Default to StartProxyRemoveUnusedRegistries behaviour

Merge pull request #3894 from github/henrymercer/require-codeql-2.19.4
Bump minimum CodeQL CLI version to 2.19.4
2026-05-24 16:14:33 +00:00 · 2026-05-18 16:17:15 +01:00 · 2026-05-18 14:55:40 +00:00 · 2026-05-18 14:27:03 +01:00 · 2026-05-15 18:13:43 +01:00 · 2026-05-15 14:58:30 +00:00
148 changed files with 77668 additions and 1370735 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"
@@ -16,12 +16,23 @@ No user facing changes.
 """

 # NB: This exact commit message is used to find commits for reverting during backports.
-# Changing it requires a transition period where both old and new versions are supported.
+# Changing it requires a transition period where both old and new versions are supported.
 BACKPORT_COMMIT_MESSAGE = 'Update version and changelog for v'

 # Name of the remote
 ORIGIN = 'origin'

+# Environment variables to check for a GitHub API token.
+TOKEN_ENVIRONMENT_VARIABLES = ('GH_TOKEN', 'GITHUB_TOKEN')
+
+# Gets a GitHub API token from one of the supported environment variables.
+def get_github_token():
+  for variable_name in TOKEN_ENVIRONMENT_VARIABLES:
+    token = os.environ.get(variable_name, '').strip()
+    if token:
+      return token
+  raise Exception('Missing GitHub token. Set GITHUB_TOKEN or GH_TOKEN.')
+
 # Runs git with the given args and returns the stdout.
 # Raises an error if git does not exit successfully (unless passed
 # allow_non_zero_exit_code=True).
@@ -270,12 +281,6 @@ def update_changelog(version):
 def main():
  parser = argparse.ArgumentParser('update-release-branch.py')

-  parser.add_argument(
-    '--github-token',
-    type=str,
-    required=True,
-    help='GitHub token, typically from GitHub Actions.'
-  )
  parser.add_argument(
    '--repository-nwo',
    type=str,
@@ -313,7 +318,7 @@ def main():
  target_branch = args.target_branch
  is_primary_release = args.is_primary_release

-  repo = Github(args.github_token).get_repo(args.repository_nwo)
+  repo = Github(get_github_token()).get_repo(args.repository_nwo)

  # the target branch will be of the form releases/vN, where N is the major version number
  target_branch_major_version = target_branch.strip('releases/v')
@@ -49,10 +49,6 @@ jobs:
      fail-fast: false
      matrix:
        include:
-          - os: ubuntu-latest
-            version: stable-v2.17.6
-          - os: ubuntu-latest
-            version: stable-v2.18.4
          - os: ubuntu-latest
            version: stable-v2.19.4
          - os: ubuntu-latest
@@ -61,6 +57,10 @@ jobs:
            version: stable-v2.21.4
          - os: ubuntu-latest
            version: stable-v2.22.4
+          - os: ubuntu-latest
+            version: stable-v2.23.9
+          - os: ubuntu-latest
+            version: stable-v2.24.3
          - os: ubuntu-latest
            version: default
          - os: ubuntu-latest
@@ -49,10 +49,6 @@ jobs:
      fail-fast: false
      matrix:
        include:
-          - os: ubuntu-latest
-            version: stable-v2.17.6
-          - os: ubuntu-latest
-            version: stable-v2.18.4
          - os: ubuntu-latest
            version: stable-v2.19.4
          - os: ubuntu-latest
@@ -61,6 +57,10 @@ jobs:
            version: stable-v2.21.4
          - os: ubuntu-latest
            version: stable-v2.22.4
+          - os: ubuntu-latest
+            version: stable-v2.23.9
+          - os: ubuntu-latest
+            version: stable-v2.24.3
          - os: ubuntu-latest
            version: default
          - os: ubuntu-latest
@@ -49,10 +49,6 @@ jobs:
      fail-fast: false
      matrix:
        include:
-          - os: ubuntu-latest
-            version: stable-v2.17.6
-          - os: ubuntu-latest
-            version: stable-v2.18.4
          - os: ubuntu-latest
            version: stable-v2.19.4
          - os: ubuntu-latest
@@ -61,6 +57,10 @@ jobs:
            version: stable-v2.21.4
          - os: ubuntu-latest
            version: stable-v2.22.4
+          - os: ubuntu-latest
+            version: stable-v2.23.9
+          - os: ubuntu-latest
+            version: stable-v2.24.3
          - os: ubuntu-latest
            version: default
          - os: ubuntu-latest
@@ -59,41 +59,41 @@ jobs:
      fail-fast: false
      matrix:
        include:
-          - os: ubuntu-latest
-            version: stable-v2.17.6
-          - os: macos-latest
-            version: stable-v2.17.6
-          - os: ubuntu-latest
-            version: stable-v2.18.4
-          - os: macos-latest
-            version: stable-v2.18.4
          - os: ubuntu-latest
            version: stable-v2.19.4
-          - os: macos-latest
+          - os: macos-latest-xlarge
            version: stable-v2.19.4
          - os: ubuntu-latest
            version: stable-v2.20.7
-          - os: macos-latest
+          - os: macos-latest-xlarge
            version: stable-v2.20.7
          - os: ubuntu-latest
            version: stable-v2.21.4
-          - os: macos-latest
+          - os: macos-latest-xlarge
            version: stable-v2.21.4
          - os: ubuntu-latest
            version: stable-v2.22.4
-          - os: macos-latest
+          - os: macos-latest-xlarge
            version: stable-v2.22.4
+          - os: ubuntu-latest
+            version: stable-v2.23.9
+          - os: macos-latest-xlarge
+            version: stable-v2.23.9
+          - os: ubuntu-latest
+            version: stable-v2.24.3
+          - os: macos-latest-xlarge
+            version: stable-v2.24.3
          - os: ubuntu-latest
            version: default
-          - os: macos-latest
+          - os: macos-latest-xlarge
            version: default
          - os: ubuntu-latest
            version: linked
-          - os: macos-latest
+          - os: macos-latest-xlarge
            version: linked
          - os: ubuntu-latest
            version: nightly-latest
-          - os: macos-latest
+          - os: macos-latest-xlarge
            version: nightly-latest
    name: Multi-language repository
    if: github.triggering_actor != 'dependabot[bot]'
@@ -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
@@ -40,7 +40,7 @@ jobs:
      matrix:
        include:
          - os: ubuntu-latest
-            version: stable-v2.19.3
+            version: stable-v2.19.4
          - os: ubuntu-latest
            version: stable-v2.22.1
          - os: ubuntu-latest
@@ -39,7 +39,7 @@ jobs:
      fail-fast: false
      matrix:
        include:
-          - os: macos-latest
+          - os: macos-latest-xlarge
            version: nightly-latest
    name: Swift analysis using autobuild
    if: github.triggering_actor != 'dependabot[bot]'
@@ -77,7 +77,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        os: [ubuntu-22.04,ubuntu-24.04,windows-2022,windows-2025,macos-14,macos-15]
+        os: [ubuntu-22.04,ubuntu-24.04,windows-2022,windows-2025,macos-14-xlarge,macos-15-xlarge]
        tools: ${{ fromJson(needs.check-codeql-versions.outputs.versions) }}
    runs-on: ${{ matrix.os }}

@@ -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
@@ -64,11 +64,12 @@ jobs:

    - name: Update current release branch
      if: github.event_name == 'workflow_dispatch'
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      run: |
        echo SOURCE_BRANCH=${REF_NAME}
        echo TARGET_BRANCH=releases/${MAJOR_VERSION}
        python .github/update-release-branch.py \
-          --github-token ${{ secrets.GITHUB_TOKEN }} \
          --repository-nwo ${{ github.repository }} \
          --source-branch '${{ env.REF_NAME }}' \
          --target-branch 'releases/${{ env.MAJOR_VERSION }}' \
@@ -93,7 +94,7 @@ 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 }}
@@ -107,11 +108,12 @@ jobs:
    - uses: ./.github/actions/release-initialise

    - name: Update older release branch
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      run: |
        echo SOURCE_BRANCH=${SOURCE_BRANCH}
        echo TARGET_BRANCH=${TARGET_BRANCH}
        python .github/update-release-branch.py \
-          --github-token ${{ secrets.GITHUB_TOKEN }} \
          --repository-nwo ${{ github.repository }} \
          --source-branch ${SOURCE_BRANCH} \
          --target-branch ${TARGET_BRANCH} \
@@ -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}`,",
@@ -2,6 +2,30 @@

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

+## [UNRELEASED]
+
+- _Breaking change_: Bump the minimum required CodeQL bundle version to 2.19.4. [#3894](https://github.com/github/codeql-action/pull/3894)
+- Add support for SHA-256 Git object IDs. [#3893](https://github.com/github/codeql-action/pull/3893)
+
+## 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)
@@ -71,7 +71,7 @@ Once the mergeback and backport pull request have been merged, the release is co

 Since the `codeql-action` runs most of its testing through individual Actions workflows, there are over two hundred required jobs that need to pass in order for a PR to turn green. It would be too tedious to maintain that list manually. You can regenerate the set of required checks automatically by running the [sync-checks.ts](pr-checks/sync-checks.ts) script:

- At a minimum, you must provide an argument for the `--token` input. For example, `--token "$(gh auth token)"` to use the same token that `gh` uses. If no token is provided or the token has insufficient permissions, the script will fail.
+- At a minimum, you must provide a token with permissions to update branch protection rules. For example, `gh auth token | pr-checks/sync-checks.ts --token-stdin` uses the same token that `gh` uses. You can also set the `GH_TOKEN` or `GITHUB_TOKEN` environment variable. If no token is provided or the token has insufficient permissions, the script will fail.
 - By default, the script performs a dry run and outputs information about the changes it would make to the branch protection rules. To actually apply the changes, specify the `--apply` flag.
 - If you run the script without any other arguments, it will retrieve the set of workflows that ran for the latest commit on `main`.
 - You can specify a different git ref with the `--ref` input. You will likely want to use this if you have a PR that removes or adds PR checks. For example, `--ref "some/branch/name"` to use the HEAD of the `some/branch/name` branch.
@@ -72,13 +72,12 @@ 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 | |
 | `v3.28.12` | `2.20.7` | Enterprise Server 3.17 | |
 | `v3.28.6` | `2.20.3` | Enterprise Server 3.16 | |
-| `v3.28.6` | `2.20.3` | Enterprise Server 3.15 | |
-| `v3.28.6` | `2.20.3` | Enterprise Server 3.14 | |

 See the full list of GHES release and deprecation dates at [GitHub Enterprise Server releases](https://docs.github.com/en/enterprise-server/admin/all-releases#releases-of-github-enterprise-server).

@@ -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 identified 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-v2.25.2",
-  "cliVersion": "2.25.2",
-  "priorBundleVersion": "codeql-bundle-v2.25.1",
-  "priorCliVersion": "2.25.1"
+  "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 +1,19 @@
 {
  "name": "codeql",
-  "version": "4.35.2",
+  "version": "4.36.0",
  "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",
+    "update-pr-checks": "./pr-checks/sync.sh"
  },
  "license": "MIT",
  "workspaces": [
@@ -32,7 +33,7 @@
    "@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 +41,35 @@
    "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": "^22.0.0",
+    "typescript": "^6.0.3",
+    "typescript-eslint": "^8.59.2"
  },
  "overrides": {
    "@actions/tool-cache": {
@@ -89,7 +90,7 @@
    "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"
  }
 }
@@ -2,7 +2,8 @@ name: "Multi-language repository"
 description: "An end-to-end integration test of a multi-language repository using automatic language detection"
 operatingSystems:
  - ubuntu
-  - macos
+  - os: macos
+    runner-image: macos-latest-xlarge
 env:
  CODEQL_ACTION_RESOLVE_SUPPORTED_LANGUAGES_USING_CLI: true
 installGo: true
@@ -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
@@ -2,7 +2,7 @@ name: "Rust analysis"
 description: "Tests creation of a Rust database"
 versions:
  # experimental rust support introduced, requires action to set `CODEQL_ENABLE_EXPERIMENTAL_FEATURES`
-  - stable-v2.19.3
+  - stable-v2.19.4
  # first public preview version
  - stable-v2.22.1
  - linked
@@ -3,7 +3,8 @@ description: "Tests creation of a Swift database using autobuild"
 versions:
  - nightly-latest
 operatingSystems:
-  - macos
+  - os: macos
+    runner-image: macos-latest-xlarge
 steps:
  - uses: ./../action/init
    id: init
@@ -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"
  }
 }
@@ -7,7 +7,13 @@ Tests for the sync-checks.ts script
 import * as assert from "node:assert/strict";
 import { describe, it } from "node:test";

-import { CheckInfo, Exclusions, Options, removeExcluded } from "./sync-checks";
+import {
+  CheckInfo,
+  Exclusions,
+  Options,
+  removeExcluded,
+  resolveToken,
+} from "./sync-checks";

 const defaultOptions: Options = {
  apply: false,
@@ -58,3 +64,46 @@ describe("removeExcluded", async () => {
    assert.deepEqual(retained, expectedExactMatches);
  });
 });
+
+describe("resolveToken", async () => {
+  await it("reads the token from standard input", async () => {
+    const token = await resolveToken(
+      { tokenStdin: true },
+      { env: {}, readStdin: async () => " stdin-token\n" },
+    );
+    assert.equal(token, "stdin-token");
+  });
+
+  await it("reads the token from the GH_TOKEN environment variable", async () => {
+    const token = await resolveToken(
+      {},
+      { env: { GH_TOKEN: "env-token" }, readStdin: async () => "" },
+    );
+    assert.equal(token, "env-token");
+  });
+
+  await it("reads the token from the GITHUB_TOKEN environment variable", async () => {
+    const token = await resolveToken(
+      {},
+      { env: { GITHUB_TOKEN: "env-token" }, readStdin: async () => "" },
+    );
+    assert.equal(token, "env-token");
+  });
+
+  await it("rejects an empty standard input token", async () => {
+    await assert.rejects(
+      resolveToken(
+        { tokenStdin: true },
+        { env: {}, readStdin: async () => "\n" },
+      ),
+      /No token received on standard input/,
+    );
+  });
+
+  await it("rejects missing token sources", async () => {
+    await assert.rejects(
+      resolveToken({}, { env: {}, readStdin: async () => "" }),
+      /Missing authentication token/,
+    );
+  });
+});
@@ -15,8 +15,8 @@ import {

 /** Represents the command-line options. */
 export interface Options {
-  /** The token to use to authenticate to the GitHub API. */
-  token?: string;
+  /** Whether to read the GitHub API token from standard input. */
+  tokenStdin?: boolean;
  /** The git ref to use the checks for. */
  ref?: string;
  /** Whether to actually apply the changes or not. */
@@ -31,6 +31,65 @@ const codeqlActionRepo = {
  repo: "codeql-action",
 };

+/** Environment variables to check for a GitHub API token. */
+const TOKEN_ENVIRONMENT_VARIABLES = ["GH_TOKEN", "GITHUB_TOKEN"];
+
+/** Represents the sources from which we can retrieve the GitHub API token. */
+interface TokenSource {
+  /** Environment variables to inspect. */
+  env: NodeJS.ProcessEnv;
+  /** Reads a token from standard input. */
+  readStdin: () => Promise<string>;
+}
+
+/** Reads the GitHub API token from standard input. */
+async function readTokenFromStdin(): Promise<string> {
+  let token = "";
+  process.stdin.setEncoding("utf8");
+  for await (const chunk of process.stdin) {
+    token += chunk;
+  }
+  return token.trim();
+}
+
+/** Gets a GitHub API token from one of the supported environment variables. */
+function getTokenFromEnvironment(env: NodeJS.ProcessEnv): string | undefined {
+  for (const variableName of TOKEN_ENVIRONMENT_VARIABLES) {
+    const token = env[variableName]?.trim();
+    if (token) {
+      return token;
+    }
+  }
+  return undefined;
+}
+
+/** Gets the token to use to authenticate to the GitHub API. */
+export async function resolveToken(
+  options: Pick<Options, "tokenStdin">,
+  tokenSource: TokenSource = {
+    env: process.env,
+    readStdin: readTokenFromStdin,
+  },
+): Promise<string> {
+  if (options.tokenStdin) {
+    const token = (await tokenSource.readStdin()).trim();
+    if (token.length === 0) {
+      throw new Error("No token received on standard input.");
+    }
+    return token;
+  }
+
+  const environmentToken = getTokenFromEnvironment(tokenSource.env);
+  if (environmentToken !== undefined) {
+    return environmentToken;
+  }
+
+  throw new Error(
+    "Missing authentication token. Set GH_TOKEN/GITHUB_TOKEN or pipe a token " +
+      "to --token-stdin.",
+  );
+}
+
 /** Represents a configuration of which checks should not be set up as required checks. */
 export interface Exclusions {
  /** A list of strings that, if contained in a check name, are excluded. */
@@ -205,9 +264,10 @@ async function updateBranch(
 async function main(): Promise<void> {
  const { values: options } = parseArgs({
    options: {
-      // The token to use to authenticate to the API.
-      token: {
-        type: "string",
+      // Read the token to use to authenticate to the API from standard input.
+      "token-stdin": {
+        type: "boolean",
+        default: false,
      },
      // The git ref for which to retrieve the check runs.
      ref: {
@@ -228,16 +288,16 @@ async function main(): Promise<void> {
    strict: true,
  });

-  if (options.token === undefined) {
-    throw new Error("Missing --token");
-  }
+  const token = await resolveToken({
+    tokenStdin: options["token-stdin"],
+  });

  console.info(
    `Oldest supported major version is: ${OLDEST_SUPPORTED_MAJOR_VERSION}`,
  );

  // Initialise the API client.
-  const client = getApiClient(options.token);
+  const client = getApiClient(token);

  // Find the check runs for the specified `ref` that we will later set as the required checks
  // for the main and release branches.
@@ -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 {
@@ -28,6 +28,24 @@ interface WorkflowInput {
 /** A partial mapping from known input names to input definitions. */
 type WorkflowInputs = Partial<Record<KnownInputName, WorkflowInput>>;

+/** An operating system identifier. */
+type OperatingSystemIdentifier = "ubuntu" | "macos" | "windows";
+
+/**
+ * Represents an operating system matrix entry for a generated PR check workflow.
+ *
+ * Either a string containing the OS identifier or an object containing the OS identifier and an
+ * optional runner image label.
+ */
+type OperatingSystem =
+  | OperatingSystemIdentifier
+  | {
+      /** OS identifier. */
+      os: OperatingSystemIdentifier;
+      /** Optional runner image label. */
+      "runner-image"?: string;
+    };
+
 /**
 * Represents PR check specifications.
 */
@@ -36,8 +54,8 @@ interface Specification extends JobSpecification {
  inputs?: Record<string, WorkflowInput>;
  /** CodeQL bundle versions to test against. Defaults to `DEFAULT_TEST_VERSIONS`. */
  versions?: string[];
-  /** Operating system prefixes used to select runner images (e.g. `["ubuntu", "macos"]`). */
-  operatingSystems?: string[];
+  /** Operating system prefixes, either as strings or with explicit runner image labels. */
+  operatingSystems?: OperatingSystem[];
  /** Per-OS version overrides. If specified for an OS, only those versions are tested on that OS. */
  osCodeQlVersions?: Record<string, string[]>;
  /** Whether to use the all-platform CodeQL bundle. */
@@ -91,16 +109,12 @@ 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 = [
  // The oldest supported CodeQL version. If bumping, update `CODEQL_MINIMUM_VERSION` in `codeql.ts`
-  "stable-v2.17.6",
-  // The last CodeQL release in the 2.18 series.
-  "stable-v2.18.4",
-  // The last CodeQL release in the 2.19 series.
  "stable-v2.19.4",
  // The last CodeQL release in the 2.20 series.
  "stable-v2.20.7",
@@ -108,6 +122,10 @@ const defaultTestVersions = [
  "stable-v2.21.4",
  // The last CodeQL release in the 2.22 series.
  "stable-v2.22.4",
+  // The last CodeQL release in the 2.23 series.
+  "stable-v2.23.9",
+  // The last CodeQL release in the 2.24 series.
+  "stable-v2.24.3",
  // The default version of CodeQL for Dotcom, as determined by feature flags.
  "default",
  // The version of CodeQL shipped with the Action in `defaults.json`. During the release process
@@ -125,7 +143,7 @@ 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 = {
@@ -311,10 +329,19 @@ function generateJobMatrix(
      );
    }

-    const runnerImages = ["ubuntu-latest", "macos-latest", "windows-latest"];
+    const defaultRunnerImages = [
+      "ubuntu-latest",
+      "macos-latest",
+      "windows-latest",
+    ];
    const operatingSystems = checkSpecification.operatingSystems ?? ["ubuntu"];

-    for (const operatingSystem of operatingSystems) {
+    for (const operatingSystemConfig of operatingSystems) {
+      const operatingSystem =
+        typeof operatingSystemConfig === "string"
+          ? operatingSystemConfig
+          : operatingSystemConfig.os;
+
      // If osCodeQlVersions is set for this OS, only include the specified CodeQL versions.
      const allowedVersions =
        checkSpecification.osCodeQlVersions?.[operatingSystem];
@@ -322,9 +349,13 @@ function generateJobMatrix(
        continue;
      }

-      const runnerImagesForOs = runnerImages.filter((image) =>
-        image.startsWith(operatingSystem),
-      );
+      const runnerImagesForOs =
+        typeof operatingSystemConfig === "string" ||
+        operatingSystemConfig["runner-image"] === undefined
+          ? defaultRunnerImages.filter((image) =>
+              image.startsWith(operatingSystem),
+            )
+          : [operatingSystemConfig["runner-image"]];

      for (const runnerImage of runnerImagesForOs) {
        matrix.push({
@@ -364,7 +395,7 @@ 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;
@@ -1,90 +0,0 @@
-import test from "ava";
-import * as sinon from "sinon";
-
-import * as actionsUtil from "./actions-util";
-import * as analyze from "./analyze";
-import * as api from "./api-client";
-import * as configUtils from "./config-utils";
-import * as gitUtils from "./git-utils";
-import * as statusReport from "./status-report";
-import {
-  setupTests,
-  setupActionsVars,
-  mockFeatureFlagApiEndpoint,
-} from "./testing-utils";
-import * as util from "./util";
-
-setupTests(test);
-
-// This test needs to be in its own file so that ava would run it in its own
-// nodejs process. The code being tested is in analyze-action.ts, which runs
-// immediately on load. So the file needs to be loaded during part of the test,
-// and that can happen only once per nodejs process. If multiple such tests are
-// in the same test file, ava would run them in the same nodejs process, and all
-// but the first test would fail.
-
-test("analyze action with RAM & threads from environment variables", async (t) => {
-  // This test frequently times out on Windows with the default timeout, so we bump
-  // it a bit to 20s.
-  t.timeout(1000 * 20);
-  await util.withTmpDir(async (tmpDir) => {
-    setupActionsVars(tmpDir, tmpDir);
-    sinon
-      .stub(statusReport, "createStatusReportBase")
-      .resolves({} as statusReport.StatusReportBase);
-    sinon.stub(statusReport, "sendStatusReport").resolves();
-    sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);
-
-    const gitHubVersion: util.GitHubVersion = {
-      type: util.GitHubVariant.DOTCOM,
-    };
-    sinon.stub(configUtils, "getConfig").resolves({
-      gitHubVersion,
-      augmentationProperties: {},
-      languages: [],
-      packs: [],
-      trapCaches: {},
-    } as unknown as configUtils.Config);
-    const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
-    requiredInputStub.withArgs("token").returns("fake-token");
-    requiredInputStub.withArgs("upload-database").returns("false");
-    requiredInputStub.withArgs("output").returns("out");
-    const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
-    optionalInputStub.withArgs("expect-error").returns("false");
-    sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
-    mockFeatureFlagApiEndpoint(200, {});
-
-    // When there are no action inputs for RAM and threads, the action uses
-    // environment variables (passed down from the init action) to set RAM and
-    // threads usage.
-    process.env["CODEQL_THREADS"] = "-1";
-    process.env["CODEQL_RAM"] = "4992";
-
-    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;
-
-    t.assert(
-      runFinalizeStub.calledOnceWith(
-        sinon.match.any,
-        sinon.match.any,
-        "--threads=-1",
-        "--ram=4992",
-      ),
-    );
-    t.assert(
-      runQueriesStub.calledOnceWith(
-        sinon.match.any,
-        "--ram=4992",
-        "--threads=-1",
-      ),
-    );
-  });
-});
@@ -1,88 +0,0 @@
-import test from "ava";
-import * as sinon from "sinon";
-
-import * as actionsUtil from "./actions-util";
-import * as analyze from "./analyze";
-import * as api from "./api-client";
-import * as configUtils from "./config-utils";
-import * as gitUtils from "./git-utils";
-import * as statusReport from "./status-report";
-import {
-  setupTests,
-  setupActionsVars,
-  mockFeatureFlagApiEndpoint,
-} from "./testing-utils";
-import * as util from "./util";
-
-setupTests(test);
-
-// This test needs to be in its own file so that ava would run it in its own
-// nodejs process. The code being tested is in analyze-action.ts, which runs
-// immediately on load. So the file needs to be loaded during part of the test,
-// and that can happen only once per nodejs process. If multiple such tests are
-// in the same test file, ava would run them in the same nodejs process, and all
-// but the first test would fail.
-
-test("analyze action with RAM & threads from action inputs", async (t) => {
-  t.timeout(1000 * 20);
-  await util.withTmpDir(async (tmpDir) => {
-    setupActionsVars(tmpDir, tmpDir);
-    sinon
-      .stub(statusReport, "createStatusReportBase")
-      .resolves({} as statusReport.StatusReportBase);
-    sinon.stub(statusReport, "sendStatusReport").resolves();
-    const gitHubVersion: util.GitHubVersion = {
-      type: util.GitHubVariant.DOTCOM,
-    };
-    sinon.stub(configUtils, "getConfig").resolves({
-      gitHubVersion,
-      augmentationProperties: {},
-      languages: [],
-      packs: [],
-      trapCaches: {},
-    } as unknown as configUtils.Config);
-    const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
-    requiredInputStub.withArgs("token").returns("fake-token");
-    requiredInputStub.withArgs("upload-database").returns("false");
-    requiredInputStub.withArgs("output").returns("out");
-    const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
-    optionalInputStub.withArgs("expect-error").returns("false");
-    sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
-    sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);
-    mockFeatureFlagApiEndpoint(200, {});
-
-    process.env["CODEQL_THREADS"] = "1";
-    process.env["CODEQL_RAM"] = "4992";
-
-    // Action inputs have precedence over environment variables.
-    optionalInputStub.withArgs("threads").returns("-1");
-    optionalInputStub.withArgs("ram").returns("3012");
-
-    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;
-
-    t.assert(
-      runFinalizeStub.calledOnceWith(
-        sinon.match.any,
-        sinon.match.any,
-        "--threads=-1",
-        "--ram=3012",
-      ),
-    );
-    t.assert(
-      runQueriesStub.calledOnceWith(
-        sinon.match.any,
-        "--ram=3012",
-        "--threads=-1",
-      ),
-    );
-  });
-});
@@ -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();
@@ -0,0 +1,142 @@
+import test from "ava";
+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";
+import * as statusReport from "./status-report";
+import {
+  setupTests,
+  setupActionsVars,
+  mockFeatureFlagApiEndpoint,
+} from "./testing-utils";
+import * as util from "./util";
+
+setupTests(test);
+
+test.serial(
+  "analyze action with RAM & threads from environment variables",
+  async (t) => {
+    // This test frequently times out on Windows with the default timeout, so we bump
+    // it a bit to 20s.
+    t.timeout(1000 * 20);
+    await util.withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      sinon
+        .stub(statusReport, "createStatusReportBase")
+        .resolves({} as statusReport.StatusReportBase);
+      sinon.stub(statusReport, "sendStatusReport").resolves();
+      sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);
+
+      const gitHubVersion: util.GitHubVersion = {
+        type: util.GitHubVariant.DOTCOM,
+      };
+      sinon.stub(configUtils, "getConfig").resolves({
+        gitHubVersion,
+        augmentationProperties: {},
+        languages: [],
+        packs: [],
+        trapCaches: {},
+      } as unknown as configUtils.Config);
+      const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
+      requiredInputStub.withArgs("token").returns("fake-token");
+      requiredInputStub.withArgs("upload-database").returns("false");
+      requiredInputStub.withArgs("output").returns("out");
+      const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
+      optionalInputStub.withArgs("expect-error").returns("false");
+      sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
+      mockFeatureFlagApiEndpoint(200, {});
+
+      // When there are no action inputs for RAM and threads, the action uses
+      // environment variables (passed down from the init action) to set RAM and
+      // threads usage.
+      process.env["CODEQL_THREADS"] = "-1";
+      process.env["CODEQL_RAM"] = "4992";
+
+      const runFinalizeStub = sinon.stub(analyze, "runFinalize");
+      const runQueriesStub = sinon.stub(analyze, "runQueries");
+
+      await runWrapper();
+
+      t.assert(
+        runFinalizeStub.calledOnceWith(
+          sinon.match.any,
+          sinon.match.any,
+          "--threads=-1",
+          "--ram=4992",
+        ),
+      );
+      t.assert(
+        runQueriesStub.calledOnceWith(
+          sinon.match.any,
+          "--ram=4992",
+          "--threads=-1",
+        ),
+      );
+    });
+  },
+);
+
+test.serial(
+  "analyze action with RAM & threads from action inputs",
+  async (t) => {
+    t.timeout(1000 * 20);
+    await util.withTmpDir(async (tmpDir) => {
+      setupActionsVars(tmpDir, tmpDir);
+      sinon
+        .stub(statusReport, "createStatusReportBase")
+        .resolves({} as statusReport.StatusReportBase);
+      sinon.stub(statusReport, "sendStatusReport").resolves();
+      const gitHubVersion: util.GitHubVersion = {
+        type: util.GitHubVariant.DOTCOM,
+      };
+      sinon.stub(configUtils, "getConfig").resolves({
+        gitHubVersion,
+        augmentationProperties: {},
+        languages: [],
+        packs: [],
+        trapCaches: {},
+      } as unknown as configUtils.Config);
+      const requiredInputStub = sinon.stub(actionsUtil, "getRequiredInput");
+      requiredInputStub.withArgs("token").returns("fake-token");
+      requiredInputStub.withArgs("upload-database").returns("false");
+      requiredInputStub.withArgs("output").returns("out");
+      const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
+      optionalInputStub.withArgs("expect-error").returns("false");
+      sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
+      sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);
+      mockFeatureFlagApiEndpoint(200, {});
+
+      process.env["CODEQL_THREADS"] = "1";
+      process.env["CODEQL_RAM"] = "4992";
+
+      // Action inputs have precedence over environment variables.
+      optionalInputStub.withArgs("threads").returns("-1");
+      optionalInputStub.withArgs("ram").returns("3012");
+
+      const runFinalizeStub = sinon.stub(analyze, "runFinalize");
+      const runQueriesStub = sinon.stub(analyze, "runQueries");
+
+      await runWrapper();
+
+      t.assert(
+        runFinalizeStub.calledOnceWith(
+          sinon.match.any,
+          sinon.match.any,
+          "--threads=-1",
+          "--ram=3012",
+        ),
+      );
+      t.assert(
+        runQueriesStub.calledOnceWith(
+          sinon.match.any,
+          "--ram=3012",
+          "--threads=-1",
+        ),
+      );
+    });
+  },
+);
@@ -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:
@@ -1050,7 +1072,7 @@ test.serial(
 );

 test.serial(
-  "Avoids duplicating --overwrite flag if specified in CODEQL_ACTION_EXTRA_OPTIONS",
+  "Avoids duplicating --force-overwrite flag if specified in CODEQL_ACTION_EXTRA_OPTIONS",
  async (t) => {
    const runnerConstructorStub = stubToolRunnerConstructor();
    const codeqlObject = await stubCodeql();
@@ -1058,7 +1080,7 @@ test.serial(
    sinon.stub(io, "which").resolves("");

    process.env["CODEQL_ACTION_EXTRA_OPTIONS"] =
-      '{ "database": { "init": ["--overwrite"] } }';
+      '{ "database": { "init": ["--force-overwrite"] } }';

    await codeqlObject.databaseInitCluster(
      stubConfig,
@@ -1071,9 +1093,9 @@ test.serial(
    t.true(runnerConstructorStub.calledOnce);
    const args = runnerConstructorStub.firstCall.args[1] as string[];
    t.is(
-      args.filter((option: string) => option === "--overwrite").length,
+      args.filter((option: string) => option === "--force-overwrite").length,
      1,
-      "--overwrite should only be passed once",
+      "--force-overwrite should only be passed once",
    );

    // Clean up
@@ -277,22 +277,22 @@ let cachedCodeQL: CodeQL | undefined = undefined;
 * The version flags below can be used to conditionally enable certain features
 * on versions newer than this.
 */
-const CODEQL_MINIMUM_VERSION = "2.17.6";
+const CODEQL_MINIMUM_VERSION = "2.19.4";

 /**
 * 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,
    );
@@ -586,13 +592,6 @@ async function getCodeQLForCmd(
        extraArgs.push(`--qlconfig-file=${qlconfigFile}`);
      }

-      const overwriteFlag = isSupportedToolsFeature(
-        await this.getVersion(),
-        ToolsFeature.ForceOverwrite,
-      )
-        ? "--force-overwrite"
-        : "--overwrite";
-
      const overlayDatabaseMode = config.overlayDatabaseMode;
      if (overlayDatabaseMode === OverlayDatabaseMode.Overlay) {
        const overlayChangesFile = await writeOverlayChangesFile(
@@ -619,7 +618,7 @@ async function getCodeQLForCmd(
          "init",
          ...(overlayDatabaseMode === OverlayDatabaseMode.Overlay
            ? []
-            : [overwriteFlag]),
+            : ["--force-overwrite"]),
          "--db-cluster",
          config.dbLocation,
          `--source-root=${sourceRoot}`,
@@ -630,7 +629,14 @@ async function getCodeQLForCmd(
            // Some user configs specify `--no-calculate-baseline` as an additional
            // argument to `codeql database init`. Therefore ignore the baseline file
            // options here to avoid specifying the same argument twice and erroring.
-            ignoringOptions: ["--overwrite", ...baselineFilesOptions],
+            //
+            // Ignore `--overwrite` to avoid passing both `--force-overwrite` and `--overwrite` if
+            // the user has configured `--overwrite`.
+            ignoringOptions: [
+              "--force-overwrite",
+              "--overwrite",
+              ...baselineFilesOptions,
+            ],
          }),
        ],
        { stdin: externalRepositoryToken },
@@ -847,7 +853,7 @@ async function getCodeQLForCmd(
        "--sarif-group-rules-by-pack",
        "--sarif-include-query-help=always",
        "--sublanguage-file-coverage",
-        ...(await getJobRunUuidSarifOptions(this)),
+        ...(await getJobRunUuidSarifOptions()),
        ...getExtraOptionsFromEnv(["database", "interpret-results"]),
      ];
      if (sarifRunPropertyFlag !== undefined) {
@@ -1277,13 +1283,8 @@ function applyAutobuildAzurePipelinesTimeoutFix() {
  ].join(" ");
 }

-async function getJobRunUuidSarifOptions(codeql: CodeQL) {
+async function getJobRunUuidSarifOptions() {
  const jobRunUuid = process.env[EnvVar.JOB_RUN_UUID];

-  return jobRunUuid &&
-    (await codeql.supportsFeature(
-      ToolsFeature.DatabaseInterpretResultsSupportsSarifRunProperty,
-    ))
-    ? [`--sarif-run-property=jobRunUuid=${jobRunUuid}`]
-    : [];
+  return jobRunUuid ? [`--sarif-run-property=jobRunUuid=${jobRunUuid}`] : [];
 }
@@ -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-v2.25.2",
-  "cliVersion": "2.25.2",
-  "priorBundleVersion": "codeql-bundle-v2.25.1",
-  "priorCliVersion": "2.25.1"
+  "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,
  ) => {
@@ -73,39 +75,34 @@ const testShouldPerformDiffInformedAnalysis = test.macro({
        [Feature.DiffInformedQueries]: testCase.featureEnabled,
      });

-      const getGitHubVersionStub = sinon
+      sinon
        .stub(apiClient, "getGitHubVersion")
        .resolves(testCase.gitHubVersion);
-      const getPullRequestBranchesStub = sinon
+      sinon
        .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;
-
-      getGitHubVersionStub.restore();
-      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 +110,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false when CODEQL_ACTION_DIFF_INFORMED_QUERIES is set to false",
  {
    featureEnabled: true,
@@ -123,8 +119,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns true when CODEQL_ACTION_DIFF_INFORMED_QUERIES is set to true",
  {
    featureEnabled: false,
@@ -133,8 +128,7 @@ test.serial(
  true,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false for CodeQL version 2.20.0",
  {
    codeQLVersion: "2.20.0",
@@ -142,8 +136,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false for invalid GHES version",
  {
    gitHubVersion: {
@@ -154,8 +147,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false for GHES version 3.18.5",
  {
    gitHubVersion: {
@@ -166,8 +158,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns true for GHES version 3.19.0",
  {
    gitHubVersion: {
@@ -178,8 +169,7 @@ test.serial(
  true,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false when not a pull request",
  {
    pullRequestBranches: undefined,
@@ -187,6 +177,135 @@ 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,
        });

@@ -26,12 +26,38 @@ const DEFAULT_VERSION_FEATURE_FLAG_SUFFIX = "_enabled";

 /**
 * The first version of the CodeQL Bundle that shipped with zstd-compressed bundles.
+ *
+ * This is now below the minimum version of CodeQL, but we keep this around because we currently set
+ * up CodeQL before checking that the version is new enough.
 */
 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 +70,8 @@ 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 +100,19 @@ 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.
@@ -88,7 +129,6 @@ export enum Feature {
  QaTelemetryEnabled = "qa_telemetry_enabled",
  /** Note that this currently only disables baseline file coverage information. */
  SkipFileCoverageOnPrs = "skip_file_coverage_on_prs",
-  StartProxyRemoveUnusedRegistries = "start_proxy_remove_unused_registries",
  StartProxyUseFeaturesRelease = "start_proxy_use_features_release",
  UploadOverlayDbToApi = "upload_overlay_db_to_api",
  ValidateDbConfig = "validate_db_config",
@@ -124,6 +164,11 @@ 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 +322,16 @@ 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",
@@ -309,11 +364,6 @@ export const featureConfig = {
    minimumVersion: undefined,
    toolsFeature: ToolsFeature.SuppressesMissingFileBaselineWarning,
  },
-  [Feature.StartProxyRemoveUnusedRegistries]: {
-    defaultValue: false,
-    envVar: "CODEQL_ACTION_START_PROXY_REMOVE_UNUSED_REGISTRIES",
-    minimumVersion: undefined,
-  },
  [Feature.StartProxyUseFeaturesRelease]: {
    defaultValue: false,
    envVar: "CODEQL_ACTION_START_PROXY_USE_FEATURES_RELEASE",
@@ -346,8 +396,12 @@ 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 +425,11 @@ 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 +439,7 @@ 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 +571,13 @@ 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 +653,22 @@ 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 +684,7 @@ 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 +692,14 @@ 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,
    };
  }
@@ -33,7 +33,6 @@ test.serial(

      const actualRef = await gitUtils.getRef();
      t.deepEqual(actualRef, expectedRef);
-      callback.restore();
    });
  },
 );
@@ -54,7 +53,6 @@ test.serial(

      const actualRef = await gitUtils.getRef();
      t.deepEqual(actualRef, expectedRef);
-      callback.restore();
    });
  },
 );
@@ -73,7 +71,6 @@ test.serial(

      const actualRef = await gitUtils.getRef();
      t.deepEqual(actualRef, "refs/pull/1/head");
-      callback.restore();
    });
  },
 );
@@ -100,8 +97,6 @@ test.serial(

      const actualRef = await gitUtils.getRef();
      t.deepEqual(actualRef, "refs/pull/2/merge");
-      callback.restore();
-      getAdditionalInputStub.restore();
    });
  },
 );
@@ -161,7 +156,6 @@ test.serial(
            "Both 'ref' and 'sha' are required if one of them is provided.",
        },
      );
-      getAdditionalInputStub.restore();
    });
  },
 );
@@ -188,7 +182,6 @@ test.serial(
            "Both 'ref' and 'sha' are required if one of them is provided.",
        },
      );
-      getAdditionalInputStub.restore();
    });
  },
 );
@@ -242,7 +235,6 @@ test.serial("isAnalyzingDefaultBranch()", async (t) => {
    process.env["GITHUB_EVENT_NAME"] = "schedule";
    process.env["GITHUB_REF"] = "refs/heads/main";
    t.deepEqual(await gitUtils.isAnalyzingDefaultBranch(), false);
-    getAdditionalInputStub.restore();
  });
 });

@@ -254,8 +246,6 @@ test.serial("determineBaseBranchHeadCommitOid non-pullrequest", async (t) => {
  const result = await gitUtils.determineBaseBranchHeadCommitOid(__dirname);
  t.deepEqual(result, undefined);
  t.deepEqual(0, infoStub.callCount);
-
-  infoStub.restore();
 });

 test.serial(
@@ -276,8 +266,6 @@ test.serial(
      "git call failed. Will calculate the base branch SHA on the server. Error: " +
        "The checkout path provided to the action does not appear to be a git repository.",
    );
-
-    infoStub.restore();
  },
 );

@@ -301,10 +289,27 @@ test.serial("determineBaseBranchHeadCommitOid other error", async (t) => {
      "The checkout path provided to the action does not appear to be a git repository.",
    ),
  );
-
-  infoStub.restore();
 });

+test.serial(
+  "determineBaseBranchHeadCommitOid accepts SHA-256 OIDs",
+  async (t) => {
+    const mergeSha = "a".repeat(64);
+    const baseOid = "b".repeat(64);
+    const headOid = "c".repeat(64);
+
+    process.env["GITHUB_EVENT_NAME"] = "pull_request";
+    process.env["GITHUB_SHA"] = mergeSha;
+
+    sinon
+      .stub(gitUtils as any, "runGitCommand")
+      .resolves(`commit ${mergeSha}\nparent ${baseOid}\nparent ${headOid}\n`);
+
+    const result = await gitUtils.determineBaseBranchHeadCommitOid(__dirname);
+    t.deepEqual(result, baseOid);
+  },
+);
+
 test.serial("decodeGitFilePath unquoted strings", async (t) => {
  t.deepEqual(gitUtils.decodeGitFilePath("foo"), "foo");
  t.deepEqual(gitUtils.decodeGitFilePath("foo bar"), "foo bar");
@@ -436,6 +441,64 @@ test.serial("getFileOidsUnderPath handles quoted paths", async (t) => {
  });
 });

+test.serial("getFileOidsUnderPath handles SHA-256 OIDs", async (t) => {
+  await withTmpDir(async (tmpDir) => {
+    const sha256OidA =
+      "9f86d081884c7d659a2feaa0c55ad015a3bf4f1b2c0d4b7e8f9a1234567890ab";
+    const sha256OidB =
+      "aabbccddeeff00112233445566778899aabbccddeeff00112233445566778899";
+
+    sinon
+      .stub(gitUtils as any, "runGitCommand")
+      .callsFake(async (_cwd: any, args: any) => {
+        if (args[0] === "rev-parse") {
+          return `${tmpDir}\n`;
+        }
+        return (
+          `100644 ${sha256OidA} 0\tlib/sha256-file-a.js\n` +
+          `100644 ${sha256OidB} 0\tsrc/sha256-file-b.ts`
+        );
+      });
+
+    const result = await gitUtils.getFileOidsUnderPath("/fake/path");
+
+    t.deepEqual(result, {
+      "lib/sha256-file-a.js": sha256OidA,
+      "src/sha256-file-b.ts": sha256OidB,
+    });
+  });
+});
+
+test.serial(
+  "getFileOidsUnderPath rejects OIDs of unsupported length",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      // 50-char OID: not a valid SHA-1 (40) or SHA-256 (64) length. The regex
+      // must not accept this even though every character is a valid hex digit.
+      const invalidLine =
+        "100644 30d998ded095371488be3a729eb61d86ed721a1830d998ded0 0\tlib/bad.js";
+      sinon
+        .stub(gitUtils as any, "runGitCommand")
+        .callsFake(async (_cwd: any, args: any) => {
+          if (args[0] === "rev-parse") {
+            return `${tmpDir}\n`;
+          }
+          return invalidLine;
+        });
+
+      await t.throwsAsync(
+        async () => {
+          await gitUtils.getFileOidsUnderPath("/fake/path");
+        },
+        {
+          instanceOf: Error,
+          message: `Unexpected "git ls-files" output: ${invalidLine}`,
+        },
+      );
+    });
+  },
+);
+
 test.serial("getFileOidsUnderPath handles empty output", async (t) => {
  await withTmpDir(async (tmpDir) => {
    sinon
@@ -163,11 +163,12 @@ export const determineBaseBranchHeadCommitOid = async function (
      }
    }

-    // Let's confirm our assumptions: We had a merge commit and the parsed parent data looks correct
+    // Let's confirm our assumptions: We had a merge commit and the parsed parent
+    // data looks correct. OIDs are either 40 (SHA-1) or 64 (SHA-256) hex characters.
    if (
      commitOid === mergeSha &&
-      headOid.length === 40 &&
-      baseOid.length === 40
+      (headOid.length === 40 || headOid.length === 64) &&
+      (baseOid.length === 40 || baseOid.length === 64)
    ) {
      return baseOid;
    }
@@ -296,7 +297,8 @@ export const getFileOidsUnderPath = async function (
  // 100644 4c51bc1d9e86cd86e01b0f340cb8ce095c33b283 0\tsrc/git-utils.test.ts
  // 100644 6b792ea543ce75d7a8a03df591e3c85311ecb64f 0\tsrc/git-utils.ts
  // The fields are: <mode> <oid> <stage>\t<path>
-  const regex = /^[0-9]+ ([0-9a-f]{40}) [0-9]+\t(.+)$/;
+  // The OID is either 40 (SHA-1) or 64 (SHA-256) hex characters.
+  const regex = /^[0-9]+ ([0-9a-f]{40}|[0-9a-f]{64}) [0-9]+\t(.+)$/;
  for (const line of stdout.split("\n")) {
    if (line) {
      const match = line.match(regex);
@@ -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();
--- a/Show More
+++ b/Show More