
-      [KnownLanguage.cpp],
-      new RegExp(`^"${name}" is not a valid pack$`),
+      arg,
+      [BuiltInLanguage.cpp],
+      new RegExp(`^"${arg}" is not a valid pack$`),
    ),
  title: (_providedTitle: string | undefined, arg: string | undefined) =>
    `Invalid pack string: ${arg}`,
 });

-test("no packs", parsePacksMacro, "", [], undefined);
-test("two packs", parsePacksMacro, "a/b,c/d@1.2.3", [KnownLanguage.cpp], {
-  [KnownLanguage.cpp]: ["a/b", "c/d@1.2.3"],
+parsePacksMacro("no packs", "", [], undefined);
+parsePacksMacro("two packs", "a/b,c/d@1.2.3", [BuiltInLanguage.cpp], {
+  [BuiltInLanguage.cpp]: ["a/b", "c/d@1.2.3"],
 });
-test(
+parsePacksMacro(
  "two packs with spaces",
-  parsePacksMacro,
  " a/b , c/d@1.2.3 ",
-  [KnownLanguage.cpp],
+  [BuiltInLanguage.cpp],
  {
-    [KnownLanguage.cpp]: ["a/b", "c/d@1.2.3"],
+    [BuiltInLanguage.cpp]: ["a/b", "c/d@1.2.3"],
  },
 );
-test(
+parsePacksErrorMacro(
  "two packs with language",
-  parsePacksErrorMacro,
  "a/b,c/d@1.2.3",
-  [KnownLanguage.cpp, KnownLanguage.java],
+  [BuiltInLanguage.cpp, BuiltInLanguage.java],
  new RegExp(
    "Cannot specify a 'packs' input in a multi-language analysis. " +
      "Use a codeql-config.yml file instead and specify packs by language.",
  ),
 );

-test(
+parsePacksMacro(
  "packs with other valid names",
-  parsePacksMacro,
  [
    // ranges are ok
    "c/d@1.0",
@@ -106,9 +104,9 @@ test(
    // (globbing is not done)
    "c/d@1.2.3:+*)_(",
  ].join(","),
-  [KnownLanguage.cpp],
+  [BuiltInLanguage.cpp],
  {
-    [KnownLanguage.cpp]: [
+    [BuiltInLanguage.cpp]: [
      "c/d@1.0",
      "c/d@~1.0.0",
      "c/d@~1.0.0:a/b",
@@ -123,23 +121,23 @@ test(
  },
 );

-test(invalidPackNameMacro, "c"); // all packs require at least a scope and a name
-test(invalidPackNameMacro, "c-/d");
-test(invalidPackNameMacro, "-c/d");
-test(invalidPackNameMacro, "c/d_d");
-test(invalidPackNameMacro, "c/d@@");
-test(invalidPackNameMacro, "c/d@1.0.0:");
-test(invalidPackNameMacro, "c/d:");
-test(invalidPackNameMacro, "c/d:/a");
-test(invalidPackNameMacro, "@1.0.0:a");
-test(invalidPackNameMacro, "c/d@../a");
-test(invalidPackNameMacro, "c/d@b/../a");
-test(invalidPackNameMacro, "c/d:z@1");
+invalidPackNameMacro.test("c"); // all packs require at least a scope and a name
+invalidPackNameMacro.test("c-/d");
+invalidPackNameMacro.test("-c/d");
+invalidPackNameMacro.test("c/d_d");
+invalidPackNameMacro.test("c/d@@");
+invalidPackNameMacro.test("c/d@1.0.0:");
+invalidPackNameMacro.test("c/d:");
+invalidPackNameMacro.test("c/d:/a");
+invalidPackNameMacro.test("@1.0.0:a");
+invalidPackNameMacro.test("c/d@../a");
+invalidPackNameMacro.test("c/d@b/../a");
+invalidPackNameMacro.test("c/d:z@1");

 /**
 * Test macro for pretty printing pack specs
 */
-const packSpecPrettyPrintingMacro = test.macro({
+const packSpecPrettyPrintingMacro = makeMacro({
  exec: (t: ExecutionContext, packStr: string, packObj: dbConfig.Pack) => {
    const parsed = dbConfig.parsePacksSpecification(packStr);
    t.deepEqual(parsed, packObj, "parsed pack spec is correct");
@@ -163,36 +161,35 @@ const packSpecPrettyPrintingMacro = test.macro({
  ) => `Prettyprint pack spec: '${packStr}'`,
 });

-test(packSpecPrettyPrintingMacro, "a/b", {
+packSpecPrettyPrintingMacro.test("a/b", {
  name: "a/b",
  version: undefined,
  path: undefined,
 });
-test(packSpecPrettyPrintingMacro, "a/b@~1.2.3", {
+packSpecPrettyPrintingMacro.test("a/b@~1.2.3", {
  name: "a/b",
  version: "~1.2.3",
  path: undefined,
 });
-test(packSpecPrettyPrintingMacro, "a/b@~1.2.3:abc/def", {
+packSpecPrettyPrintingMacro.test("a/b@~1.2.3:abc/def", {
  name: "a/b",
  version: "~1.2.3",
  path: "abc/def",
 });
-test(packSpecPrettyPrintingMacro, "a/b:abc/def", {
+packSpecPrettyPrintingMacro.test("a/b:abc/def", {
  name: "a/b",
  version: undefined,
  path: "abc/def",
 });
-test(packSpecPrettyPrintingMacro, "    a/b:abc/def    ", {
+packSpecPrettyPrintingMacro.test("    a/b:abc/def    ", {
  name: "a/b",
  version: undefined,
  path: "abc/def",
 });

-const calculateAugmentationMacro = test.macro({
+const calculateAugmentationMacro = makeMacro({
  exec: async (
    t: ExecutionContext,
-    _title: string,
    rawPacksInput: string | undefined,
    rawQueriesInput: string | undefined,
    languages: Language[],
@@ -207,27 +204,25 @@ const calculateAugmentationMacro = test.macro({
    );
    t.deepEqual(actualAugmentationProperties, expectedAugmentationProperties);
  },
-  title: (_, title) => `Calculate Augmentation: ${title}`,
+  title: (title) => `Calculate Augmentation: ${title}`,
 });

-test(
-  calculateAugmentationMacro,
+calculateAugmentationMacro(
  "All empty",
  undefined,
  undefined,
-  [KnownLanguage.javascript],
+  [BuiltInLanguage.javascript],
  {},
  {
    ...dbConfig.defaultAugmentationProperties,
  },
 );

-test(
-  calculateAugmentationMacro,
+calculateAugmentationMacro(
  "With queries",
  undefined,
  " a, b , c, d",
-  [KnownLanguage.javascript],
+  [BuiltInLanguage.javascript],
  {},
  {
    ...dbConfig.defaultAugmentationProperties,
@@ -235,12 +230,11 @@ test(
  },
 );

-test(
-  calculateAugmentationMacro,
+calculateAugmentationMacro(
  "With queries combining",
  undefined,
  "   +   a, b , c, d ",
-  [KnownLanguage.javascript],
+  [BuiltInLanguage.javascript],
  {},
  {
    ...dbConfig.defaultAugmentationProperties,
@@ -249,12 +243,11 @@ test(
  },
 );

-test(
-  calculateAugmentationMacro,
+calculateAugmentationMacro(
  "With packs",
  "   codeql/a , codeql/b   , codeql/c  , codeql/d  ",
  undefined,
-  [KnownLanguage.javascript],
+  [BuiltInLanguage.javascript],
  {},
  {
    ...dbConfig.defaultAugmentationProperties,
@@ -262,12 +255,11 @@ test(
  },
 );

-test(
-  calculateAugmentationMacro,
+calculateAugmentationMacro(
  "With packs combining",
  "   +   codeql/a, codeql/b, codeql/c, codeql/d",
  undefined,
-  [KnownLanguage.javascript],
+  [BuiltInLanguage.javascript],
  {},
  {
    ...dbConfig.defaultAugmentationProperties,
@@ -276,12 +268,11 @@ test(
  },
 );

-test(
-  calculateAugmentationMacro,
+calculateAugmentationMacro(
  "With repo property queries",
  undefined,
  undefined,
-  [KnownLanguage.javascript],
+  [BuiltInLanguage.javascript],
  {
    "github-codeql-extra-queries": "a, b, c, d",
  },
@@ -294,12 +285,11 @@ test(
  },
 );

-test(
-  calculateAugmentationMacro,
+calculateAugmentationMacro(
  "With repo property queries combining",
  undefined,
  undefined,
-  [KnownLanguage.javascript],
+  [BuiltInLanguage.javascript],
  {
    "github-codeql-extra-queries": "+ a, b, c, d",
  },
@@ -312,10 +302,9 @@ test(
  },
 );

-const calculateAugmentationErrorMacro = test.macro({
+const calculateAugmentationErrorMacro = makeMacro({
  exec: async (
    t: ExecutionContext,
-    _title: string,
    rawPacksInput: string | undefined,
    rawQueriesInput: string | undefined,
    languages: Language[],
@@ -333,53 +322,48 @@ const calculateAugmentationErrorMacro = test.macro({
      { message: expectedError },
    );
  },
-  title: (_, title) => `Calculate Augmentation Error: ${title}`,
+  title: (title) => `Calculate Augmentation Error: ${title}`,
 });

-test(
-  calculateAugmentationErrorMacro,
+calculateAugmentationErrorMacro(
  "Plus (+) with nothing else (queries)",
  undefined,
  "   +   ",
-  [KnownLanguage.javascript],
+  [BuiltInLanguage.javascript],
  {},
  /The workflow property "queries" is invalid/,
 );

-test(
-  calculateAugmentationErrorMacro,
+calculateAugmentationErrorMacro(
  "Plus (+) with nothing else (packs)",
  "   +   ",
  undefined,
-  [KnownLanguage.javascript],
+  [BuiltInLanguage.javascript],
  {},
  /The workflow property "packs" is invalid/,
 );

-test(
-  calculateAugmentationErrorMacro,
+calculateAugmentationErrorMacro(
  "Plus (+) with nothing else (repo property queries)",
  undefined,
  undefined,
-  [KnownLanguage.javascript],
+  [BuiltInLanguage.javascript],
  {
    "github-codeql-extra-queries": "    + ",
  },
  /The repository property "github-codeql-extra-queries" is invalid/,
 );

-test(
-  calculateAugmentationErrorMacro,
+calculateAugmentationErrorMacro(
  "Packs input with multiple languages",
  "   +  a/b, c/d ",
  undefined,
-  [KnownLanguage.javascript, KnownLanguage.java],
+  [BuiltInLanguage.javascript, BuiltInLanguage.java],
  {},
  /Cannot specify a 'packs' input in a multi-language analysis/,
 );

-test(
-  calculateAugmentationErrorMacro,
+calculateAugmentationErrorMacro(
  "Packs input with no languages",
  "   +  a/b, c/d ",
  undefined,
@@ -388,12 +372,11 @@ test(
  /No languages specified/,
 );

-test(
-  calculateAugmentationErrorMacro,
+calculateAugmentationErrorMacro(
  "Invalid packs",
  " a-pack-without-a-scope ",
  undefined,
-  [KnownLanguage.javascript],
+  [BuiltInLanguage.javascript],
  {},
  /"a-pack-without-a-scope" is not a valid pack/,
 );
@@ -12,7 +12,7 @@ import { createStubCodeQL } from "./codeql";
 import { Config } from "./config-utils";
 import { cleanupAndUploadDatabases } from "./database-upload";
 import * as gitUtils from "./git-utils";
-import { KnownLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages";
 import { RepositoryNwo } from "./repository";
 import {
  checkExpectedLogMessages,
@@ -45,7 +45,7 @@ const testApiDetails: GitHubApiDetails = {

 function getTestConfig(tmpDir: string): Config {
  return createTestConfig({
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    dbLocation: tmpDir,
  });
 }
@@ -263,7 +263,7 @@ export function getArtifactSuffix(matrix: string | undefined): string {
    try {
      const matrixObject = JSON.parse(matrix);
      if (json.isObject(matrixObject)) {
-        for (const matrixKey of Object.keys(matrixObject as object).sort())
+        for (const matrixKey of Object.keys(matrixObject).sort())
          suffix += `-${matrixObject[matrixKey]}`;
      } else {
        core.warning("User-specified `matrix` input is not an object.");
@@ -1,6 +1,6 @@
 {
-  "bundleVersion": "codeql-bundle-v2.25.1",
-  "cliVersion": "2.25.1",
-  "priorBundleVersion": "codeql-bundle-v2.24.3",
-  "priorCliVersion": "2.24.3"
+  "bundleVersion": "codeql-bundle-v2.25.4",
+  "cliVersion": "2.25.4",
+  "priorBundleVersion": "codeql-bundle-v2.25.3",
+  "priorCliVersion": "2.25.3"
 }
@@ -27,7 +27,7 @@ import {
  CacheStoreResult,
 } from "./dependency-caching";
 import { Feature } from "./feature-flags";
-import { KnownLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages";
 import {
  setupTests,
  createFeatures,
@@ -179,7 +179,7 @@ test("checkHashPatterns - logs when no patterns match", async (t) => {
  const result = await checkHashPatterns(
    codeql,
    features,
-    KnownLanguage.csharp,
+    BuiltInLanguage.csharp,
    config,
    "download",
    getRecordingLogger(messages),
@@ -208,7 +208,7 @@ test("checkHashPatterns - returns patterns when patterns match", async (t) => {
    const result = await checkHashPatterns(
      codeql,
      features,
-      KnownLanguage.csharp,
+      BuiltInLanguage.csharp,
      config,
      "upload",
      getRecordingLogger(messages),
@@ -270,7 +270,7 @@ test.serial(
    const keyWithFeature = await cacheKey(
      codeql,
      createFeatures([Feature.CsharpNewCacheKey]),
-      KnownLanguage.csharp,
+      BuiltInLanguage.csharp,
      // Patterns don't matter here because we have stubbed `hashFiles` to always return a specific hash above.
      [],
    );
@@ -288,12 +288,12 @@ test.serial(
    const result = await downloadDependencyCaches(
      codeql,
      createFeatures([]),
-      [KnownLanguage.csharp],
+      [BuiltInLanguage.csharp],
      logger,
    );
    const statusReport = result.statusReport;
    t.is(statusReport.length, 1);
-    t.is(statusReport[0].language, KnownLanguage.csharp);
+    t.is(statusReport[0].language, BuiltInLanguage.csharp);
    t.is(statusReport[0].hit_kind, CacheHitKind.Miss);
    t.deepEqual(result.restoredKeys, []);
    t.assert(restoreCacheStub.calledOnce);
@@ -316,7 +316,7 @@ test.serial(
    const keyWithFeature = await cacheKey(
      codeql,
      features,
-      KnownLanguage.csharp,
+      BuiltInLanguage.csharp,
      // Patterns don't matter here because we have stubbed `hashFiles` to always return a specific hash above.
      [],
    );
@@ -334,14 +334,14 @@ test.serial(
    const result = await downloadDependencyCaches(
      codeql,
      features,
-      [KnownLanguage.csharp],
+      [BuiltInLanguage.csharp],
      logger,
    );

    // Check that the status report for telemetry indicates that one cache was restored with an exact match.
    const statusReport = result.statusReport;
    t.is(statusReport.length, 1);
-    t.is(statusReport[0].language, KnownLanguage.csharp);
+    t.is(statusReport[0].language, BuiltInLanguage.csharp);
    t.is(statusReport[0].hit_kind, CacheHitKind.Exact);

    // Check that the restored key has been returned.
@@ -380,7 +380,7 @@ test.serial(
    const keyWithFeature = await cacheKey(
      codeql,
      features,
-      KnownLanguage.csharp,
+      BuiltInLanguage.csharp,
      // Patterns don't matter here because we have stubbed `hashFiles` to always return a specific hash above.
      [],
    );
@@ -398,14 +398,14 @@ test.serial(
    const result = await downloadDependencyCaches(
      codeql,
      features,
-      [KnownLanguage.csharp],
+      [BuiltInLanguage.csharp],
      logger,
    );

    // Check that the status report for telemetry indicates that one cache was restored with a partial match.
    const statusReport = result.statusReport;
    t.is(statusReport.length, 1);
-    t.is(statusReport[0].language, KnownLanguage.csharp);
+    t.is(statusReport[0].language, BuiltInLanguage.csharp);
    t.is(statusReport[0].hit_kind, CacheHitKind.Partial);

    // Check that the restored key has been returned.
@@ -426,7 +426,7 @@ test("uploadDependencyCaches - skips upload for a language with no cache config"
  const logger = getRecordingLogger(messages);
  const features = createFeatures([]);
  const config = createTestConfig({
-    languages: [KnownLanguage.actions],
+    languages: [BuiltInLanguage.actions],
  });

  const result = await uploadDependencyCaches(codeql, features, config, logger);
@@ -444,7 +444,7 @@ test.serial(
    const logger = getRecordingLogger(messages);
    const features = createFeatures([]);
    const config = createTestConfig({
-      languages: [KnownLanguage.go],
+      languages: [BuiltInLanguage.go],
    });

    const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
@@ -457,7 +457,7 @@ test.serial(
      logger,
    );
    t.is(result.length, 1);
-    t.is(result[0].language, KnownLanguage.go);
+    t.is(result[0].language, BuiltInLanguage.go);
    t.is(result[0].result, CacheStoreResult.NoHash);
  },
 );
@@ -483,12 +483,12 @@ test.serial(
    const primaryCacheKey = await cacheKey(
      codeql,
      features,
-      KnownLanguage.csharp,
+      BuiltInLanguage.csharp,
      CSHARP_BASE_PATTERNS,
    );

    const config = createTestConfig({
-      languages: [KnownLanguage.csharp],
+      languages: [BuiltInLanguage.csharp],
      dependencyCachingRestoredKeys: [primaryCacheKey],
    });

@@ -499,7 +499,7 @@ test.serial(
      logger,
    );
    t.is(result.length, 1);
-    t.is(result[0].language, KnownLanguage.csharp);
+    t.is(result[0].language, BuiltInLanguage.csharp);
    t.is(result[0].result, CacheStoreResult.Duplicate);
  },
 );
@@ -525,7 +525,7 @@ test.serial(
    sinon.stub(cachingUtils, "getTotalCacheSize").resolves(0);

    const config = createTestConfig({
-      languages: [KnownLanguage.csharp],
+      languages: [BuiltInLanguage.csharp],
    });

    const result = await uploadDependencyCaches(
@@ -535,7 +535,7 @@ test.serial(
      logger,
    );
    t.is(result.length, 1);
-    t.is(result[0].language, KnownLanguage.csharp);
+    t.is(result[0].language, BuiltInLanguage.csharp);
    t.is(result[0].result, CacheStoreResult.Empty);

    checkExpectedLogMessages(t, messages, [
@@ -566,7 +566,7 @@ test.serial(
    sinon.stub(actionsCache, "saveCache").resolves();

    const config = createTestConfig({
-      languages: [KnownLanguage.csharp],
+      languages: [BuiltInLanguage.csharp],
    });

    const result = await uploadDependencyCaches(
@@ -576,7 +576,7 @@ test.serial(
      logger,
    );
    t.is(result.length, 1);
-    t.is(result[0].language, KnownLanguage.csharp);
+    t.is(result[0].language, BuiltInLanguage.csharp);
    t.is(result[0].result, CacheStoreResult.Stored);
    t.is(result[0].upload_size_bytes, 1024);

@@ -608,7 +608,7 @@ test.serial(
      .throws(new actionsCache.ReserveCacheError("Already in use"));

    const config = createTestConfig({
-      languages: [KnownLanguage.csharp],
+      languages: [BuiltInLanguage.csharp],
    });

    await t.notThrowsAsync(async () => {
@@ -619,7 +619,7 @@ test.serial(
        logger,
      );
      t.is(result.length, 1);
-      t.is(result[0].language, KnownLanguage.csharp);
+      t.is(result[0].language, BuiltInLanguage.csharp);
      t.is(result[0].result, CacheStoreResult.Duplicate);

      checkExpectedLogMessages(t, messages, ["Not uploading cache for"]);
@@ -647,7 +647,7 @@ test.serial("uploadDependencyCaches - throws other exceptions", async (t) => {
  sinon.stub(actionsCache, "saveCache").throws();

  const config = createTestConfig({
-    languages: [KnownLanguage.csharp],
+    languages: [BuiltInLanguage.csharp],
  });

  await t.throwsAsync(async () => {
@@ -659,7 +659,7 @@ test("getFeaturePrefix - returns empty string if no features are enabled", async
  const codeql = createStubCodeQL({});
  const features = createFeatures([]);

-  for (const knownLanguage of Object.values(KnownLanguage)) {
+  for (const knownLanguage of Object.values(BuiltInLanguage)) {
    const result = await getFeaturePrefix(codeql, features, knownLanguage);
    t.deepEqual(result, "", `Expected no feature prefix for ${knownLanguage}`);
  }
@@ -669,7 +669,11 @@ test("getFeaturePrefix - C# - returns prefix if CsharpNewCacheKey is enabled", a
  const codeql = createStubCodeQL({});
  const features = createFeatures([Feature.CsharpNewCacheKey]);

-  const result = await getFeaturePrefix(codeql, features, KnownLanguage.csharp);
+  const result = await getFeaturePrefix(
+    codeql,
+    features,
+    BuiltInLanguage.csharp,
+  );
  t.notDeepEqual(result, "");
  t.assert(result.endsWith("-"));
  // Check the length of the prefix, which should correspond to `cacheKeyHashLength` + 1 for the trailing `-`.
@@ -680,9 +684,9 @@ test("getFeaturePrefix - non-C# - returns '' if CsharpNewCacheKey is enabled", a
  const codeql = createStubCodeQL({});
  const features = createFeatures([Feature.CsharpNewCacheKey]);

-  for (const knownLanguage of Object.values(KnownLanguage)) {
+  for (const knownLanguage of Object.values(BuiltInLanguage)) {
    // Skip C# since we expect a result for it, which is tested in the previous test.
-    if (knownLanguage === KnownLanguage.csharp) {
+    if (knownLanguage === BuiltInLanguage.csharp) {
      continue;
    }
    const result = await getFeaturePrefix(codeql, features, knownLanguage);
@@ -694,7 +698,11 @@ test("getFeaturePrefix - C# - returns prefix if CsharpCacheBuildModeNone is enab
  const codeql = createStubCodeQL({});
  const features = createFeatures([Feature.CsharpCacheBuildModeNone]);

-  const result = await getFeaturePrefix(codeql, features, KnownLanguage.csharp);
+  const result = await getFeaturePrefix(
+    codeql,
+    features,
+    BuiltInLanguage.csharp,
+  );
  t.notDeepEqual(result, "");
  t.assert(result.endsWith("-"));
  // Check the length of the prefix, which should correspond to `cacheKeyHashLength` + 1 for the trailing `-`.
@@ -705,9 +713,9 @@ test("getFeaturePrefix - non-C# - returns '' if CsharpCacheBuildModeNone is enab
  const codeql = createStubCodeQL({});
  const features = createFeatures([Feature.CsharpCacheBuildModeNone]);

-  for (const knownLanguage of Object.values(KnownLanguage)) {
+  for (const knownLanguage of Object.values(BuiltInLanguage)) {
    // Skip C# since we expect a result for it, which is tested in the previous test.
-    if (knownLanguage === KnownLanguage.csharp) {
+    if (knownLanguage === BuiltInLanguage.csharp) {
      continue;
    }
    const result = await getFeaturePrefix(codeql, features, knownLanguage);
@@ -11,7 +11,7 @@ import { CodeQL } from "./codeql";
 import { Config } from "./config-utils";
 import { EnvVar } from "./environment";
 import { Feature, FeatureEnablement } from "./feature-flags";
-import { KnownLanguage, Language } from "./languages";
+import { BuiltInLanguage, Language } from "./languages";
 import { Logger } from "./logging";
 import { getErrorMessage, getRequiredEnvParam } from "./util";

@@ -541,7 +541,7 @@ export async function getFeaturePrefix(
    }
  };

-  if (language === KnownLanguage.csharp) {
+  if (language === BuiltInLanguage.csharp) {
    await addFeatureIfEnabled(Feature.CsharpNewCacheKey);
    await addFeatureIfEnabled(Feature.CsharpCacheBuildModeNone);
  }
@@ -72,6 +72,13 @@ let unwrittenDiagnostics: UnwrittenDiagnostic[] = [];
 */
 let unwrittenDefaultLanguageDiagnostics: DiagnosticMessage[] = [];

+/**
+ * Counter used to generate a unique suffix for each diagnostic filename, so that
+ * two diagnostics produced within the same millisecond do not overwrite each
+ * other on disk.
+ */
+let diagnosticCounter = 0;
+
 /**
 * Constructs a new diagnostic message with the specified id and name, as well as optional additional data.
 *
@@ -167,10 +174,18 @@ function writeDiagnostic(
    // Create the directory if it doesn't exist yet.
    mkdirSync(diagnosticsPath, { recursive: true });

+    // Include a monotonically increasing suffix to avoid filename collisions
+    // between diagnostics produced within the same millisecond.
+    const uniqueSuffix = (diagnosticCounter++).toString();
+    // We should only need to remove colons, but to be defensive, only allow a restricted set of
+    // characters.
+    const sanitizedTimestamp = diagnostic.timestamp.replace(
+      /[^a-zA-Z0-9.-]/g,
+      "",
+    );
    const jsonPath = path.resolve(
      diagnosticsPath,
-      // Remove colons from the timestamp as these are not allowed in Windows filenames.
-      `codeql-action-${diagnostic.timestamp.replaceAll(":", "")}.json`,
+      `codeql-action-${sanitizedTimestamp}-${uniqueSuffix}.json`,
    );

    writeFileSync(jsonPath, JSON.stringify(diagnostic));
@@ -5,17 +5,20 @@ import * as actionsUtil from "./actions-util";
 import type { PullRequestBranches } from "./actions-util";
 import * as apiClient from "./api-client";
 import {
-  shouldPerformDiffInformedAnalysis,
+  getDiffInformedAnalysisBranches,
+  prepareDiffInformedAnalysis,
  exportedForTesting,
 } from "./diff-informed-analysis-utils";
-import { Feature, initFeatures } from "./feature-flags";
+import { Feature, FeatureEnablement, initFeatures } from "./feature-flags";
 import { getRunnerLogger } from "./logging";
 import { parseRepositoryNwo } from "./repository";
 import {
  setupTests,
+  createFeatures,
  mockCodeQLVersion,
  mockFeatureFlagApiEndpoint,
  setupActionsVars,
+  makeMacro,
 } from "./testing-utils";
 import { GitHubVariant, withTmpDir } from "./util";
 import type { GitHubVersion } from "./util";
@@ -42,10 +45,9 @@ const defaultTestCase: DiffInformedAnalysisTestCase = {
  codeQLVersion: "2.21.0",
 };

-const testShouldPerformDiffInformedAnalysis = test.macro({
+const testShouldPerformDiffInformedAnalysis = makeMacro({
  exec: async (
    t: ExecutionContext,
-    _title: string,
    partialTestCase: Partial<DiffInformedAnalysisTestCase>,
    expectedResult: boolean,
  ) => {
@@ -80,13 +82,13 @@ const testShouldPerformDiffInformedAnalysis = test.macro({
        .stub(actionsUtil, "getPullRequestBranches")
        .returns(testCase.pullRequestBranches);

-      const result = await shouldPerformDiffInformedAnalysis(
+      const branches = await getDiffInformedAnalysisBranches(
        codeql,
        features,
        logger,
      );

-      t.is(result, expectedResult);
+      t.is(branches !== undefined, expectedResult);

      delete process.env.CODEQL_ACTION_DIFF_INFORMED_QUERIES;

@@ -94,18 +96,16 @@ const testShouldPerformDiffInformedAnalysis = test.macro({
      getPullRequestBranchesStub.restore();
    });
  },
-  title: (_, title) => `shouldPerformDiffInformedAnalysis: ${title}`,
+  title: (title) => `getDiffInformedAnalysisBranches: ${title}`,
 });

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns true in the default test case",
  {},
  true,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false when feature flag is disabled from the API",
  {
    featureEnabled: false,
@@ -113,8 +113,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false when CODEQL_ACTION_DIFF_INFORMED_QUERIES is set to false",
  {
    featureEnabled: true,
@@ -123,8 +122,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns true when CODEQL_ACTION_DIFF_INFORMED_QUERIES is set to true",
  {
    featureEnabled: false,
@@ -133,8 +131,7 @@ test.serial(
  true,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false for CodeQL version 2.20.0",
  {
    codeQLVersion: "2.20.0",
@@ -142,8 +139,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false for invalid GHES version",
  {
    gitHubVersion: {
@@ -154,8 +150,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false for GHES version 3.18.5",
  {
    gitHubVersion: {
@@ -166,8 +161,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns true for GHES version 3.19.0",
  {
    gitHubVersion: {
@@ -178,8 +172,7 @@ test.serial(
  true,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false when not a pull request",
  {
    pullRequestBranches: undefined,
@@ -187,6 +180,135 @@ test.serial(
  false,
 );

+test.serial(
+  "prepareDiffInformedAnalysis: returns false when not a pull request",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      const logger = getRunnerLogger(true);
+      const codeql = mockCodeQLVersion("2.21.0");
+      const features = createFeatures([Feature.DiffInformedQueries]);
+
+      sinon.stub(actionsUtil, "getPullRequestBranches").returns(undefined);
+      sinon
+        .stub(apiClient, "getGitHubVersion")
+        .resolves({ type: GitHubVariant.DOTCOM });
+
+      const result = await prepareDiffInformedAnalysis(
+        codeql,
+        features,
+        logger,
+      );
+
+      t.false(result);
+    });
+  },
+);
+
+test.serial(
+  "prepareDiffInformedAnalysis: returns false when applicability check throws",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      const logger = getRunnerLogger(true);
+      const codeql = mockCodeQLVersion("2.21.0");
+      // A features implementation whose getValue rejects, simulating an
+      // unexpected failure when determining whether diff-informed analysis
+      // should run.
+      const features: FeatureEnablement = {
+        getEnabledDefaultCliVersions: async () => {
+          throw new Error("not implemented");
+        },
+        getValue: async () => {
+          throw new Error("feature flag lookup failed");
+        },
+      };
+
+      const result = await prepareDiffInformedAnalysis(
+        codeql,
+        features,
+        logger,
+      );
+
+      t.false(result);
+    });
+  },
+);
+
+test.serial(
+  "prepareDiffInformedAnalysis: returns true when the diff is fetched successfully",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      const logger = getRunnerLogger(true);
+      const codeql = mockCodeQLVersion("2.21.0");
+      const features = createFeatures([Feature.DiffInformedQueries]);
+
+      sinon
+        .stub(actionsUtil, "getPullRequestBranches")
+        .returns({ base: "main", head: "feature" });
+      sinon
+        .stub(apiClient, "getGitHubVersion")
+        .resolves({ type: GitHubVariant.DOTCOM });
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-argument
+      sinon.stub(apiClient, "getApiClient").returns({
+        rest: {
+          repos: {
+            compareCommitsWithBasehead: sinon
+              .stub()
+              .resolves({ data: { files: [] } }),
+          },
+        },
+      } as any);
+
+      const result = await prepareDiffInformedAnalysis(
+        codeql,
+        features,
+        logger,
+      );
+
+      t.true(result);
+    });
+  },
+);
+
+test.serial(
+  "prepareDiffInformedAnalysis: returns false when the diff API call fails",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      const logger = getRunnerLogger(true);
+      const codeql = mockCodeQLVersion("2.21.0");
+      const features = createFeatures([Feature.DiffInformedQueries]);
+
+      sinon
+        .stub(actionsUtil, "getPullRequestBranches")
+        .returns({ base: "main", head: "feature" });
+      sinon
+        .stub(apiClient, "getGitHubVersion")
+        .resolves({ type: GitHubVariant.DOTCOM });
+      const notFoundError: any = new Error("Not Found");
+      notFoundError.status = 404;
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-argument
+      sinon.stub(apiClient, "getApiClient").returns({
+        rest: {
+          repos: {
+            compareCommitsWithBasehead: sinon.stub().rejects(notFoundError),
+          },
+        },
+      } as any);
+
+      const result = await prepareDiffInformedAnalysis(
+        codeql,
+        features,
+        logger,
+      );
+
+      t.false(result);
+    });
+  },
+);
+
 function runGetDiffRanges(changes: number, patch: string[] | undefined): any {
  return exportedForTesting.getDiffRanges(
    {
@@ -5,9 +5,9 @@ import type { PullRequestBranches } from "./actions-util";
 import { getApiClient, getGitHubVersion } from "./api-client";
 import type { CodeQL } from "./codeql";
 import { Feature, FeatureEnablement } from "./feature-flags";
-import { Logger } from "./logging";
+import { Logger, withGroupAsync } from "./logging";
 import { getRepositoryNwoFromEnv } from "./repository";
-import { GitHubVariant, satisfiesGHESVersion } from "./util";
+import { getErrorMessage, GitHubVariant, satisfiesGHESVersion } from "./util";

 /**
 * This interface is an abbreviated version of the file diff object returned by
@@ -21,20 +21,6 @@ interface FileDiff {
  patch?: string | undefined;
 }

-/**
- * Check if the action should perform diff-informed analysis.
- */
-export async function shouldPerformDiffInformedAnalysis(
-  codeql: CodeQL,
-  features: FeatureEnablement,
-  logger: Logger,
-): Promise<boolean> {
-  return (
-    (await getDiffInformedAnalysisBranches(codeql, features, logger)) !==
-    undefined
-  );
-}
-
 /**
 * Get the branches to use for diff-informed analysis.
 *
@@ -69,6 +55,46 @@ export async function getDiffInformedAnalysisBranches(
  return branches;
 }

+/**
+ * Prepares the diff ranges needed for diff-informed analysis for the current
+ * run.
+ *
+ * @returns `true` if the diff ranges were successfully computed and persisted
+ *   and are therefore available for use, `false` otherwise.
+ */
+export async function prepareDiffInformedAnalysis(
+  codeql: CodeQL,
+  features: FeatureEnablement,
+  logger: Logger,
+): Promise<boolean> {
+  let branches: PullRequestBranches | undefined;
+  try {
+    branches = await getDiffInformedAnalysisBranches(codeql, features, logger);
+  } catch (e) {
+    // If we cannot determine whether diff-informed analysis applies (for
+    // example, because a feature-flag lookup failed), treat it as not
+    // applicable rather than triggering the overlay fallback.
+    logger.warning(
+      `Failed to determine branch information for diff-informed analysis: ${getErrorMessage(e)}`,
+    );
+    return false;
+  }
+  if (!branches) {
+    return false;
+  }
+
+  return await withGroupAsync("Computing PR diff ranges", async () => {
+    try {
+      return await computeAndPersistDiffRanges(branches, logger);
+    } catch (e) {
+      logger.warning(
+        `Failed to compute diff-informed analysis ranges: ${getErrorMessage(e)}`,
+      );
+      return false;
+    }
+  });
+}
+
 export interface DiffThunkRange {
  /** Relative path from the repository root, using forward slashes as separators. */
  path: string;
@@ -151,6 +177,33 @@ export async function getPullRequestEditedDiffRanges(
  return results;
 }

+/**
+ * Compute and persist the diff ranges for a pull request. This fetches the
+ * diff from the GitHub API and writes it to the diff ranges JSON file so that
+ * CodeQL can use it for diff-informed analysis.
+ *
+ * @param branches The base and head branches of the pull request, as returned
+ *   by `getDiffInformedAnalysisBranches`.
+ * @param logger
+ * @returns `true` if the diff ranges were successfully computed and persisted,
+ *   otherwise `false`.
+ */
+export async function computeAndPersistDiffRanges(
+  branches: PullRequestBranches,
+  logger: Logger,
+): Promise<boolean> {
+  const ranges = await getPullRequestEditedDiffRanges(branches, logger);
+  if (ranges === undefined) {
+    return false;
+  }
+  writeDiffRangesJsonFile(logger, ranges);
+  const distinctFiles = new Set(ranges.map((r) => r.path)).size;
+  logger.info(
+    `Persisted ${ranges.length} diff range(s) across ${distinctFiles} file(s).`,
+  );
+  return true;
+}
+
 async function getFileDiffsWithBasehead(
  branches: PullRequestBranches,
  logger: Logger,
@@ -8,6 +8,7 @@ export enum DocUrl {
  CODEQL_BUILD_MODES = "https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages#codeql-build-modes",
  DEFINE_ENV_VARIABLES = "https://docs.github.com/en/actions/learn-github-actions/variables#defining-environment-variables-for-a-single-workflow",
  DELETE_ACTIONS_CACHE_ENTRIES = "https://docs.github.com/en/actions/how-tos/manage-workflow-runs/manage-caches#deleting-cache-entries",
+  PRIVATE_REGISTRY_LOGS = "https://docs.github.com/en/code-security/reference/code-scanning/code-scanning-logs#diagnostic-information-for-private-package-registries",
  SCANNING_ON_PUSH = "https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning#scanning-on-push",
  SPECIFY_BUILD_STEPS_MANUALLY = "https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages#about-specifying-build-steps-manually",
  SYSTEM_REQUIREMENTS = "https://codeql.github.com/docs/codeql-overview/system-requirements/",
@@ -0,0 +1,3 @@
+export async function run__ACTION__() {
+  return await __ACTION__.runWrapper();
+}
@@ -451,12 +451,16 @@ test.serial(`selects CLI from defaults.json on GHES`, async (t) => {
  await withTmpDir(async (tmpDir) => {
    const features = setUpFeatureFlagTests(tmpDir);

-    const defaultCliVersion = await features.getDefaultCliVersion(
+    const defaultCliVersion = await features.getEnabledDefaultCliVersions(
      GitHubVariant.GHES,
    );
    t.deepEqual(defaultCliVersion, {
-      cliVersion: defaults.cliVersion,
-      tagName: defaults.bundleVersion,
+      enabledVersions: [
+        {
+          cliVersion: defaults.cliVersion,
+          tagName: defaults.bundleVersion,
+        },
+      ],
    });
  });
 });
@@ -482,10 +486,13 @@ for (const variant of [GitHubVariant.DOTCOM, GitHubVariant.GHEC_DR]) {
          false;
        mockFeatureFlagApiEndpoint(200, expectedFeatureEnablement);

-        const defaultCliVersion = await features.getDefaultCliVersion(variant);
+        const defaultCliVersion =
+          await features.getEnabledDefaultCliVersions(variant);
        t.deepEqual(defaultCliVersion, {
-          cliVersion: "2.20.1",
-          tagName: "codeql-bundle-v2.20.1",
+          enabledVersions: [
+            { cliVersion: "2.20.1", tagName: "codeql-bundle-v2.20.1" },
+            { cliVersion: "2.20.0", tagName: "codeql-bundle-v2.20.0" },
+          ],
          toolsFeatureFlagsValid: true,
        });
      });
@@ -500,10 +507,15 @@ for (const variant of [GitHubVariant.DOTCOM, GitHubVariant.GHEC_DR]) {
        const expectedFeatureEnablement = initializeFeatures(true);
        mockFeatureFlagApiEndpoint(200, expectedFeatureEnablement);

-        const defaultCliVersion = await features.getDefaultCliVersion(variant);
+        const defaultCliVersion =
+          await features.getEnabledDefaultCliVersions(variant);
        t.deepEqual(defaultCliVersion, {
-          cliVersion: defaults.cliVersion,
-          tagName: defaults.bundleVersion,
+          enabledVersions: [
+            {
+              cliVersion: defaults.cliVersion,
+              tagName: defaults.bundleVersion,
+            },
+          ],
          toolsFeatureFlagsValid: false,
        });
      });
@@ -529,10 +541,13 @@ for (const variant of [GitHubVariant.DOTCOM, GitHubVariant.GHEC_DR]) {
        ] = true;
        mockFeatureFlagApiEndpoint(200, expectedFeatureEnablement);

-        const defaultCliVersion = await features.getDefaultCliVersion(variant);
+        const defaultCliVersion =
+          await features.getEnabledDefaultCliVersions(variant);
        t.deepEqual(defaultCliVersion, {
-          cliVersion: "2.20.1",
-          tagName: "codeql-bundle-v2.20.1",
+          enabledVersions: [
+            { cliVersion: "2.20.1", tagName: "codeql-bundle-v2.20.1" },
+            { cliVersion: "2.20.0", tagName: "codeql-bundle-v2.20.0" },
+          ],
          toolsFeatureFlagsValid: true,
        });

@@ -29,9 +29,32 @@ const DEFAULT_VERSION_FEATURE_FLAG_SUFFIX = "_enabled";
 */
 export const CODEQL_VERSION_ZSTD_BUNDLE = "2.19.0";

-export interface CodeQLDefaultVersionInfo {
+const LINKED_CODEQL_VERSION: CodeQLVersionInfo = {
+  cliVersion: defaults.cliVersion,
+  tagName: defaults.bundleVersion,
+};
+
+export interface CodeQLVersionInfo {
+  /** The version number of the CodeQL CLI, e.g. `2.19.0`. */
  cliVersion: string;
+  /**
+   * The tag name of the CodeQL Bundle associated with this version, e.g. `codeql-bundle-v2.19.0`.
+   */
  tagName: string;
+}
+
+export interface CodeQLDefaultVersionInfo {
+  /**
+   * CodeQL CLI versions that are enabled as defaults, sorted from highest to lowest.
+   *
+   * Guaranteed to be non-empty. When feature flags are unavailable, this falls back to a single
+   * entry containing the version pinned in `defaults.json`.
+   */
+  enabledVersions: CodeQLVersionInfo[];
+  /**
+   * If accessed, whether the tools feature flags are valid, i.e. contain at least one enabled
+   * version.
+   */
  toolsFeatureFlagsValid?: boolean;
 }

@@ -44,6 +67,8 @@ export interface CodeQLDefaultVersionInfo {
 * Legacy features should end with `_enabled`.
 */
 export enum Feature {
+  /** Controls whether we allow multiple values for the `analysis-kinds` input. */
+  AllowMultipleAnalysisKinds = "allow_multiple_analysis_kinds",
  AllowToolcacheInput = "allow_toolcache_input",
  CleanupTrapCaches = "cleanup_trap_caches",
  CppDependencyInstallation = "cpp_dependency_installation_enabled",
@@ -72,6 +97,19 @@ export enum Feature {
  OverlayAnalysisGo = "overlay_analysis_go",
  OverlayAnalysisJava = "overlay_analysis_java",
  OverlayAnalysisJavascript = "overlay_analysis_javascript",
+  /**
+   * When set, chooses the default CodeQL CLI version as the highest version that is both enabled by
+   * feature flags and present as an overlay-base database in the Actions cache for the configured
+   * languages. Falls back to the highest feature flagged version if no intersecting overlay-base
+   * database exists in the cache.
+   */
+  OverlayAnalysisMatchCodeqlVersion = "overlay_analysis_match_codeql_version",
+  /**
+   * Like `OverlayAnalysisMatchCodeqlVersion`, but only logs a diagnostic with the version that
+   * would have been chosen instead of actually changing the default CodeQL CLI version.
+   * `OverlayAnalysisMatchCodeqlVersion` overrides this flag.
+   */
+  OverlayAnalysisMatchCodeqlVersionDryRun = "overlay_analysis_match_codeql_version_dry_run",
  OverlayAnalysisPython = "overlay_analysis_python",
  /**
   * Controls whether lower disk space requirements are used for overlay hardware checks.
@@ -124,6 +162,11 @@ export type FeatureConfig = {
 };

 export const featureConfig = {
+  [Feature.AllowMultipleAnalysisKinds]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_ALLOW_MULTIPLE_ANALYSIS_KINDS",
+    minimumVersion: undefined,
+  },
  [Feature.AllowToolcacheInput]: {
    defaultValue: false,
    envVar: "CODEQL_ACTION_ALLOW_TOOLCACHE_INPUT",
@@ -277,6 +320,16 @@ export const featureConfig = {
    envVar: "CODEQL_ACTION_OVERLAY_ANALYSIS_DISABLE_TRAP_CACHING",
    minimumVersion: undefined,
  },
+  [Feature.OverlayAnalysisMatchCodeqlVersion]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_OVERLAY_ANALYSIS_MATCH_CODEQL_VERSION",
+    minimumVersion: undefined,
+  },
+  [Feature.OverlayAnalysisMatchCodeqlVersionDryRun]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_OVERLAY_ANALYSIS_MATCH_CODEQL_VERSION_DRY_RUN",
+    minimumVersion: undefined,
+  },
  [Feature.OverlayAnalysisResourceChecksV2]: {
    defaultValue: false,
    envVar: "CODEQL_ACTION_OVERLAY_ANALYSIS_RESOURCE_CHECKS_V2",
@@ -346,8 +399,12 @@ export type FeatureWithoutCLI = {
 }[keyof typeof featureConfig];

 export interface FeatureEnablement {
-  /** Gets the default version of the CodeQL tools. */
-  getDefaultCliVersion(
+  /**
+   * Returns the set of default CodeQL CLI versions to consider, sorted from
+   * highest to lowest. The first entry is the version that the CodeQL Action
+   * will use by default. The list is always non-empty.
+   */
+  getEnabledDefaultCliVersions(
    variant: util.GitHubVariant,
  ): Promise<CodeQLDefaultVersionInfo>;
  getValue(feature: FeatureWithoutCLI): Promise<boolean>;
@@ -371,12 +428,11 @@ export const FEATURE_FLAGS_FILE_NAME = "cached-feature-flags.json";
 class OfflineFeatures implements FeatureEnablement {
  constructor(protected readonly logger: Logger) {}

-  async getDefaultCliVersion(
+  async getEnabledDefaultCliVersions(
    _variant: util.GitHubVariant,
  ): Promise<CodeQLDefaultVersionInfo> {
    return {
-      cliVersion: defaults.cliVersion,
-      tagName: defaults.bundleVersion,
+      enabledVersions: [LINKED_CODEQL_VERSION],
    };
  }

@@ -386,7 +442,7 @@ class OfflineFeatures implements FeatureEnablement {
  getFeatureConfig(feature: Feature): FeatureConfig {
    // Narrow the type to FeatureConfig to avoid type errors. To avoid unsafe use of `as`, we
    // check that the required properties exist using `satisfies`.
-    return featureConfig[feature] satisfies FeatureConfig as FeatureConfig;
+    return featureConfig[feature] satisfies FeatureConfig;
  }

  /**
@@ -518,13 +574,13 @@ class Features extends OfflineFeatures {
    );
  }

-  async getDefaultCliVersion(
+  async getEnabledDefaultCliVersions(
    variant: util.GitHubVariant,
  ): Promise<CodeQLDefaultVersionInfo> {
    if (supportsFeatureFlags(variant)) {
-      return await this.gitHubFeatureFlags.getDefaultCliVersionFromFlags();
+      return await this.gitHubFeatureFlags.getEnabledDefaultCliVersionsFromFlags();
    }
-    return super.getDefaultCliVersion(variant);
+    return super.getEnabledDefaultCliVersions(variant);
  }

  /**
@@ -600,16 +656,22 @@ class GitHubFeatureFlags {
    return version;
  }

-  async getDefaultCliVersionFromFlags(): Promise<CodeQLDefaultVersionInfo> {
+  /**
+   * Returns CLI versions enabled by `default_codeql_version_*_enabled` feature
+   * flags, sorted from highest to lowest. Falls back to the version pinned in
+   * `defaults.json` if no such flags are enabled.
+   */
+  async getEnabledDefaultCliVersionsFromFlags(): Promise<CodeQLDefaultVersionInfo> {
    const response = await this.getAllFeatures();

-    const enabledFeatureFlagCliVersions = Object.entries(response)
+    const sortedCliVersions = Object.entries(response)
      .map(([f, isEnabled]) =>
        isEnabled ? this.getCliVersionFromFeatureFlag(f) : undefined,
      )
-      .filter((f): f is string => f !== undefined);
+      .filter((f): f is string => f !== undefined)
+      .sort(semver.rcompare);

-    if (enabledFeatureFlagCliVersions.length === 0) {
+    if (sortedCliVersions.length === 0) {
      // We expect at least one default CLI version to be enabled on Dotcom at any time. However if
      // the feature flags are misconfigured, rather than crashing, we fall back to the CLI version
      // shipped with the Action in defaults.json. This has the effect of immediately rolling out
@@ -625,8 +687,7 @@ class GitHubFeatureFlags {
          `shipped with the Action. This is ${defaults.cliVersion}.`,
      );
      const result: CodeQLDefaultVersionInfo = {
-        cliVersion: defaults.cliVersion,
-        tagName: defaults.bundleVersion,
+        enabledVersions: [LINKED_CODEQL_VERSION],
      };
      if (this.hasAccessedRemoteFeatureFlags) {
        result.toolsFeatureFlagsValid = false;
@@ -634,17 +695,14 @@ class GitHubFeatureFlags {
      return result;
    }

-    const maxCliVersion = enabledFeatureFlagCliVersions.reduce(
-      (maxVersion, currentVersion) =>
-        currentVersion > maxVersion ? currentVersion : maxVersion,
-      enabledFeatureFlagCliVersions[0],
-    );
    this.logger.debug(
-      `Derived default CLI version of ${maxCliVersion} from feature flags.`,
+      `Derived default CLI version of ${sortedCliVersions[0]} from feature flags.`,
    );
    return {
-      cliVersion: maxCliVersion,
-      tagName: `codeql-bundle-v${maxCliVersion}`,
+      enabledVersions: sortedCliVersions.map((cliVersion) => ({
+        cliVersion,
+        tagName: `codeql-bundle-v${cliVersion}`,
+      })),
      toolsFeatureFlagsValid: true,
    };
  }
@@ -19,6 +19,7 @@ import {
  createFeatures,
  createTestConfig,
  DEFAULT_ACTIONS_VARS,
+  makeMacro,
  makeVersionInfo,
  RecordingLogger,
  setupActionsVars,
@@ -601,7 +602,7 @@ async function testFailedSarifUpload(
  uploadFiles.resolves({
    sarifID: "42",
    statusReport: { raw_upload_size_bytes: 20, zipped_upload_size_bytes: 10 },
-  } as uploadLib.UploadResult);
+  });
  const waitForProcessing = sinon.stub(uploadLib, "waitForProcessing");

  const features = [] as Feature[];
@@ -796,7 +797,7 @@ test.serial(
  },
 );

-const skippedUploadTest = test.macro({
+const skippedUploadTest = makeMacro({
  exec: async (
    t: ExecutionContext<unknown>,
    config: Partial<configUtils.Config>,
@@ -823,9 +824,8 @@ const skippedUploadTest = test.macro({
    `tryUploadSarifIfRunFailed - skips upload ${providedTitle}`,
 });

-test.serial(
+skippedUploadTest.serial(
  "without CodeQL command",
-  skippedUploadTest,
  // No codeQLCmd
  {
    analysisKinds: [AnalysisKind.RiskAssessment],
@@ -834,9 +834,8 @@ test.serial(
  "CodeQL command not found",
 );

-test.serial(
+skippedUploadTest.serial(
  "if no language is configured",
-  skippedUploadTest,
  // No explicit language configuration
  {
    analysisKinds: [AnalysisKind.RiskAssessment],
@@ -845,9 +844,8 @@ test.serial(
  "Unexpectedly, the configuration is not for a single language.",
 );

-test.serial(
+skippedUploadTest.serial(
  "if multiple languages is configured",
-  skippedUploadTest,
  // Multiple explicit languages configured
  {
    analysisKinds: [AnalysisKind.RiskAssessment],
@@ -207,7 +207,7 @@ function getJobStatusFromEnvironment(): JobStatus | undefined {
  return undefined;
 }

-async function runWrapper() {
+export async function runWrapper() {
  const startedAt = new Date();
  const logger = getActionsLogger();
  try {
@@ -222,5 +222,3 @@ async function runWrapper() {
    );
  }
 }
-
-void runWrapper();
@@ -37,11 +37,6 @@ import {
  makeDiagnostic,
  makeTelemetryDiagnostic,
 } from "./diagnostics";
-import {
-  getDiffInformedAnalysisBranches,
-  getPullRequestEditedDiffRanges,
-  writeDiffRangesJsonFile,
-} from "./diff-informed-analysis-utils";
 import { EnvVar } from "./environment";
 import { Feature, FeatureEnablement, initFeatures } from "./feature-flags";
 import {
@@ -58,7 +53,7 @@ import {
  initConfig,
  runDatabaseInitCluster,
 } from "./init";
-import { JavaEnvVars, KnownLanguage } from "./languages";
+import { JavaEnvVars, BuiltInLanguage } from "./languages";
 import { getActionsLogger, Logger, withGroupAsync } from "./logging";
 import {
  downloadOverlayBaseDatabaseFromCache,
@@ -281,7 +276,7 @@ async function run(startedAt: Date) {
    // successful, the results are cached so that we don't duplicate the work in normal runs.
    let analysisKinds: AnalysisKind[] | undefined;
    try {
-      analysisKinds = await getAnalysisKinds(logger);
+      analysisKinds = await getAnalysisKinds(logger, features);
    } catch (err) {
      logger.debug(
        `Failed to parse analysis kinds for 'starting' status report: ${getErrorMessage(err)}`,
@@ -298,16 +293,23 @@ async function run(startedAt: Date) {
      );
    }

-    const codeQLDefaultVersionInfo = await features.getDefaultCliVersion(
-      gitHubVersion.type,
-    );
+    const codeQLDefaultVersionInfo =
+      await features.getEnabledDefaultCliVersions(gitHubVersion.type);
    toolsFeatureFlagsValid = codeQLDefaultVersionInfo.toolsFeatureFlagsValid;
+    const rawLanguages = configUtils.getRawLanguagesNoAutodetect(
+      getOptionalInput("languages"),
+    );
+    const useOverlayAwareDefaultCliVersion =
+      analysisKinds?.length === 1 &&
+      analysisKinds[0] === AnalysisKind.CodeScanning;
    const initCodeQLResult = await initCodeQL(
      getOptionalInput("tools"),
      apiDetails,
      getTemporaryDirectory(),
      gitHubVersion.type,
      codeQLDefaultVersionInfo,
+      rawLanguages,
+      useOverlayAwareDefaultCliVersion,
      features,
      logger,
    );
@@ -330,7 +332,7 @@ async function run(startedAt: Date) {
      // requested rust - don't enable it via language autodetection.
      configUtils
        .getRawLanguagesNoAutodetect(getOptionalInput("languages"))
-        .includes(KnownLanguage.rust)
+        .includes(BuiltInLanguage.rust)
    ) {
      const experimental = "2.19.3";
      const publicPreview = "2.22.1";
@@ -346,7 +348,7 @@ async function run(startedAt: Date) {
      }
    }

-    analysisKinds = await getAnalysisKinds(logger);
+    analysisKinds = await getAnalysisKinds(logger, features);
    const debugMode = getOptionalInput("debug") === "true" || core.isDebug();
    const repositoryProperties = repositoryPropertiesResult.orElse({});
    const fileCoverageResult = await getFileCoverageInformationEnabled(
@@ -390,7 +392,7 @@ async function run(startedAt: Date) {
    });

    if (
-      config.languages.includes(KnownLanguage.swift) &&
+      config.languages.includes(BuiltInLanguage.swift) &&
      process.platform !== "darwin"
    ) {
      throw new ConfigurationError(
@@ -427,7 +429,6 @@ async function run(startedAt: Date) {
    }

    await checkInstallPython311(config.languages, codeql);
-    await computeAndPersistDiffRanges(codeql, features, logger);
  } catch (unwrappedError) {
    const error = wrapError(unwrappedError);
    core.setFailed(error.message);
@@ -465,18 +466,23 @@ async function run(startedAt: Date) {
      // necessary preparations. So, in that mode, we would assume that
      // everything is in order and let the analysis fail if that turns out not
      // to be the case.
-      overlayBaseDatabaseStats = await downloadOverlayBaseDatabaseFromCache(
-        codeql,
-        config,
-        logger,
+      await withGroupAsync(
+        "Checking cache for overlay-base database",
+        async () => {
+          overlayBaseDatabaseStats = await downloadOverlayBaseDatabaseFromCache(
+            codeql,
+            config,
+            logger,
+          );
+          if (!overlayBaseDatabaseStats) {
+            config.overlayDatabaseMode = OverlayDatabaseMode.None;
+            logger.info(
+              "No overlay-base database found in cache, " +
+                `reverting overlay database mode to ${OverlayDatabaseMode.None}.`,
+            );
+          }
+        },
      );
-      if (!overlayBaseDatabaseStats) {
-        config.overlayDatabaseMode = OverlayDatabaseMode.None;
-        logger.info(
-          "No overlay-base database found in cache, " +
-            `reverting overlay database mode to ${OverlayDatabaseMode.None}.`,
-        );
-      }
    }

    if (config.overlayDatabaseMode !== OverlayDatabaseMode.Overlay) {
@@ -509,7 +515,7 @@ async function run(startedAt: Date) {
    }

    if (
-      config.languages.includes(KnownLanguage.go) &&
+      config.languages.includes(BuiltInLanguage.go) &&
      process.platform === "linux"
    ) {
      try {
@@ -567,7 +573,7 @@ async function run(startedAt: Date) {
        if (e instanceof FileCmdNotFoundError) {
          addDiagnostic(
            config,
-            KnownLanguage.go,
+            BuiltInLanguage.go,
            makeDiagnostic(
              "go/workflow/file-program-unavailable",
              "The `file` program is required on Linux, but does not appear to be installed",
@@ -661,7 +667,7 @@ async function run(startedAt: Date) {
      (await codeQlVersionAtLeast(codeql, CODEQL_VERSION_JAR_MINIMIZATION)) &&
      config.dependencyCachingEnabled &&
      config.buildMode === BuildMode.None &&
-      config.languages.includes(KnownLanguage.java)
+      config.languages.includes(BuiltInLanguage.java)
    ) {
      core.exportVariable(
        EnvVar.JAVA_EXTRACTOR_MINIMIZE_DEPENDENCY_JARS,
@@ -818,42 +824,6 @@ async function loadRepositoryProperties(
  }
 }

-/**
- * Compute and persist diff ranges when diff-informed analysis is enabled
- * (feature flag + PR context). This writes the standard pr-diff-range.json
- * file for later reuse in the analyze step. Failures are logged but non-fatal.
- */
-async function computeAndPersistDiffRanges(
-  codeql: CodeQL,
-  features: FeatureEnablement,
-  logger: Logger,
-): Promise<void> {
-  await withGroupAsync("Computing PR diff ranges", async () => {
-    try {
-      const branches = await getDiffInformedAnalysisBranches(
-        codeql,
-        features,
-        logger,
-      );
-      if (!branches) {
-        return;
-      }
-      const ranges = await getPullRequestEditedDiffRanges(branches, logger);
-      if (ranges === undefined) {
-        return;
-      }
-      writeDiffRangesJsonFile(logger, ranges);
-      const distinctFiles = new Set(ranges.map((r) => r.path)).size;
-      logger.info(
-        `Persisted ${ranges.length} diff range(s) across ${distinctFiles} file(s).`,
-      );
-    } catch (e) {
-      logger.warning(
-        `Failed to compute and persist PR diff ranges: ${getErrorMessage(e)}`,
-      );
-    }
-  });
-}
 async function recordZstdAvailability(
  config: configUtils.Config,
  zstdAvailability: ZstdAvailability,
@@ -868,7 +838,7 @@ async function recordZstdAvailability(
  );
 }

-async function runWrapper() {
+export async function runWrapper() {
  const startedAt = new Date();
  const logger = getActionsLogger();
  try {
@@ -884,5 +854,3 @@ async function runWrapper() {
  }
  await checkForTimeout();
 }
-
-void runWrapper();
@@ -15,13 +15,14 @@ import {
  getFileCoverageInformationEnabled,
  logFileCoverageOnPrsDeprecationWarning,
 } from "./init";
-import { KnownLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages";
 import {
  createFeatures,
  LoggedMessage,
  createTestConfig,
  getRecordingLogger,
  setupTests,
+  makeMacro,
 } from "./testing-utils";
 import { ConfigurationError, withTmpDir } from "./util";

@@ -152,16 +153,15 @@ test("cleanupDatabaseClusterDirectory can disable warning with options", async (
 });

 type PackInfo = {
-  language: KnownLanguage;
+  language: BuiltInLanguage;
  packinfoContents: string | undefined;
  sourceOnlyPack?: boolean;
  qlpackFileName?: string;
 };

-const testCheckPacksForOverlayCompatibility = test.macro({
+const testCheckPacksForOverlayCompatibility = makeMacro({
  exec: async (
    t: ExecutionContext,
-    _title: string,
    {
      cliOverlayVersion,
      languages,
@@ -169,13 +169,13 @@ const testCheckPacksForOverlayCompatibility = test.macro({
      expectedResult,
    }: {
      cliOverlayVersion: number | undefined;
-      languages: KnownLanguage[];
+      languages: BuiltInLanguage[];
      packs: Record<string, PackInfo>;
      expectedResult: boolean;
    },
  ) => {
    await withTmpDir(async (tmpDir) => {
-      const packDirsByLanguage = new Map<KnownLanguage, string[]>();
+      const packDirsByLanguage = new Map<BuiltInLanguage, string[]>();

      for (const [packName, packInfo] of Object.entries(packs)) {
        const packPath = path.join(tmpDir, packName);
@@ -234,18 +234,17 @@ const testCheckPacksForOverlayCompatibility = test.macro({
      );
    });
  },
-  title: (_, title) => `checkPacksForOverlayCompatibility: ${title}`,
+  title: (title) => `checkPacksForOverlayCompatibility: ${title}`,
 });

-test(
-  testCheckPacksForOverlayCompatibility,
+testCheckPacksForOverlayCompatibility(
  "returns false when CLI does not support overlay",
  {
    cliOverlayVersion: undefined,
-    languages: [KnownLanguage.java],
+    languages: [BuiltInLanguage.java],
    packs: {
      "codeql/java-queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: '{"overlayVersion":2}',
      },
    },
@@ -253,26 +252,24 @@ test(
  },
 );

-test(
-  testCheckPacksForOverlayCompatibility,
+testCheckPacksForOverlayCompatibility(
  "returns true when there are no query packs",
  {
    cliOverlayVersion: 2,
-    languages: [KnownLanguage.java],
+    languages: [BuiltInLanguage.java],
    packs: {},
    expectedResult: true,
  },
 );

-test(
-  testCheckPacksForOverlayCompatibility,
+testCheckPacksForOverlayCompatibility(
  "returns true when query pack has not been compiled",
  {
    cliOverlayVersion: 2,
-    languages: [KnownLanguage.java],
+    languages: [BuiltInLanguage.java],
    packs: {
      "codeql/java-queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: undefined,
        sourceOnlyPack: true,
      },
@@ -281,15 +278,14 @@ test(
  },
 );

-test(
-  testCheckPacksForOverlayCompatibility,
+testCheckPacksForOverlayCompatibility(
  "returns true when query pack has expected overlay version",
  {
    cliOverlayVersion: 2,
-    languages: [KnownLanguage.java],
+    languages: [BuiltInLanguage.java],
    packs: {
      "codeql/java-queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: '{"overlayVersion":2}',
      },
    },
@@ -297,19 +293,18 @@ test(
  },
 );

-test(
-  testCheckPacksForOverlayCompatibility,
+testCheckPacksForOverlayCompatibility(
  "returns true when query packs for all languages to analyze are compatible",
  {
    cliOverlayVersion: 2,
-    languages: [KnownLanguage.cpp, KnownLanguage.java],
+    languages: [BuiltInLanguage.cpp, BuiltInLanguage.java],
    packs: {
      "codeql/cpp-queries": {
-        language: KnownLanguage.cpp,
+        language: BuiltInLanguage.cpp,
        packinfoContents: '{"overlayVersion":2}',
      },
      "codeql/java-queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: '{"overlayVersion":2}',
      },
    },
@@ -317,19 +312,18 @@ test(
  },
 );

-test(
-  testCheckPacksForOverlayCompatibility,
+testCheckPacksForOverlayCompatibility(
  "returns true when query pack for a language not analyzed is incompatible",
  {
    cliOverlayVersion: 2,
-    languages: [KnownLanguage.java],
+    languages: [BuiltInLanguage.java],
    packs: {
      "codeql/cpp-queries": {
-        language: KnownLanguage.cpp,
+        language: BuiltInLanguage.cpp,
        packinfoContents: undefined,
      },
      "codeql/java-queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: '{"overlayVersion":2}',
      },
    },
@@ -337,19 +331,18 @@ test(
  },
 );

-test(
-  testCheckPacksForOverlayCompatibility,
+testCheckPacksForOverlayCompatibility(
  "returns false when query pack for a language to analyze is incompatible",
  {
    cliOverlayVersion: 2,
-    languages: [KnownLanguage.cpp, KnownLanguage.java],
+    languages: [BuiltInLanguage.cpp, BuiltInLanguage.java],
    packs: {
      "codeql/cpp-queries": {
-        language: KnownLanguage.cpp,
+        language: BuiltInLanguage.cpp,
        packinfoContents: '{"overlayVersion":1}',
      },
      "codeql/java-queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: '{"overlayVersion":2}',
      },
    },
@@ -357,19 +350,18 @@ test(
  },
 );

-test(
-  testCheckPacksForOverlayCompatibility,
+testCheckPacksForOverlayCompatibility(
  "returns false when query pack is missing .packinfo",
  {
    cliOverlayVersion: 2,
-    languages: [KnownLanguage.java],
+    languages: [BuiltInLanguage.java],
    packs: {
      "codeql/java-queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: '{"overlayVersion":2}',
      },
      "custom/queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: undefined,
      },
    },
@@ -377,19 +369,18 @@ test(
  },
 );

-test(
-  testCheckPacksForOverlayCompatibility,
+testCheckPacksForOverlayCompatibility(
  "returns false when query pack has different overlay version",
  {
    cliOverlayVersion: 2,
-    languages: [KnownLanguage.java],
+    languages: [BuiltInLanguage.java],
    packs: {
      "codeql/java-queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: '{"overlayVersion":2}',
      },
      "custom/queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: '{"overlayVersion":1}',
      },
    },
@@ -397,19 +388,18 @@ test(
  },
 );

-test(
-  testCheckPacksForOverlayCompatibility,
+testCheckPacksForOverlayCompatibility(
  "returns false when query pack is missing overlayVersion in .packinfo",
  {
    cliOverlayVersion: 2,
-    languages: [KnownLanguage.java],
+    languages: [BuiltInLanguage.java],
    packs: {
      "codeql/java-queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: '{"overlayVersion":2}',
      },
      "custom/queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: "{}",
      },
    },
@@ -417,19 +407,18 @@ test(
  },
 );

-test(
-  testCheckPacksForOverlayCompatibility,
+testCheckPacksForOverlayCompatibility(
  "returns false when .packinfo is not valid JSON",
  {
    cliOverlayVersion: 2,
-    languages: [KnownLanguage.java],
+    languages: [BuiltInLanguage.java],
    packs: {
      "codeql/java-queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: '{"overlayVersion":2}',
      },
      "custom/queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: "this_is_not_valid_json",
      },
    },
@@ -437,15 +426,14 @@ test(
  },
 );

-test(
-  testCheckPacksForOverlayCompatibility,
+testCheckPacksForOverlayCompatibility(
  "returns true when query pack uses codeql-pack.yml filename",
  {
    cliOverlayVersion: 2,
-    languages: [KnownLanguage.java],
+    languages: [BuiltInLanguage.java],
    packs: {
      "codeql/java-queries": {
-        language: KnownLanguage.java,
+        language: BuiltInLanguage.java,
        packinfoContents: '{"overlayVersion":2}',
        qlpackFileName: "codeql-pack.yml",
      },
@@ -26,7 +26,7 @@ import {
  RepositoryProperties,
  RepositoryPropertyName,
 } from "./feature-flags/properties";
-import { KnownLanguage, Language } from "./languages";
+import { BuiltInLanguage, Language } from "./languages";
 import { Logger, withGroupAsync } from "./logging";
 import { ToolsSource } from "./setup-codeql";
 import { ZstdAvailability } from "./tar";
@@ -39,6 +39,8 @@ export async function initCodeQL(
  tempDir: string,
  variant: util.GitHubVariant,
  defaultCliVersion: CodeQLDefaultVersionInfo,
+  rawLanguages: string[] | undefined,
+  useOverlayAwareDefaultCliVersion: boolean,
  features: FeatureEnablement,
  logger: Logger,
 ): Promise<{
@@ -61,6 +63,8 @@ export async function initCodeQL(
    tempDir,
    variant,
    defaultCliVersion,
+    rawLanguages,
+    useOverlayAwareDefaultCliVersion,
    features,
    logger,
    true,
@@ -235,7 +239,7 @@ export async function checkInstallPython311(
  codeql: CodeQL,
 ) {
  if (
-    languages.includes(KnownLanguage.python) &&
+    languages.includes(BuiltInLanguage.python) &&
    process.platform === "win32" &&
    !(await codeql.getVersion()).features?.supportsPython312
  ) {
@@ -0,0 +1,46 @@
+import test from "ava";
+
+import { setupTests } from "../testing-utils";
+
+import * as json from ".";
+
+setupTests(test);
+
+const testSchema = {
+  requiredKey: json.string,
+};
+
+const optionalSchema = {
+  optionalKey: json.optional(json.string),
+};
+
+test("validateSchema - required properties are required", async (t) => {
+  t.false(json.validateSchema(testSchema, {}));
+  t.false(json.validateSchema(testSchema, { requiredKey: undefined }));
+  t.false(json.validateSchema(testSchema, { requiredKey: null }));
+  t.false(json.validateSchema(testSchema, { requiredKey: 0 }));
+  t.false(json.validateSchema(testSchema, { requiredKey: 123 }));
+  t.false(json.validateSchema(testSchema, { requiredKey: false }));
+  t.false(json.validateSchema(testSchema, { requiredKey: true }));
+  t.false(json.validateSchema(testSchema, { requiredKey: [] }));
+  t.false(json.validateSchema(testSchema, { requiredKey: {} }));
+  t.true(json.validateSchema(testSchema, { requiredKey: "" }));
+  t.true(json.validateSchema(testSchema, { requiredKey: "foo" }));
+});
+
+test("validateSchema - optional properties are optional", async (t) => {
+  // Optional fields may be absent
+  t.true(json.validateSchema(optionalSchema, {}));
+  t.true(json.validateSchema(optionalSchema, { optionalKey: undefined }));
+  t.true(json.validateSchema(optionalSchema, { optionalKey: null }));
+
+  // But, if present, should have the expected type
+  t.false(json.validateSchema(optionalSchema, { optionalKey: 0 }));
+  t.false(json.validateSchema(optionalSchema, { optionalKey: 123 }));
+  t.false(json.validateSchema(optionalSchema, { optionalKey: false }));
+  t.false(json.validateSchema(optionalSchema, { optionalKey: true }));
+  t.false(json.validateSchema(optionalSchema, { optionalKey: [] }));
+  t.false(json.validateSchema(optionalSchema, { optionalKey: {} }));
+  t.true(json.validateSchema(optionalSchema, { optionalKey: "" }));
+  t.true(json.validateSchema(optionalSchema, { optionalKey: "foo" }));
+});
@@ -36,3 +36,82 @@ export function isStringOrUndefined(
 ): value is string | undefined {
  return value === undefined || isString(value);
 }
+
+/**
+ * Represents a field of type `T` in a schema.
+ * Carries a validation function and flag indicating whether the field is required or not.
+ */
+export type Validator<T> = {
+  validate: (val: unknown) => val is T;
+  required: boolean;
+};
+
+/** Extracts `T` from `Validator<T>`. */
+export type UnwrapValidator<V> = V extends Validator<infer A> ? A : never;
+
+/** A validator for string fields in schemas. */
+export const string = {
+  validate: isString,
+  required: true,
+} as const satisfies Validator<string>;
+
+/** Transforms a validator to be optional. */
+export function optional<T>(validator: Validator<T>) {
+  return {
+    validate: (val: unknown) => {
+      return val === undefined || val === null || validator.validate(val);
+    },
+    required: false,
+  } as const satisfies Validator<T | undefined | null>;
+}
+
+/** Represents an arbitrary object schema. */
+export type Schema = Record<string, Validator<any>>;
+
+/** Extracts the required keys from `S`. */
+export type RequiredKeys<S extends Schema> = {
+  [K in keyof S]: S[K]["required"] extends true ? K : never;
+}[keyof S];
+
+/** Extracts optional keys from `S`. */
+export type OptionalKeys<S extends Schema> = {
+  [K in keyof S]: S[K]["required"] extends true ? never : K;
+}[keyof S];
+
+/** Constructs an object type corresponding to a schema. */
+export type FromSchema<S extends Schema> = {
+  [K in RequiredKeys<S>]: UnwrapValidator<S[K]>;
+} & { [K in OptionalKeys<S>]?: UnwrapValidator<S[K]> };
+
+/**
+ * Validates that `obj` satisfies at least `schema`. Additional keys are accepted.
+ *
+ * @param schema The schema to validate against.
+ * @param obj The object to validate.
+ * @returns Asserts that `obj` is of the `schema`'s type if validation is successful.
+ */
+export function validateSchema<S extends Schema>(
+  schema: S,
+  obj: UnvalidatedObject<any>,
+): obj is FromSchema<S> {
+  for (const [key, validator] of Object.entries(schema)) {
+    const hasKey = key in obj;
+
+    // If the property is required, but absent, fail.
+    if (validator.required && !hasKey) {
+      return false;
+    }
+
+    // If the property is required, but undefined or null, fail.
+    if (validator.required && (obj[key] === undefined || obj[key] === null)) {
+      return false;
+    }
+
+    // If the property is present, validate it.
+    if (hasKey && !validator.validate(obj[key])) {
+      return false;
+    }
+  }
+
+  return true;
+}
@@ -0,0 +1,106 @@
+import { ExecutionContext } from "ava";
+
+import * as json from ".";
+
+/**
+ * Constructs an object based on `schema` for unit tests.
+ * Assumes that all keys in `schema` have string values.
+ *
+ * @param includeOptional Whether to include optional properties.
+ * @param schema The schema to base the object on.
+ * @returns An object that satisfies `schema`.
+ */
+export function makeFromSchema<S extends json.Schema>(
+  includeOptional: boolean,
+  schema: S,
+): json.FromSchema<S> {
+  const result = {};
+  for (const [key, validator] of Object.entries(schema)) {
+    if (!validator.required && !includeOptional) {
+      continue;
+    }
+    result[key] = `value-for-${key}`;
+  }
+  return result as json.FromSchema<S>;
+}
+
+/** Options for `withSchemaMatrix`. */
+export interface SchemaMatrixOptions {
+  /** Whether cases where the properties are entirely absent should be excluded. */
+  excludeAbsent?: boolean;
+}
+
+/**
+ * Constructs a test matrix of possible objects for `schema`: all required properties
+ * plus all permutations of possible states for the optional properties.
+ *
+ * @param schema The schema to construct a test matrix for.
+ * @param body The test body to call with each value from the test matrix.
+ */
+export function withSchemaMatrix<S extends json.Schema>(
+  t: ExecutionContext<any>,
+  schema: S,
+  opts: SchemaMatrixOptions,
+  body: (value: json.FromSchema<S>) => void,
+): void {
+  // Construct a base object that includes all required properties.
+  const required = makeFromSchema(false, schema);
+
+  // Identify optional properties.
+  const optionalKeys: Array<keyof S> = [];
+
+  for (const [key, validator] of Object.entries(schema)) {
+    if (!validator.required) {
+      optionalKeys.push(key);
+    }
+  }
+
+  const optionalValues = (key: keyof S) => [
+    null,
+    undefined,
+    `value-for-${String(key)}`,
+  ];
+
+  // Constructs an array of test objects, starting with `required` and combining it with all
+  // possible states of each optional property. For example, with default settings:
+  //
+  // For { requiredKey: string }, we get: `[{ requiredKey: "some-string-value" }]`
+  //
+  // For { requiredKey: string, optionalKey?: string }, we get:
+  // [ { requiredKey: "some-string-value" },
+  //   { requiredKey: "some-string-value", optionalKey: undefined },
+  //   { requiredKey: "some-string-value", optionalKey: null },
+  //   { requiredKey: "some-string-value", optionalKey: "some-value" },
+  // ]
+  const permutations = (keys: Array<keyof S>) => {
+    if (keys.length === 0) return [required];
+
+    const bases = permutations(keys.slice(1));
+    const result: Array<json.FromSchema<S>> = [];
+
+    const optionalKey = keys[0];
+    for (const base of bases) {
+      if (!opts.excludeAbsent) {
+        // Optional keys can be absent entirely.
+        result.push(base);
+      }
+
+      // Or be present and have one of the `optionalValues`.
+      for (const optionalValue of optionalValues(optionalKey)) {
+        result.push({ ...base, [optionalKey]: optionalValue });
+      }
+    }
+    return result;
+  };
+
+  // Call `body` for all test cases.
+  const testCases = permutations(optionalKeys);
+  for (const testCase of testCases) {
+    try {
+      body(testCase);
+    } catch (err) {
+      t.log(testCase);
+      throw err;
+    }
+  }
+}
@@ -1,11 +0,0 @@
-{
-  "c": "cpp",
-  "c-c++": "cpp",
-  "c-cpp": "cpp",
-  "c#": "csharp",
-  "c++": "cpp",
-  "java-kotlin": "java",
-  "javascript-typescript": "javascript",
-  "kotlin": "java",
-  "typescript": "javascript"
-}
@@ -1,29 +0,0 @@
-/** A language to analyze with CodeQL. */
-export type Language = string;
-
-/**
- * A language supported by CodeQL that is treated specially by the Action.
- *
- * This is not an exhaustive list of languages supported by CodeQL and new
- * languages do not need to be added here.
- */
-export enum KnownLanguage {
-  actions = "actions",
-  cpp = "cpp",
-  csharp = "csharp",
-  go = "go",
-  java = "java",
-  javascript = "javascript",
-  python = "python",
-  ruby = "ruby",
-  rust = "rust",
-  swift = "swift",
-}
-
-/** Java-specific environment variable names that we may care about. */
-export enum JavaEnvVars {
-  JAVA_HOME = "JAVA_HOME",
-  JAVA_TOOL_OPTIONS = "JAVA_TOOL_OPTIONS",
-  JDK_JAVA_OPTIONS = "JDK_JAVA_OPTIONS",
-  _JAVA_OPTIONS = "_JAVA_OPTIONS",
-}
@@ -0,0 +1,25 @@
+{
+  "languages": [
+    "actions",
+    "cpp",
+    "csharp",
+    "go",
+    "java",
+    "javascript",
+    "python",
+    "ruby",
+    "rust",
+    "swift"
+  ],
+  "aliases": {
+    "c": "cpp",
+    "c-c++": "cpp",
+    "c-cpp": "cpp",
+    "c#": "csharp",
+    "c++": "cpp",
+    "java-kotlin": "java",
+    "javascript-typescript": "javascript",
+    "kotlin": "java",
+    "typescript": "javascript"
+  }
+}
@@ -0,0 +1,46 @@
+import test from "ava";
+
+import { setupTests } from "../testing-utils";
+
+import knownLanguagesData from "./builtin.json";
+
+import { isBuiltInLanguage, BuiltInLanguage, parseBuiltInLanguage } from ".";
+
+setupTests(test);
+
+test("parseBuiltInLanguage", (t) => {
+  // Exact matches
+  t.is(parseBuiltInLanguage("csharp"), BuiltInLanguage.csharp);
+  t.is(parseBuiltInLanguage("cpp"), BuiltInLanguage.cpp);
+  t.is(parseBuiltInLanguage("go"), BuiltInLanguage.go);
+  t.is(parseBuiltInLanguage("java"), BuiltInLanguage.java);
+  t.is(parseBuiltInLanguage("javascript"), BuiltInLanguage.javascript);
+  t.is(parseBuiltInLanguage("python"), BuiltInLanguage.python);
+  t.is(parseBuiltInLanguage("rust"), BuiltInLanguage.rust);
+
+  // Aliases
+  t.is(parseBuiltInLanguage("  \t\nCsHaRp\t\t"), BuiltInLanguage.csharp);
+  t.is(parseBuiltInLanguage("c"), BuiltInLanguage.cpp);
+  t.is(parseBuiltInLanguage("c++"), BuiltInLanguage.cpp);
+  t.is(parseBuiltInLanguage("kotlin"), BuiltInLanguage.java);
+  t.is(parseBuiltInLanguage("typescript"), BuiltInLanguage.javascript);
+
+  // spaces and case-insensitivity
+  t.is(parseBuiltInLanguage("  \t\nkOtLin\t\t"), BuiltInLanguage.java);
+
+  // Not matches
+  t.is(parseBuiltInLanguage(BuiltInLanguage.python), BuiltInLanguage.python);
+  t.is(parseBuiltInLanguage("foo"), undefined);
+  t.is(parseBuiltInLanguage(" "), undefined);
+  t.is(parseBuiltInLanguage(""), undefined);
+});
+
+test("isBuiltInLanguage matches the curated built-in language set", (t) => {
+  t.true(isBuiltInLanguage(BuiltInLanguage.actions));
+  t.true(isBuiltInLanguage(BuiltInLanguage.swift));
+  t.false(isBuiltInLanguage("typescript"));
+});
+
+test("BuiltInLanguage enum matches builtin.json", (t) => {
+  t.deepEqual(Object.values(BuiltInLanguage), knownLanguagesData.languages);
+});
@@ -0,0 +1,57 @@
+import knownLanguagesData from "./builtin.json";
+
+/** A language to analyze with CodeQL. */
+export type Language = string;
+
+/** A language built into the `defaults.json` CodeQL distribution. */
+export enum BuiltInLanguage {
+  actions = "actions",
+  cpp = "cpp",
+  csharp = "csharp",
+  go = "go",
+  java = "java",
+  javascript = "javascript",
+  python = "python",
+  ruby = "ruby",
+  rust = "rust",
+  swift = "swift",
+}
+
+/** Java-specific environment variable names that we may care about. */
+export enum JavaEnvVars {
+  JAVA_HOME = "JAVA_HOME",
+  JAVA_TOOL_OPTIONS = "JAVA_TOOL_OPTIONS",
+  JDK_JAVA_OPTIONS = "JDK_JAVA_OPTIONS",
+  _JAVA_OPTIONS = "_JAVA_OPTIONS",
+}
+
+const builtInLanguageSet = new Set<string>(knownLanguagesData.languages);
+
+export function isBuiltInLanguage(
+  language: string,
+): language is BuiltInLanguage {
+  return builtInLanguageSet.has(language);
+}
+
+/**
+ * Parse a language input corresponding to a built-in language into its canonical CodeQL language
+ * name.
+ *
+ * This uses the language aliases shipped with the Action and will not be able to resolve aliases
+ * added by third-party CodeQL language support or versions of the CodeQL CLI newer than the one
+ * mentioned in `defaults.json`. Therefore, this function should only be used when the CodeQL CLI is
+ * not available.
+ */
+export function parseBuiltInLanguage(
+  language: string,
+): BuiltInLanguage | undefined {
+  language = language.trim().toLowerCase();
+  language =
+    knownLanguagesData.aliases[
+      language as keyof typeof knownLanguagesData.aliases
+    ] ?? language;
+  if (isBuiltInLanguage(language)) {
+    return language;
+  }
+  return undefined;
+}
@@ -7,12 +7,13 @@ import * as sinon from "sinon";

 import * as actionsUtil from "../actions-util";
 import * as apiClient from "../api-client";
-import { ResolveDatabaseOutput } from "../codeql";
+import type { ResolveDatabaseOutput } from "../codeql";
 import * as gitUtils from "../git-utils";
-import { KnownLanguage } from "../languages";
+import { BuiltInLanguage } from "../languages";
 import { getRunnerLogger } from "../logging";
 import {
  createTestConfig,
+  makeMacro,
  mockCodeQLVersion,
  setupTests,
 } from "../testing-utils";
@@ -23,6 +24,7 @@ import {
  downloadOverlayBaseDatabaseFromCache,
  getCacheRestoreKeyPrefix,
  getCacheSaveKey,
+  getCodeQlVersionsForOverlayBaseDatabases,
 } from "./caching";
 import { OverlayDatabaseMode } from "./overlay-database-mode";

@@ -50,10 +52,9 @@ const defaultDownloadTestCase: DownloadOverlayBaseDatabaseTestCase = {
  resolveDatabaseOutput: { overlayBaseSpecifier: "20250626:XXX" },
 };

-const testDownloadOverlayBaseDatabaseFromCache = test.macro({
+const testDownloadOverlayBaseDatabaseFromCache = makeMacro({
  exec: async (
    t,
-    _title: string,
    partialTestCase: Partial<DownloadOverlayBaseDatabaseTestCase>,
    expectDownloadSuccess: boolean,
  ) => {
@@ -65,7 +66,7 @@ const testDownloadOverlayBaseDatabaseFromCache = test.macro({
      const testCase = { ...defaultDownloadTestCase, ...partialTestCase };
      const config = createTestConfig({
        dbLocation,
-        languages: [KnownLanguage.java],
+        languages: [BuiltInLanguage.java],
      });

      config.overlayDatabaseMode = testCase.overlayDatabaseMode;
@@ -141,18 +142,16 @@ const testDownloadOverlayBaseDatabaseFromCache = test.macro({
      }
    });
  },
-  title: (_, title) => `downloadOverlayBaseDatabaseFromCache: ${title}`,
+  title: (title) => `downloadOverlayBaseDatabaseFromCache: ${title}`,
 });

-test.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
+testDownloadOverlayBaseDatabaseFromCache.serial(
  "returns stats when successful",
  {},
  true,
 );

-test.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
+testDownloadOverlayBaseDatabaseFromCache.serial(
  "returns undefined when mode is OverlayDatabaseMode.OverlayBase",
  {
    overlayDatabaseMode: OverlayDatabaseMode.OverlayBase,
@@ -160,8 +159,7 @@ test.serial(
  false,
 );

-test.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
+testDownloadOverlayBaseDatabaseFromCache.serial(
  "returns undefined when mode is OverlayDatabaseMode.None",
  {
    overlayDatabaseMode: OverlayDatabaseMode.None,
@@ -169,8 +167,7 @@ test.serial(
  false,
 );

-test.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
+testDownloadOverlayBaseDatabaseFromCache.serial(
  "returns undefined when caching is disabled",
  {
    useOverlayDatabaseCaching: false,
@@ -178,8 +175,7 @@ test.serial(
  false,
 );

-test.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
+testDownloadOverlayBaseDatabaseFromCache.serial(
  "returns undefined in test mode",
  {
    isInTestMode: true,
@@ -187,8 +183,7 @@ test.serial(
  false,
 );

-test.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
+testDownloadOverlayBaseDatabaseFromCache.serial(
  "returns undefined when cache miss",
  {
    restoreCacheResult: undefined,
@@ -196,8 +191,7 @@ test.serial(
  false,
 );

-test.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
+testDownloadOverlayBaseDatabaseFromCache.serial(
  "returns undefined when download fails",
  {
    restoreCacheResult: new Error("Download failed"),
@@ -205,8 +199,7 @@ test.serial(
  false,
 );

-test.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
+testDownloadOverlayBaseDatabaseFromCache.serial(
  "returns undefined when downloaded database is invalid",
  {
    hasBaseDatabaseOidsFile: false,
@@ -214,8 +207,7 @@ test.serial(
  false,
 );

-test.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
+testDownloadOverlayBaseDatabaseFromCache.serial(
  "returns undefined when downloaded database doesn't have an overlayBaseSpecifier",
  {
    resolveDatabaseOutput: {},
@@ -223,8 +215,7 @@ test.serial(
  false,
 );

-test.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
+testDownloadOverlayBaseDatabaseFromCache.serial(
  "returns undefined when resolving database metadata fails",
  {
    resolveDatabaseOutput: new Error("Failed to resolve database metadata"),
@@ -232,8 +223,7 @@ test.serial(
  false,
 );

-test.serial(
-  testDownloadOverlayBaseDatabaseFromCache,
+testDownloadOverlayBaseDatabaseFromCache.serial(
  "returns undefined when filesystem error occurs",
  {
    tryGetFolderBytesSucceeds: false,
@@ -285,3 +275,160 @@ test.serial("overlay-base database cache keys remain stable", async (t) => {
    `Expected save key "${saveKey}" to start with restore key prefix "${restoreKeyPrefix}"`,
  );
 });
+
+test.serial(
+  "getCodeQlVersionsForOverlayBaseDatabases returns unique versions sorted latest first",
+  async (t) => {
+    const logger = getRunnerLogger(true);
+
+    sinon.stub(apiClient, "getAutomationID").resolves("test-automation-id/");
+    sinon.stub(apiClient, "listActionsCaches").resolves([
+      {
+        key: "codeql-overlay-base-database-1-c5666c509a2d9895-javascript_python-2.23.0-abc123-1-1",
+      },
+      {
+        key: "codeql-overlay-base-database-1-c5666c509a2d9895-javascript_python-2.24.1-def456-2-1",
+      },
+      {
+        key: "codeql-overlay-base-database-1-c5666c509a2d9895-javascript_python-2.23.0-ghi789-3-1",
+      },
+    ]);
+
+    const result = await getCodeQlVersionsForOverlayBaseDatabases(
+      ["javascript", "python"],
+      logger,
+    );
+    t.deepEqual(result, ["2.24.1", "2.23.0"]);
+  },
+);
+
+test.serial(
+  "getCodeQlVersionsForOverlayBaseDatabases returns empty list when no caches exist",
+  async (t) => {
+    const logger = getRunnerLogger(true);
+
+    sinon.stub(apiClient, "getAutomationID").resolves("test-automation-id/");
+    sinon.stub(apiClient, "listActionsCaches").resolves([]);
+
+    const result = await getCodeQlVersionsForOverlayBaseDatabases(
+      ["python"],
+      logger,
+    );
+    t.deepEqual(result, []);
+  },
+);
+
+test.serial(
+  "getCodeQlVersionsForOverlayBaseDatabases returns empty list when cache keys are unparseable",
+  async (t) => {
+    const logger = getRunnerLogger(true);
+
+    sinon.stub(apiClient, "getAutomationID").resolves("test-automation-id/");
+    sinon.stub(apiClient, "listActionsCaches").resolves([
+      {
+        key: "codeql-overlay-base-database-1-c5666c509a2d9895-python-malformed",
+      },
+      { key: undefined },
+    ]);
+
+    const result = await getCodeQlVersionsForOverlayBaseDatabases(
+      ["python"],
+      logger,
+    );
+    t.deepEqual(result, []);
+  },
+);
+
+test.serial(
+  "getCodeQlVersionsForOverlayBaseDatabases returns the single version when only one cache exists",
+  async (t) => {
+    const logger = getRunnerLogger(true);
+
+    sinon.stub(apiClient, "getAutomationID").resolves("test-automation-id/");
+    sinon.stub(apiClient, "listActionsCaches").resolves([
+      {
+        key: "codeql-overlay-base-database-1-c5666c509a2d9895-cpp-2.25.0-abc123-1-1",
+      },
+    ]);
+
+    const result = await getCodeQlVersionsForOverlayBaseDatabases(
+      ["cpp"],
+      logger,
+    );
+    t.deepEqual(result, ["2.25.0"]);
+  },
+);
+
+test.serial(
+  "getCodeQlVersionsForOverlayBaseDatabases resolves language aliases",
+  async (t) => {
+    const logger = getRunnerLogger(true);
+    // The alias `c++` should be resolved to "cpp" and match cache entries keyed with "cpp"
+
+    sinon.stub(apiClient, "getAutomationID").resolves("test-automation-id/");
+    sinon.stub(apiClient, "listActionsCaches").resolves([
+      {
+        key: "codeql-overlay-base-database-1-c5666c509a2d9895-cpp-2.25.0-abc123-1-1",
+      },
+    ]);
+
+    const result = await getCodeQlVersionsForOverlayBaseDatabases(
+      ["c++"],
+      logger,
+    );
+    t.deepEqual(result, ["2.25.0"]);
+  },
+);
+
+test.serial(
+  "getCodeQlVersionsForOverlayBaseDatabases de-duplicates resolved language aliases",
+  async (t) => {
+    const logger = getRunnerLogger(true);
+
+    sinon.stub(apiClient, "getAutomationID").resolves("test-automation-id/");
+    const listActionsCachesStub = sinon
+      .stub(apiClient, "listActionsCaches")
+      .resolves([
+        {
+          key: "codeql-overlay-base-database-1-c5666c509a2d9895-javascript_python-2.25.0-abc123-1-1",
+        },
+      ]);
+
+    const result = await getCodeQlVersionsForOverlayBaseDatabases(
+      ["javascript", "typescript", "Python", "python"],
+      logger,
+    );
+    t.deepEqual(result, ["2.25.0"]);
+    sinon.assert.calledOnceWithExactly(
+      listActionsCachesStub,
+      "codeql-overlay-base-database-1-c5666c509a2d9895-javascript_python-",
+    );
+  },
+);
+
+test.serial(
+  "getCodeQlVersionsForOverlayBaseDatabases ignores nightly versions with build metadata",
+  async (t) => {
+    const logger = getRunnerLogger(true);
+
+    sinon.stub(apiClient, "getAutomationID").resolves("test-automation-id/");
+    sinon.stub(apiClient, "listActionsCaches").resolves([
+      {
+        key: "codeql-overlay-base-database-1-c5666c509a2d9895-python-2.25.0-abc123-1-1",
+      },
+      {
+        // Nightly release with semver build metadata; should be ignored.
+        key: "codeql-overlay-base-database-1-c5666c509a2d9895-python-2.26.0+202604211234-def456-2-1",
+      },
+      {
+        key: "codeql-overlay-base-database-1-c5666c509a2d9895-python-2.24.0-ghi789-3-1",
+      },
+    ]);
+
+    const result = await getCodeQlVersionsForOverlayBaseDatabases(
+      ["python"],
+      logger,
+    );
+    t.deepEqual(result, ["2.25.0", "2.24.0"]);
+  },
+);
@@ -1,18 +1,20 @@
 import * as fs from "fs";

 import * as actionsCache from "@actions/cache";
+import * as semver from "semver";

 import {
  getRequiredInput,
  getWorkflowRunAttempt,
  getWorkflowRunID,
 } from "../actions-util";
-import { getAutomationID } from "../api-client";
+import { getAutomationID, listActionsCaches } from "../api-client";
 import { createCacheKeyHash } from "../caching-utils";
 import { type CodeQL } from "../codeql";
 import { type Config } from "../config-utils";
 import { getCommitOid } from "../git-utils";
-import { Logger, withGroupAsync } from "../logging";
+import { type Language, parseBuiltInLanguage } from "../languages";
+import { type Logger, withGroupAsync } from "../logging";
 import {
  CleanupLevel,
  getBaseDatabaseOidsFilePath,
@@ -404,7 +406,17 @@ export async function getCacheRestoreKeyPrefix(
  config: Config,
  codeQlVersion: string,
 ): Promise<string> {
-  const languages = [...config.languages].sort().join("_");
+  return `${await getCacheKeyPrefixBase(config.languages)}${codeQlVersion}-`;
+}
+
+/**
+ * Computes the cache key prefix for overlay-base databases, excluding the
+ * CodeQL version.
+ */
+async function getCacheKeyPrefixBase(
+  parsedLanguages: Language[],
+): Promise<string> {
+  const languagesComponent = [...parsedLanguages].sort().join("_");

  const cacheKeyComponents = {
    automationID: await getAutomationID(),
@@ -412,17 +424,98 @@ export async function getCacheRestoreKeyPrefix(
  };
  const componentsHash = createCacheKeyHash(cacheKeyComponents);

-  // For a cached overlay-base database to be considered compatible for overlay
-  // analysis, all components in the cache restore key must match:
-  //
  // CACHE_PREFIX: distinguishes overlay-base databases from other cache objects
  // CACHE_VERSION: cache format version
  // componentsHash: hash of additional components (see above for details)
-  // languages: the languages included in the overlay-base database
-  // codeQlVersion: CodeQL bundle version
+  // languagesComponent: the languages included in the overlay-base database
  //
-  // Technically we can also include languages and codeQlVersion in the
-  // componentsHash, but including them explicitly in the cache key makes it
-  // easier to debug and understand the cache key structure.
-  return `${CACHE_PREFIX}-${CACHE_VERSION}-${componentsHash}-${languages}-${codeQlVersion}-`;
+  // Technically we can also include languages in the componentsHash, but
+  // including them explicitly in the cache key makes it easier to debug and
+  // understand the cache key structure.
+  return `${CACHE_PREFIX}-${CACHE_VERSION}-${componentsHash}-${languagesComponent}-`;
+}
+
+/**
+ * Searches the GitHub Actions cache for overlay-base databases matching the given languages, and
+ * returns all stable CodeQL versions found across matching cache entries.
+ *
+ * Note that we do not guarantee that the cache entry for these versions of CodeQL will still be
+ * present by the time we attempt to restore the cache. We could achieve that with a download retry
+ * loop, but we expect that if there is sufficient Actions cache contention that an overlay-base
+ * cache entry for a particular CodeQL version is evicted before we can use it, then it is likely
+ * that the same thing will happen to other overlay-base cache entries, and therefore we will not be
+ * able to use overlay.
+ *
+ * @returns Unique stable CodeQL versions found in cached overlay-base databases, sorted from latest to
+ * earliest, or undefined if one of the languages is not a built-in language.
+ */
+export async function getCodeQlVersionsForOverlayBaseDatabases(
+  rawLanguages: string[],
+  logger: Logger,
+): Promise<string[] | undefined> {
+  const languages = rawLanguages.map(parseBuiltInLanguage);
+  if (languages.includes(undefined)) {
+    logger.warning(
+      "One or more provided languages are not recognized as built-in languages. " +
+        "Skipping searching for overlay-base databases in cache.",
+    );
+    return undefined;
+  }
+  const dedupedLanguages = [
+    ...new Set(languages.filter((l) => l !== undefined)),
+  ];
+  const cacheKeyPrefix = await getCacheKeyPrefixBase(dedupedLanguages);
+
+  logger.debug(
+    `Searching for overlay-base databases in Actions cache with ` +
+      `prefix ${cacheKeyPrefix}`,
+  );
+
+  const caches = await listActionsCaches(cacheKeyPrefix);
+
+  if (caches.length === 0) {
+    logger.info("No overlay-base databases found in Actions cache.");
+    return [];
+  }
+
+  logger.info(
+    `Found ${caches.length} overlay-base ` +
+      `${caches.length === 1 ? "database" : "databases"} in the Actions cache.`,
+  );
+
+  // Parse CodeQL versions from cache keys, matching only stable releases.
+  //
+  // After the prefix, the remaining key format starts with `${codeQlVersion}-`. Nightlies will have
+  // a suffix like `+202604201548` that will break the match.
+  //
+  // Caveat: this relies on the fact that we haven't released any CodeQL bundles with the
+  // `x.y.z-<pre-release>` semver format which does not interact well with the current overlay base
+  // DB cache key format.
+  const versionRegex = /^([\d.]+)-/;
+  const versionSet = new Set<string>();
+
+  for (const cache of caches) {
+    if (!cache.key) continue;
+    const suffix = cache.key.substring(cacheKeyPrefix.length);
+    const match = suffix.match(versionRegex);
+    if (match && semver.valid(match[1])) {
+      versionSet.add(match[1]);
+    }
+  }
+
+  if (versionSet.size === 0) {
+    logger.info(
+      "Could not parse any CodeQL versions from overlay-base database " +
+        "cache keys.",
+    );
+    return [];
+  }
+
+  const versions = [...versionSet].sort(semver.rcompare);
+
+  logger.info(
+    `Found overlay databases for the following CodeQL versions in the Actions cache: ${versions.join(", ")}`,
+  );
+
+  return versions;
 }
@@ -39,6 +39,15 @@ export enum OverlayDisabledReason {
  NotPullRequestOrDefaultBranch = "not-pull-request-or-default-branch",
  /** The top-level overlay analysis feature flag is not enabled. */
  OverallFeatureNotEnabled = "overall-feature-not-enabled",
+  /**
+   * Overlay analysis was selected for a pull request, but diff-informed
+   * analysis was not enabled for the run (for example, because the
+   * `DiffInformedQueries` feature flag is off, the GHES version is too old,
+   * or the PR diff ranges could not be computed). Overlay analysis has only
+   * been validated in combination with diff-informed analysis, so we fall
+   * back to a non-overlay analysis in this case.
+   */
+  DiffInformedAnalysisNotEnabled = "diff-informed-analysis-not-enabled",
  /** Overlay analysis was skipped because it previously failed with similar hardware resources. */
  SkippedDueToCachedStatus = "skipped-due-to-cached-status",
  /** Disk usage could not be determined during the overlay status check. */
@@ -117,7 +117,7 @@ async function run(startedAt: Date) {
  }
 }

-async function runWrapper() {
+export async function runWrapper() {
  const startedAt = new Date();
  const logger = getActionsLogger();
  try {
@@ -137,5 +137,3 @@ async function runWrapper() {
  }
  await checkForTimeout();
 }
-
-void runWrapper();
@@ -7,8 +7,10 @@ import {
  getRequiredInput,
  getTemporaryDirectory,
 } from "./actions-util";
+import { AnalysisKind, getAnalysisKinds } from "./analyses";
 import { getGitHubVersion } from "./api-client";
 import { CodeQL } from "./codeql";
+import { getRawLanguagesNoAutodetect } from "./config-utils";
 import { EnvVar } from "./environment";
 import { initFeatures } from "./feature-flags";
 import { initCodeQL } from "./init";
@@ -136,16 +138,22 @@ async function run(startedAt: Date): Promise<void> {
    if (statusReportBase !== undefined) {
      await sendStatusReport(statusReportBase);
    }
-    const codeQLDefaultVersionInfo = await features.getDefaultCliVersion(
-      gitHubVersion.type,
-    );
+    const codeQLDefaultVersionInfo =
+      await features.getEnabledDefaultCliVersions(gitHubVersion.type);
    toolsFeatureFlagsValid = codeQLDefaultVersionInfo.toolsFeatureFlagsValid;
+    const rawLanguages = getRawLanguagesNoAutodetect(
+      getOptionalInput("languages"),
+    );
+    const analysisKinds = await getAnalysisKinds(logger, features);
    const initCodeQLResult = await initCodeQL(
      getOptionalInput("tools"),
      apiDetails,
      getTemporaryDirectory(),
      gitHubVersion.type,
      codeQLDefaultVersionInfo,
+      rawLanguages,
+      analysisKinds.length === 1 &&
+        analysisKinds[0] === AnalysisKind.CodeScanning,
      features,
      logger,
    );
@@ -188,7 +196,7 @@ async function run(startedAt: Date): Promise<void> {
 }

 /** Run the action and catch any unhandled errors. */
-async function runWrapper(): Promise<void> {
+export async function runWrapper(): Promise<void> {
  const startedAt = new Date();
  const logger = getActionsLogger();
  try {
@@ -204,5 +212,3 @@ async function runWrapper(): Promise<void> {
  }
  await checkForTimeout();
 }
-
-void runWrapper();
@@ -7,8 +7,9 @@ import * as sinon from "sinon";

 import * as actionsUtil from "./actions-util";
 import * as api from "./api-client";
-import { Feature, FeatureEnablement } from "./feature-flags";
+import { Feature } from "./feature-flags";
 import { getRunnerLogger } from "./logging";
+import { getCacheRestoreKeyPrefix } from "./overlay/caching";
 import * as setupCodeql from "./setup-codeql";
 import * as tar from "./tar";
 import {
@@ -18,8 +19,9 @@ import {
  SAMPLE_DOTCOM_API_DETAILS,
  checkExpectedLogMessages,
  createFeatures,
+  createTestConfig,
  getRecordingLogger,
-  initializeFeatures,
+  makeMacro,
  mockBundleDownloadApi,
  setupActionsVars,
  setupTests,
@@ -33,14 +35,6 @@ import {

 setupTests(test);

-// TODO: Remove when when we no longer need to pass in features (https://github.com/github/codeql-action/issues/2600)
-const expectedFeatureEnablement: FeatureEnablement = initializeFeatures(
-  true,
-) as FeatureEnablement;
-expectedFeatureEnablement.getValue = function (feature: Feature) {
-  // eslint-disable-next-line @typescript-eslint/no-unsafe-return
-  return expectedFeatureEnablement[feature];
-};
 test.beforeEach(() => {
  initializeEnvironment("1.2.3");
 });
@@ -107,6 +101,8 @@ test.serial(
      const source = await setupCodeql.getCodeQLSource(
        `https://github.com/github/codeql-action/releases/download/${tagName}/codeql-bundle-linux64.tar.gz`,
        SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        SAMPLE_DOTCOM_API_DETAILS,
        GitHubVariant.DOTCOM,
        false,
@@ -130,6 +126,8 @@ test.serial(
      const source = await setupCodeql.getCodeQLSource(
        "linked",
        SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        SAMPLE_DOTCOM_API_DETAILS,
        GitHubVariant.DOTCOM,
        false,
@@ -155,6 +153,8 @@ test.serial(
      const source = await setupCodeql.getCodeQLSource(
        "latest",
        SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        SAMPLE_DOTCOM_API_DETAILS,
        GitHubVariant.DOTCOM,
        false,
@@ -211,6 +211,8 @@ test.serial(
        "tmp/codeql_action_test/",
        GitHubVariant.DOTCOM,
        SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        features,
        logger,
      );
@@ -266,6 +268,8 @@ test.serial(
        "tmp/codeql_action_test/",
        GitHubVariant.DOTCOM,
        SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        features,
        logger,
      );
@@ -317,6 +321,8 @@ test.serial(
      const source = await setupCodeql.getCodeQLSource(
        "nightly",
        SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        SAMPLE_DOTCOM_API_DETAILS,
        GitHubVariant.DOTCOM,
        false,
@@ -378,6 +384,8 @@ test.serial(
      const source = await setupCodeql.getCodeQLSource(
        undefined,
        SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        SAMPLE_DOTCOM_API_DETAILS,
        GitHubVariant.DOTCOM,
        false,
@@ -432,6 +440,8 @@ test.serial(
      const source = await setupCodeql.getCodeQLSource(
        "toolcache",
        SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        SAMPLE_DOTCOM_API_DETAILS,
        GitHubVariant.DOTCOM,
        false,
@@ -473,7 +483,7 @@ test.serial(
  },
 );

-const toolcacheInputFallbackMacro = test.macro({
+const toolcacheInputFallbackMacro = makeMacro({
  exec: async (
    t: ExecutionContext<unknown>,
    featureList: Feature[],
@@ -499,6 +509,8 @@ const toolcacheInputFallbackMacro = test.macro({
      const source = await setupCodeql.getCodeQLSource(
        "toolcache",
        SAMPLE_DEFAULT_CLI_VERSION,
+        undefined, // rawLanguages
+        false, // useOverlayAwareDefaultCliVersion
        SAMPLE_DOTCOM_API_DETAILS,
        GitHubVariant.DOTCOM,
        false,
@@ -514,7 +526,10 @@ const toolcacheInputFallbackMacro = test.macro({

      // Check that `sourceType` and `toolsVersion` match expectations.
      t.is(source.sourceType, "download");
-      t.is(source.toolsVersion, SAMPLE_DEFAULT_CLI_VERSION.cliVersion);
+      t.is(
+        source.toolsVersion,
+        SAMPLE_DEFAULT_CLI_VERSION.enabledVersions[0].cliVersion,
+      );

      // Check that key messages we would expect to find in the log are present.
      for (const expectedMessage of expectedMessages) {
@@ -533,9 +548,8 @@ const toolcacheInputFallbackMacro = test.macro({
    `getCodeQLSource falls back to downloading the CLI if ${providedTitle}`,
 });

-test.serial(
+toolcacheInputFallbackMacro.serial(
  "the toolcache doesn't have a CodeQL CLI when tools == toolcache",
-  toolcacheInputFallbackMacro,
  [Feature.AllowToolcacheInput],
  { GITHUB_EVENT_NAME: "dynamic" },
  [],
@@ -545,9 +559,8 @@ test.serial(
  ],
 );

-test.serial(
+toolcacheInputFallbackMacro.serial(
  "the workflow trigger is not `dynamic`",
-  toolcacheInputFallbackMacro,
  [Feature.AllowToolcacheInput],
  { GITHUB_EVENT_NAME: "pull_request" },
  [],
@@ -556,9 +569,8 @@ test.serial(
  ],
 );

-test.serial(
+toolcacheInputFallbackMacro.serial(
  "the feature flag is not enabled",
-  toolcacheInputFallbackMacro,
  [],
  { GITHUB_EVENT_NAME: "dynamic" },
  [],
@@ -598,3 +610,288 @@ test.serial(
    t.is(setupCodeql.getLatestToolcacheVersion(getRunnerLogger(true)), "3.2.1");
  },
 );
+
+const overlayMatchEnabledVersions = {
+  enabledVersions: [
+    { cliVersion: "2.20.2", tagName: "codeql-bundle-v2.20.2" },
+    { cliVersion: "2.20.1", tagName: "codeql-bundle-v2.20.1" },
+    { cliVersion: "2.20.0", tagName: "codeql-bundle-v2.20.0" },
+  ],
+  toolsFeatureFlagsValid: true,
+};
+
+async function fakeOverlayBaseCacheKey(
+  language: string,
+  cliVersion: string,
+  suffix: string,
+): Promise<string> {
+  const prefix = await getCacheRestoreKeyPrefix(
+    createTestConfig({ languages: [language] }),
+    cliVersion,
+  );
+  return `${prefix}${suffix}`;
+}
+
+test.serial(
+  "getCodeQLSource uses overlay-aware default version when requested for a PR",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      process.env["CODE_SCANNING_REF"] = "refs/heads/feature-branch";
+      process.env["CODE_SCANNING_BASE_BRANCH"] = "main";
+
+      sinon.stub(api, "getAutomationID").resolves("test/");
+      const listStub = sinon.stub(api, "listActionsCaches").resolves([
+        {
+          key: await fakeOverlayBaseCacheKey("javascript", "2.20.1", "abc-1-1"),
+        },
+      ]);
+      sinon
+        .stub(toolcache, "find")
+        .withArgs("CodeQL", "2.20.1")
+        .returns("/path/to/codeql-2.20.1");
+
+      const source = await setupCodeql.getCodeQLSource(
+        undefined,
+        overlayMatchEnabledVersions,
+        ["javascript"],
+        true,
+        SAMPLE_DOTCOM_API_DETAILS,
+        GitHubVariant.DOTCOM,
+        false,
+        createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+        getRunnerLogger(true),
+      );
+
+      t.assert(listStub.calledOnce);
+      t.is(source.sourceType, "toolcache");
+      t.is(source.toolsVersion, "2.20.1");
+    });
+  },
+);
+
+test.serial(
+  "getCodeQLSource skips overlay-aware default version when not requested",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      process.env["CODE_SCANNING_REF"] = "refs/heads/feature-branch";
+      process.env["CODE_SCANNING_BASE_BRANCH"] = "main";
+
+      sinon.stub(api, "getAutomationID").resolves("test/");
+      const listStub = sinon.stub(api, "listActionsCaches").resolves([
+        {
+          key: await fakeOverlayBaseCacheKey("javascript", "2.20.1", "abc-1-1"),
+        },
+      ]);
+      sinon
+        .stub(toolcache, "find")
+        .withArgs("CodeQL", "2.20.2")
+        .returns("/path/to/codeql-2.20.2");
+
+      const source = await setupCodeql.getCodeQLSource(
+        undefined,
+        overlayMatchEnabledVersions,
+        ["javascript"],
+        false,
+        SAMPLE_DOTCOM_API_DETAILS,
+        GitHubVariant.DOTCOM,
+        false,
+        createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+        getRunnerLogger(true),
+      );
+
+      t.assert(listStub.notCalled);
+      t.is(source.sourceType, "toolcache");
+      t.is(source.toolsVersion, "2.20.2");
+    });
+  },
+);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases returns flag-enabled versions present in cache, sorted desc",
+  async (t) => {
+    sinon.stub(api, "getAutomationID").resolves("test/");
+    sinon.stub(api, "listActionsCaches").resolves([
+      // Flag-enabled versions present in the cache, listed in non-descending
+      // order so the test exercises the sort.
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.20.0", "ghi-3-1"),
+      },
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.20.1", "def-2-1"),
+      },
+      // Newer than any flag-enabled version: should be filtered out.
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.21.0", "abc-1-1"),
+      },
+    ]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, [
+      { cliVersion: "2.20.1", tagName: "codeql-bundle-v2.20.1" },
+      { cliVersion: "2.20.0", tagName: "codeql-bundle-v2.20.0" },
+    ]);
+  },
+);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases returns empty when no cached version is flag-enabled",
+  async (t) => {
+    sinon.stub(api, "getAutomationID").resolves("test/");
+    sinon.stub(api, "listActionsCaches").resolves([
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.19.0", "abc-1-1"),
+      },
+    ]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, []);
+  },
+);
+
+const noLanguagesMacro = makeMacro({
+  exec: async (
+    t: ExecutionContext<unknown>,
+    rawLanguages: string[] | undefined,
+  ) => {
+    const listStub = sinon.stub(api, "listActionsCaches").resolves([]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      rawLanguages,
+      createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, []);
+    t.assert(
+      listStub.notCalled,
+      "Should not list Actions caches without any rawLanguages.",
+    );
+  },
+  title: (providedTitle = "") =>
+    `getEnabledVersionsWithOverlayBaseDatabases does not list caches when rawLanguages is ${providedTitle}`,
+});
+
+noLanguagesMacro.serial("undefined", undefined);
+noLanguagesMacro.serial("an empty array", []);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases returns empty when listing caches throws",
+  async (t) => {
+    sinon.stub(api, "getAutomationID").resolves("test/");
+    sinon.stub(api, "listActionsCaches").rejects(new Error("listing failed"));
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, []);
+  },
+);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases returns versions present in the cache",
+  async (t) => {
+    sinon.stub(api, "getAutomationID").resolves("test/");
+    sinon.stub(api, "listActionsCaches").resolves([
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.20.2", "abc-1-1"),
+      },
+    ]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([Feature.OverlayAnalysisMatchCodeqlVersion]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, [
+      { cliVersion: "2.20.2", tagName: "codeql-bundle-v2.20.2" },
+    ]);
+  },
+);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases does not list caches when both gates are off",
+  async (t) => {
+    const listStub = sinon.stub(api, "listActionsCaches").resolves([]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, []);
+    t.assert(
+      listStub.notCalled,
+      "Should not list Actions caches when both gating feature flags are off.",
+    );
+  },
+);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases dry-run returns empty but lists caches",
+  async (t) => {
+    sinon.stub(api, "getAutomationID").resolves("test/");
+    const listStub = sinon.stub(api, "listActionsCaches").resolves([
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.20.1", "abc-1-1"),
+      },
+    ]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([Feature.OverlayAnalysisMatchCodeqlVersionDryRun]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(
+      result,
+      [],
+      "Dry-run should return an empty list so the caller falls back.",
+    );
+    t.assert(
+      listStub.calledOnce,
+      "Dry-run should still list Actions caches to populate the diagnostic.",
+    );
+  },
+);
+
+test.serial(
+  "getEnabledVersionsWithOverlayBaseDatabases match flag wins over dry-run",
+  async (t) => {
+    sinon.stub(api, "getAutomationID").resolves("test/");
+    sinon.stub(api, "listActionsCaches").resolves([
+      {
+        key: await fakeOverlayBaseCacheKey("javascript", "2.20.1", "abc-1-1"),
+      },
+    ]);
+
+    const result = await setupCodeql.getEnabledVersionsWithOverlayBaseDatabases(
+      overlayMatchEnabledVersions,
+      ["javascript"],
+      createFeatures([
+        Feature.OverlayAnalysisMatchCodeqlVersion,
+        Feature.OverlayAnalysisMatchCodeqlVersionDryRun,
+      ]),
+      getRunnerLogger(true),
+    );
+    t.deepEqual(result, [
+      { cliVersion: "2.20.1", tagName: "codeql-bundle-v2.20.1" },
+    ]);
+  },
+);
@@ -7,17 +7,27 @@ import { default as deepEqual } from "fast-deep-equal";
 import * as semver from "semver";
 import { v4 as uuidV4 } from "uuid";

-import { isDynamicWorkflow, isRunningLocalAction } from "./actions-util";
+import {
+  isAnalyzingPullRequest,
+  isDynamicWorkflow,
+  isRunningLocalAction,
+} from "./actions-util";
 import * as api from "./api-client";
 import * as defaults from "./defaults.json";
-import { addNoLanguageDiagnostic, makeDiagnostic } from "./diagnostics";
+import {
+  addNoLanguageDiagnostic,
+  makeDiagnostic,
+  makeTelemetryDiagnostic,
+} from "./diagnostics";
 import {
  CODEQL_VERSION_ZSTD_BUNDLE,
  CodeQLDefaultVersionInfo,
+  CodeQLVersionInfo,
  Feature,
  FeatureEnablement,
 } from "./feature-flags";
 import { Logger } from "./logging";
+import { getCodeQlVersionsForOverlayBaseDatabases } from "./overlay/caching";
 import * as tar from "./tar";
 import {
  downloadAndExtract,
@@ -264,12 +274,131 @@ async function findOverridingToolsInCache(
  return undefined;
 }

+/**
+ * Returns the sorted set of enabled versions that have cached overlay-base databases for the
+ * given languages, or an empty list if neither the `OverlayAnalysisMatchCodeqlVersion` nor the
+ * `OverlayAnalysisMatchCodeqlVersionDryRun` feature flag is enabled. When only the dry-run flag
+ * is enabled, this performs the lookup and emits a telemetry diagnostic with the version that
+ * would have been chosen, but still returns an empty list so the caller falls back.
+ */
+export async function getEnabledVersionsWithOverlayBaseDatabases(
+  defaultCliVersion: CodeQLDefaultVersionInfo,
+  rawLanguages: string[] | undefined,
+  features: FeatureEnablement,
+  logger: Logger,
+): Promise<CodeQLVersionInfo[]> {
+  if (rawLanguages === undefined || rawLanguages.length === 0) {
+    return [];
+  }
+  const isEnabled = await features.getValue(
+    Feature.OverlayAnalysisMatchCodeqlVersion,
+  );
+  const isDryRun =
+    !isEnabled &&
+    (await features.getValue(Feature.OverlayAnalysisMatchCodeqlVersionDryRun));
+  if (!isEnabled && !isDryRun) {
+    return [];
+  }
+
+  let cachedVersions: string[] | undefined;
+  try {
+    cachedVersions = await getCodeQlVersionsForOverlayBaseDatabases(
+      rawLanguages,
+      logger,
+    );
+  } catch (e) {
+    logger.warning(
+      "Could not list overlay-base databases in the Actions cache while choosing a default " +
+        `CodeQL CLI version, falling back to the highest enabled version. Details: ${util.getErrorMessage(e)}`,
+    );
+    return [];
+  }
+
+  if (cachedVersions === undefined || cachedVersions.length === 0) {
+    return [];
+  }
+
+  const cachedVersionsSet = new Set(cachedVersions);
+  const overlayVersions = defaultCliVersion.enabledVersions.filter((v) =>
+    cachedVersionsSet.has(v.cliVersion),
+  );
+
+  if (overlayVersions.length === 0) {
+    return [];
+  }
+
+  const isCachedVersionDifferent =
+    overlayVersions[0].cliVersion !==
+    defaultCliVersion.enabledVersions[0].cliVersion;
+
+  if (isCachedVersionDifferent) {
+    addNoLanguageDiagnostic(
+      undefined,
+      makeTelemetryDiagnostic(
+        "codeql-action/overlay-aware-default-codeql-version",
+        "Overlay-aware default CodeQL version selection",
+        {
+          cachedVersions,
+          enabledVersions: defaultCliVersion.enabledVersions.map(
+            (v) => v.cliVersion,
+          ),
+          isDryRun,
+          overlayAwareVersion: overlayVersions[0].cliVersion,
+        },
+      ),
+    );
+  }
+
+  if (isDryRun) {
+    logger.debug(
+      `Overlay-aware default CodeQL version selection is running in dry-run mode. Would have used version ${overlayVersions[0].cliVersion}.`,
+    );
+    return [];
+  }
+
+  return overlayVersions;
+}
+
+/**
+ * Resolves the newest enabled default CLI version that has a cached overlay-base database for the
+ * relevant languages, if running a Code Scanning analysis for a pull request and one exists.
+ * Otherwise, falls back to the newest enabled default CLI version.
+ */
+async function resolveDefaultCliVersion(
+  defaultCliVersion: CodeQLDefaultVersionInfo,
+  rawLanguages: string[] | undefined,
+  useOverlayAwareDefaultCliVersion: boolean,
+  features: FeatureEnablement,
+  logger: Logger,
+): Promise<CodeQLVersionInfo> {
+  if (!useOverlayAwareDefaultCliVersion || !isAnalyzingPullRequest()) {
+    return defaultCliVersion.enabledVersions[0];
+  }
+
+  const overlayVersions = await getEnabledVersionsWithOverlayBaseDatabases(
+    defaultCliVersion,
+    rawLanguages,
+    features,
+    logger,
+  );
+  if (overlayVersions.length > 0) {
+    logger.info(
+      `Using CodeQL version ${overlayVersions[0].cliVersion} since this is the ` +
+        `highest enabled version that has a cached overlay-base database.`,
+    );
+    return overlayVersions[0];
+  }
+  return defaultCliVersion.enabledVersions[0];
+}
+
 /**
 * Determines where the CodeQL CLI we want to use comes from. This can be from a local file,
 * the Actions toolcache, or a download.
 *
 * @param toolsInput The argument provided for the `tools` input, if any.
 * @param defaultCliVersion The default CLI version that's linked to the CodeQL Action.
+ * @param rawLanguages Raw set of languages.
+ * @param useOverlayAwareDefaultCliVersion Whether to select an overlay-aware default CLI version.
 * @param apiDetails Information about the GitHub API.
 * @param variant The GitHub variant we are running on.
 * @param tarSupportsZstd Whether zstd is supported by `tar`.
@@ -281,6 +410,8 @@ async function findOverridingToolsInCache(
 export async function getCodeQLSource(
  toolsInput: string | undefined,
  defaultCliVersion: CodeQLDefaultVersionInfo,
+  rawLanguages: string[] | undefined,
+  useOverlayAwareDefaultCliVersion: boolean,
  apiDetails: api.GitHubApiDetails,
  variant: util.GitHubVariant,
  tarSupportsZstd: boolean,
@@ -438,8 +569,15 @@ export async function getCodeQLSource(
        }
      }

-      cliVersion = defaultCliVersion.cliVersion;
-      tagName = defaultCliVersion.tagName;
+      const version = await resolveDefaultCliVersion(
+        defaultCliVersion,
+        rawLanguages,
+        useOverlayAwareDefaultCliVersion,
+        features,
+        logger,
+      );
+      cliVersion = version.cliVersion;
+      tagName = version.tagName;
    }
  } else if (toolsInput !== undefined) {
    // If a tools URL was provided, then use that.
@@ -454,9 +592,15 @@ export async function getCodeQLSource(
      }
    }
  } else {
-    // Otherwise, use the default CLI version passed in.
-    cliVersion = defaultCliVersion.cliVersion;
-    tagName = defaultCliVersion.tagName;
+    const version = await resolveDefaultCliVersion(
+      defaultCliVersion,
+      rawLanguages,
+      useOverlayAwareDefaultCliVersion,
+      features,
+      logger,
+    );
+    cliVersion = version.cliVersion;
+    tagName = version.tagName;
  }

  const bundleVersion =
@@ -791,6 +935,8 @@ export async function setupCodeQLBundle(
  tempDir: string,
  variant: util.GitHubVariant,
  defaultCliVersion: CodeQLDefaultVersionInfo,
+  rawLanguages: string[] | undefined,
+  useOverlayAwareDefaultCliVersion: boolean,
  features: FeatureEnablement,
  logger: Logger,
 ): Promise<SetupCodeQLResult> {
@@ -804,6 +950,8 @@ export async function setupCodeQLBundle(
  const source = await getCodeQLSource(
    toolsInput,
    defaultCliVersion,
+    rawLanguages,
+    useOverlayAwareDefaultCliVersion,
    apiDetails,
    variant,
    zstdAvailability.available,
--- a/Show More
+++ b/Show More