Improve tests

Improve error message
Remove dead code
2026-05-09 07:10:22 +00:00 · 2026-05-08 19:16:48 +01:00 · 2026-05-08 19:16:47 +01:00 · 2026-05-08 19:16:46 +01:00 · 2026-05-08 19:14:05 +01:00 · 2026-05-08 19:14:05 +01:00
138 changed files with 36184 additions and 311914 deletions
@@ -16,5 +16,5 @@ inputs:
      Comma separated list of query ids that should NOT be included in this SARIF file.

 runs:
-  using: node20
+  using: node24
  main: index.js
@@ -22,7 +22,8 @@ runs:
        MAJOR_VERSION: ${{ inputs.major_version }}
        LATEST_TAG: ${{ inputs.latest_tag }}
      run: |
-        python ${{ github.action_path }}/release-branches.py \
+        npm ci
+        npx tsx ./pr-checks/release-branches.ts \
            --major-version "$MAJOR_VERSION" \
            --latest-tag "$LATEST_TAG"
      shell: bash
@@ -1,55 +0,0 @@
-import argparse
-import json
-import os
-import configparser
-
-# Name of the remote
-ORIGIN = 'origin'
-
-script_dir = os.path.dirname(os.path.realpath(__file__))
-grandparent_dir = os.path.dirname(os.path.dirname(script_dir))
-
-config = configparser.ConfigParser()
-with open(os.path.join(grandparent_dir, 'releases.ini')) as stream:
-    config.read_string('[default]\n' + stream.read())
-
-OLDEST_SUPPORTED_MAJOR_VERSION = int(config['default']['OLDEST_SUPPORTED_MAJOR_VERSION'])
-
-def main():
-
-  parser = argparse.ArgumentParser()
-  parser.add_argument("--major-version", required=True, type=str, help="The major version of the release")
-  parser.add_argument("--latest-tag", required=True, type=str, help="The most recent tag published to the repository")
-  args = parser.parse_args()
-
-  major_version = args.major_version
-  latest_tag = args.latest_tag
-
-  print("major_version: " + major_version)
-  print("latest_tag: " + latest_tag)
-
-  # If this is a primary release, we backport to all supported branches,
-  # so we check whether the major_version taken from the package.json
-  # is greater than or equal to the latest tag pulled from the repo.
-  # For example...
-  #     'v1' >= 'v2' is False # we're operating from an older release branch and should not backport
-  #     'v2' >= 'v2' is True  # the normal case where we're updating the current version
-  #     'v3' >= 'v2' is True  # in this case we are making the first release of a new major version
-  consider_backports = ( major_version >= latest_tag.split(".")[0] )
-
-  with open(os.environ["GITHUB_OUTPUT"], "a") as f:
-
-    f.write(f"backport_source_branch=releases/{major_version}\n")
-
-    backport_target_branches = []
-
-    if consider_backports:
-      for i in range(int(major_version.strip("v"))-1, 0, -1):
-        branch_name = f"releases/v{i}"
-        if i >= OLDEST_SUPPORTED_MAJOR_VERSION:
-          backport_target_branches.append(branch_name)
-
-    f.write("backport_target_branches="+json.dumps(backport_target_branches)+"\n")
-
-if __name__ == "__main__":
-  main()
@@ -15,6 +15,12 @@ runs:
      run: echo "$GITHUB_CONTEXT"
      shell: bash

+    - name: Set up Node
+      uses: actions/setup-node@v6
+      with:
+        node-version: 20
+        cache: 'npm'
+
    - name: Set up Python
      uses: actions/setup-python@v6
      with:
@@ -1,6 +1,6 @@
 name: Verify that the best-effort debug artifact scan completed
 description: Verifies that the best-effort debug artifact scan completed successfully during tests
 runs:
-  using: node20
+  using: node24
  main: index.js
  post: post.js
@@ -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"
@@ -1,7 +1,9 @@
 version: 2
 updates:
  - package-ecosystem: npm
-    directory: "/"
+    directories:
+      - "/"
+      - "/pr-checks"
    schedule:
      interval: weekly
    cooldown:
@@ -1 +0,0 @@
-OLDEST_SUPPORTED_MAJOR_VERSION=3
@@ -60,12 +60,12 @@ jobs:
          setup-kotlin: 'true'
      - uses: ./../action/init
        with:
-          languages: C#,java-kotlin,swift,typescript
+          languages: C#,java-kotlin,typescript
          tools: ${{ steps.prepare-test.outputs.tools-url }}

      - name: 'Check languages'
        run: |
-          expected_languages="csharp,java,swift,javascript"
+          expected_languages="csharp,java,javascript"
          actual_languages=$(jq -r '.languages | join(",")' "$RUNNER_TEMP"/config)

          if [ "$expected_languages" != "$actual_languages" ]; then
@@ -59,7 +59,7 @@ jobs:
          use-all-platform-bundle: 'false'
          setup-kotlin: 'true'
      - name: Set up Ruby
-        uses: ruby/setup-ruby@09a7688d3b55cf0e976497ff046b70949eeaccfd # v1.288.0
+        uses: ruby/setup-ruby@c4e5b1316158f92e3d49443a9d58b31d25ac0f8f # v1.306.0
        with:
          ruby-version: 2.6
      - name: Install Code Scanning integration
@@ -71,7 +71,17 @@ jobs:
        id: proxy
        uses: ./../action/start-proxy
        with:
-          registry_secrets: '[{ "type": "nuget_feed", "url": "https://api.nuget.org/v3/index.json" }]'
+          registry_secrets: |
+            [
+              {
+                "type": "maven_repository",
+                "url": "https://repo.maven.apache.org/maven2/"
+              },
+              {
+                "type": "maven_repository",
+                "url": "https://repo1.maven.org/maven2"
+              }
+            ]

      - name: Print proxy outputs
        run: |
@@ -82,5 +92,12 @@ jobs:
      - name: Fail if proxy outputs are not set
        if: (!steps.proxy.outputs.proxy_host) || (!steps.proxy.outputs.proxy_port) || (!steps.proxy.outputs.proxy_ca_certificate) || (!steps.proxy.outputs.proxy_urls)
        run: exit 1
+
+      - name: Fail if proxy_urls does not contain all registries
+        if: |
+          join(fromJSON(steps.proxy.outputs.proxy_urls)[*].type, ',') != 'maven_repository,maven_repository'
+          || !contains(steps.proxy.outputs.proxy_urls, 'https://repo.maven.apache.org/maven2/')
+          || !contains(steps.proxy.outputs.proxy_urls, 'https://repo1.maven.org/maven2')
+        run: exit 1
    env:
      CODEQL_ACTION_TEST_MODE: true
@@ -66,6 +66,7 @@ jobs:
        uses: ./../action/.github/actions/verify-debug-artifact-scan-completed
      - uses: ./../action/init
        with:
+          languages: cpp,csharp,go,java,javascript,python
          tools: ${{ steps.prepare-test.outputs.tools-url }}
          debug: true
          debug-artifact-name: my-debug-artifacts
@@ -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"
@@ -24,7 +24,7 @@ defaults:

 jobs:
  merge-back:
-    runs-on: ubuntu-slim
+    runs-on: ubuntu-latest
    environment: Automation
    if: github.repository == 'github/codeql-action'
    env:
@@ -131,7 +131,7 @@ jobs:
          echo "::endgroup::"

      - name: Generate token
-        uses: actions/create-github-app-token@v3.0.0
+        uses: actions/create-github-app-token@v3.1.1
        id: app-token
        with:
          app-id: ${{ vars.AUTOMATION_APP_ID }}
@@ -29,7 +29,7 @@ defaults:
 jobs:
  prepare:
    name: "Prepare release"
-    runs-on: ubuntu-slim
+    runs-on: ubuntu-latest
    if: github.repository == 'github/codeql-action'

    permissions:
@@ -136,7 +136,7 @@ jobs:

      - name: Generate token
        if: github.event_name == 'workflow_dispatch'
-        uses: actions/create-github-app-token@v3.0.0
+        uses: actions/create-github-app-token@v3.1.1
        id: app-token
        with:
          app-id: ${{ vars.AUTOMATION_APP_ID }}
@@ -1,64 +0,0 @@
-#!/usr/bin/env bash
-# Update the required checks based on the current branch.
-
-set -euo pipefail
-
-SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-REPO_DIR="$(dirname "$SCRIPT_DIR")"
-GRANDPARENT_DIR="$(dirname "$REPO_DIR")"
-source "$GRANDPARENT_DIR/releases.ini"
-
-if ! gh auth status 2>/dev/null; then
-  gh auth status
-  echo "Failed: Not authorized. This script requires admin access to github/codeql-action through the gh CLI."
-  exit 1
-fi
-
-if [ "$#" -eq 1 ]; then
-  # If we were passed an argument, use that as the SHA
-  GITHUB_SHA="$1"
-elif [ "$#" -gt 1 ]; then
-  echo "Usage: $0 [SHA]"
-  echo "Update the required checks based on the SHA, or main."
-  exit 1
-elif [ -z "$GITHUB_SHA" ]; then
-  # If we don't have a SHA, use main
-  GITHUB_SHA="$(git rev-parse main)"
-fi
-
-echo "Getting checks for $GITHUB_SHA"
-
-# Ignore any checks with "https://", CodeQL, LGTM, Update, and ESLint checks.
-CHECKS="$(gh api repos/github/codeql-action/commits/"${GITHUB_SHA}"/check-runs --paginate | jq --slurp --compact-output --raw-output '[.[].check_runs.[] | select(.conclusion != "skipped") | .name | select(contains("https://") or . == "CodeQL" or . == "Dependabot" or . == "check-expected-release-files" or contains("Update") or contains("ESLint") or contains("update") or contains("test-setup-python-scripts") or . == "Agent" or . == "Cleanup artifacts" or . == "Prepare" or . == "Upload results" or . == "Label PR with size" | not)] | unique | sort')"
-
-echo "$CHECKS" | jq
-
-# Fail if there are no checks
-if [ -z "$CHECKS" ] || [ "$(echo "$CHECKS" | jq '. | length')" -eq 0 ]; then
-  echo "No checks found for $GITHUB_SHA"
-  exit 1
-fi
-
-echo "{\"contexts\": ${CHECKS}}" > checks.json
-
-echo "Updating main"
-gh api --silent -X "PATCH" "repos/github/codeql-action/branches/main/protection/required_status_checks" --input checks.json
-
-# list all branchs on origin remote matching releases/v*
-BRANCHES="$(git ls-remote --heads origin 'releases/v*' | sed 's?.*refs/heads/??' | sort -V)"
-
-for BRANCH in $BRANCHES; do
-
-  # strip exact 'releases/v' prefix from $BRANCH using count of characters
-  VERSION="${BRANCH:10}"
-
-  if [ "$VERSION" -lt "$OLDEST_SUPPORTED_MAJOR_VERSION" ]; then
-    echo "Skipping $BRANCH"
-    continue
-  fi
-
-  echo "Updating $BRANCH"
-  gh api --silent -X "PATCH" "repos/github/codeql-action/branches/$BRANCH/protection/required_status_checks" --input checks.json
-done
-
-rm checks.json
@@ -20,7 +20,7 @@ defaults:
 jobs:
  update-bundle:
    if: github.event.release.prerelease && startsWith(github.event.release.tag_name, 'codeql-bundle-')
-    runs-on: ubuntu-slim
+    runs-on: ubuntu-latest
    permissions:
      contents: write # needed to push commits
      pull-requests: write # needed to create pull requests
@@ -57,6 +57,17 @@ jobs:
      - name: Update bundle
        uses: ./.github/actions/update-bundle

+      - name: Set up CodeQL CLI from new bundle
+        id: setup-codeql
+        uses: ./setup-codeql
+        with:
+          tools: https://github.com/github/codeql-action/releases/download/${{ github.event.release.tag_name }}/codeql-bundle-linux64.tar.gz
+
+      - name: Update built-in languages
+        run: npx tsx pr-checks/update-builtin-languages.ts "$CODEQL_PATH"
+        env:
+          CODEQL_PATH: ${{ steps.setup-codeql.outputs.codeql-path }}
+
      - name: Bump Action minor version if new CodeQL minor version series
        id: bump-action-version
        run: |
@@ -26,7 +26,7 @@ jobs:

  update:
    timeout-minutes: 45
-    runs-on: ubuntu-slim
+    runs-on: ubuntu-latest
    if: github.event_name == 'workflow_dispatch'
    needs: [prepare]
    env:
@@ -77,7 +77,7 @@ jobs:

  backport:
    timeout-minutes: 45
-    runs-on: ubuntu-slim
+    runs-on: ubuntu-latest
    environment: Automation
    needs: [prepare]
    if: ${{ (github.event_name == 'push') && needs.prepare.outputs.backport_target_branches != '[]' }}
@@ -93,7 +93,7 @@ jobs:
      pull-requests: write # needed to create pull request
    steps:
    - name: Generate token
-      uses: actions/create-github-app-token@v3.0.0
+      uses: actions/create-github-app-token@v3.1.1
      id: app-token
      with:
        app-id: ${{ vars.AUTOMATION_APP_ID }}
@@ -11,3 +11,5 @@ build/
 eslint.sarif
 # for local incremental compilation
 tsconfig.tsbuildinfo
+# esbuild metadata file
+meta.json
@@ -0,0 +1,30 @@
+{
+  // Place your codeql-action workspace snippets here. Each snippet is defined under a snippet name and has a scope, prefix, body and
+  // description. Add comma separated ids of the languages where the snippet is applicable in the scope field. If scope
+  // is left empty or omitted, the snippet gets applied to all languages. The prefix is what is
+  // used to trigger the snippet and the body will be expanded and inserted. Possible variables are:
+  // $1, $2 for tab stops, $0 for the final cursor position, and ${1:label}, ${2:another} for placeholders.
+  // Placeholders with the same ids are connected.
+  // Example:
+  // "Print to console": {
+  // 	"scope": "javascript,typescript",
+  // 	"prefix": "log",
+  // 	"body": [
+  // 		"console.log('$1');",
+  // 		"$2"
+  // 	],
+  // 	"description": "Log output to console"
+  // }
+  "Test Macro": {
+    "scope": "javascript, typescript",
+    "prefix": "testMacro",
+    "body": [
+      "const ${1:nameMacro} = makeMacro({",
+      "  exec: async (t: ExecutionContext<unknown>) => {},",
+      "",
+      "  title: (providedTitle = \"\") => `${2:common title} - \\${providedTitle}`,",
+      "});",
+    ],
+    "description": "An Ava test macro",
+  },
+}
@@ -2,19 +2,53 @@

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

-## 3.34.1 - 20 Mar 2026
+## [UNRELEASED]
+
+- Added an experimental change which, when running a Code Scanning analysis for a PR with [improved incremental analysis](https://github.com/github/roadmap/issues/1158) enabled, prefers CodeQL CLI versions that have a cached overlay-base database for the configured languages. This speeds up analysis for a repository when there is not yet a cached overlay-base database for the latest CLI version. We expect to roll this change out to everyone in May. [#3880](https://github.com/github/codeql-action/pull/3880)
+
+## 4.35.4 - 07 May 2026
+
+- Update default CodeQL bundle version to [2.25.4](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.25.4). [#3881](https://github.com/github/codeql-action/pull/3881)
+
+## 4.35.3 - 01 May 2026
+
+- _Upcoming breaking change_: Add a deprecation warning for customers using CodeQL version 2.19.3 and earlier. These versions of CodeQL were discontinued on 9 April 2026 alongside GitHub Enterprise Server 3.15, and will be unsupported by the next minor release of the CodeQL Action. [#3837](https://github.com/github/codeql-action/pull/3837)
+- Configurations for private registries that use Cloudsmith or GCP OIDC are now accepted. [#3850](https://github.com/github/codeql-action/pull/3850)
+- Best-effort connection tests for private registries now use `GET` requests instead of `HEAD` for better compatibility with various registry implementations. For NuGet feeds, the test is now always performed against the service index. [#3853](https://github.com/github/codeql-action/pull/3853)
+- Fixed a bug where two diagnostics produced within the same millisecond could overwrite each other on disk, causing one of them to be lost. [#3852](https://github.com/github/codeql-action/pull/3852)
+- Update default CodeQL bundle version to [2.25.3](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.25.3). [#3865](https://github.com/github/codeql-action/pull/3865)
+
+## 4.35.2 - 15 Apr 2026
+
+- The undocumented TRAP cache cleanup feature that could be enabled using the `CODEQL_ACTION_CLEANUP_TRAP_CACHES` environment variable is deprecated and will be removed in May 2026. If you are affected by this, we recommend disabling TRAP caching by passing the `trap-caching: false` input to the `init` Action. [#3795](https://github.com/github/codeql-action/pull/3795)
+- The Git version 2.36.0 requirement for improved incremental analysis now only applies to repositories that contain submodules. [#3789](https://github.com/github/codeql-action/pull/3789)
+- Python analysis on GHES no longer extracts the standard library, relying instead on models of the standard library. This should result in significantly faster extraction and analysis times, while the effect on alerts should be minimal. [#3794](https://github.com/github/codeql-action/pull/3794)
+- Fixed a bug in the validation of OIDC configurations for private registries that was added in CodeQL Action 4.33.0 / 3.33.0. [#3807](https://github.com/github/codeql-action/pull/3807)
+- Update default CodeQL bundle version to [2.25.2](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.25.2). [#3823](https://github.com/github/codeql-action/pull/3823)
+
+## 4.35.1 - 27 Mar 2026
+
+- Fix incorrect minimum required Git version for [improved incremental analysis](https://github.com/github/roadmap/issues/1158): it should have been 2.36.0, not 2.11.0. [#3781](https://github.com/github/codeql-action/pull/3781)
+
+## 4.35.0 - 27 Mar 2026
+
+- Reduced the minimum Git version required for [improved incremental analysis](https://github.com/github/roadmap/issues/1158) from 2.38.0 to 2.11.0. [#3767](https://github.com/github/codeql-action/pull/3767)
+- Update default CodeQL bundle version to [2.25.1](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.25.1). [#3773](https://github.com/github/codeql-action/pull/3773)
+
+## 4.34.1 - 20 Mar 2026

 - Downgrade default CodeQL bundle version to [2.24.3](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.24.3) due to issues with a small percentage of Actions and JavaScript analyses. [#3762](https://github.com/github/codeql-action/pull/3762)

-## 3.34.0 - 20 Mar 2026
+## 4.34.0 - 20 Mar 2026

 - Added an experimental change which disables TRAP caching when [improved incremental analysis](https://github.com/github/roadmap/issues/1158) is enabled, since improved incremental analysis supersedes TRAP caching. This will improve performance and reduce Actions cache usage. We expect to roll this change out to everyone in March. [#3569](https://github.com/github/codeql-action/pull/3569)
 - We are rolling out improved incremental analysis to C/C++ analyses that use build mode `none`. We expect this rollout to be complete by the end of April 2026. [#3584](https://github.com/github/codeql-action/pull/3584)
 - Update default CodeQL bundle version to [2.25.0](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.25.0). [#3585](https://github.com/github/codeql-action/pull/3585)

-## 3.33.0 - 16 Mar 2026
+## 4.33.0 - 16 Mar 2026

 - Upcoming change: Starting April 2026, the CodeQL Action will skip collecting file coverage information on pull requests to improve analysis performance. File coverage information will still be computed on non-PR analyses. Pull request analyses will log a warning about this upcoming change. [#3562](https://github.com/github/codeql-action/pull/3562)
+
  To opt out of this change:
  - **Repositories owned by an organization:** Create a custom repository property with the name `github-codeql-file-coverage-on-prs` and the type "True/false", then set this property to `true` in the repository's settings. For more information, see [Managing custom properties for repositories in your organization](https://docs.github.com/en/organizations/managing-organization-settings/managing-custom-properties-for-repositories-in-your-organization). Alternatively, if you are using an advanced setup workflow, you can set the `CODEQL_ACTION_FILE_COVERAGE_ON_PRS` environment variable to `true` in your workflow.
  - **User-owned repositories using default setup:** Switch to an advanced setup workflow and set the `CODEQL_ACTION_FILE_COVERAGE_ON_PRS` environment variable to `true` in your workflow.
@@ -25,11 +59,11 @@ See the [releases page](https://github.com/github/codeql-action/releases) for th
 - Fixed the retry mechanism for database uploads. Previously this would fail with the error "Response body object should not be disturbed or locked". [#3564](https://github.com/github/codeql-action/pull/3564)
 - A warning is now emitted if the CodeQL Action detects a repository property whose name suggests that it relates to the CodeQL Action, but which is not one of the properties recognised by the current version of the CodeQL Action. [#3570](https://github.com/github/codeql-action/pull/3570)

-## 3.32.6 - 05 Mar 2026
+## 4.32.6 - 05 Mar 2026

 - Update default CodeQL bundle version to [2.24.3](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.24.3). [#3548](https://github.com/github/codeql-action/pull/3548)

-## 3.32.5 - 02 Mar 2026
+## 4.32.5 - 02 Mar 2026

 - Repositories owned by an organization can now set up the `github-codeql-disable-overlay` custom repository property to disable [improved incremental analysis for CodeQL](https://github.com/github/roadmap/issues/1158). First, create a custom repository property with the name `github-codeql-disable-overlay` and the type "True/false" in the organization's settings. Then in the repository's settings, set this property to `true` to disable improved incremental analysis. For more information, see [Managing custom properties for repositories in your organization](https://docs.github.com/en/organizations/managing-organization-settings/managing-custom-properties-for-repositories-in-your-organization). This feature is not yet available on GitHub Enterprise Server. [#3507](https://github.com/github/codeql-action/pull/3507)
 - Added an experimental change so that when [improved incremental analysis](https://github.com/github/roadmap/issues/1158) fails on a runner — potentially due to insufficient disk space — the failure is recorded in the Actions cache so that subsequent runs will automatically skip improved incremental analysis until something changes (e.g. a larger runner is provisioned or a new CodeQL version is released). We expect to roll this change out to everyone in March. [#3487](https://github.com/github/codeql-action/pull/3487)
@@ -39,7 +73,7 @@ See the [releases page](https://github.com/github/codeql-action/releases) for th
 - Added an experimental change which allows the `start-proxy` action to resolve the CodeQL CLI version from feature flags instead of using the linked CLI bundle version. We expect to roll this change out to everyone in March. [#3512](https://github.com/github/codeql-action/pull/3512)
 - The previously experimental changes from versions 4.32.3, 4.32.4, 3.32.3 and 3.32.4 are now enabled by default. [#3503](https://github.com/github/codeql-action/pull/3503), [#3504](https://github.com/github/codeql-action/pull/3504)

-## 3.32.4 - 20 Feb 2026
+## 4.32.4 - 20 Feb 2026

 - Update default CodeQL bundle version to [2.24.2](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.24.2). [#3493](https://github.com/github/codeql-action/pull/3493)
 - Added an experimental change which improves how certificates are generated for the authentication proxy that is used by the CodeQL Action in Default Setup when [private package registries are configured](https://docs.github.com/en/code-security/how-tos/secure-at-scale/configure-organization-security/manage-usage-and-access/giving-org-access-private-registries). This is expected to generate more widely compatible certificates and should have no impact on analyses which are working correctly already. We expect to roll this change out to everyone in February. [#3473](https://github.com/github/codeql-action/pull/3473)
@@ -47,88 +81,88 @@ See the [releases page](https://github.com/github/codeql-action/releases) for th
 - Added a setting which allows the CodeQL Action to enable network debugging for Java programs. This will help GitHub staff support customers with troubleshooting issues in GitHub-managed CodeQL workflows, such as Default Setup. This setting can only be enabled by GitHub staff. [#3485](https://github.com/github/codeql-action/pull/3485)
 - Added a setting which enables GitHub-managed workflows, such as Default Setup, to use a [nightly CodeQL CLI release](https://github.com/dsp-testing/codeql-cli-nightlies) instead of the latest, stable release that is used by default. This will help GitHub staff support customers whose analyses for a given repository or organization require early access to a change in an upcoming CodeQL CLI release. This setting can only be enabled by GitHub staff. [#3484](https://github.com/github/codeql-action/pull/3484)

-## 3.32.3 - 13 Feb 2026
+## 4.32.3 - 13 Feb 2026

 - Added experimental support for testing connections to [private package registries](https://docs.github.com/en/code-security/how-tos/secure-at-scale/configure-organization-security/manage-usage-and-access/giving-org-access-private-registries). This feature is not currently enabled for any analysis. In the future, it may be enabled by default for Default Setup. [#3466](https://github.com/github/codeql-action/pull/3466)

-## 3.32.2 - 05 Feb 2026
+## 4.32.2 - 05 Feb 2026

 - Update default CodeQL bundle version to [2.24.1](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.24.1). [#3460](https://github.com/github/codeql-action/pull/3460)

-## 3.32.1 - 02 Feb 2026
+## 4.32.1 - 02 Feb 2026

 - A warning is now shown in Default Setup workflow logs if a [private package registry is configured](https://docs.github.com/en/code-security/how-tos/secure-at-scale/configure-organization-security/manage-usage-and-access/giving-org-access-private-registries) using a GitHub Personal Access Token (PAT), but no username is configured. [#3422](https://github.com/github/codeql-action/pull/3422)
 - Fixed a bug which caused the CodeQL Action to fail when repository properties cannot successfully be retrieved. [#3421](https://github.com/github/codeql-action/pull/3421)

-## 3.32.0 - 26 Jan 2026
+## 4.32.0 - 26 Jan 2026

 - Update default CodeQL bundle version to [2.24.0](https://github.com/github/codeql-action/releases/tag/codeql-bundle-v2.24.0). [#3425](https://github.com/github/codeql-action/pull/3425)

-## 3.31.11 - 23 Jan 2026
+## 4.31.11 - 23 Jan 2026

 - When running a Default Setup workflow with [Actions debugging enabled](https://docs.github.com/en/actions/how-tos/monitor-workflows/enable-debug-logging), the CodeQL Action will now use more unique names when uploading logs from the Dependabot authentication proxy as workflow artifacts. This ensures that the artifact names do not clash between multiple jobs in a build matrix. [#3409](https://github.com/github/codeql-action/pull/3409)
 - Improved error handling throughout the CodeQL Action. [#3415](https://github.com/github/codeql-action/pull/3415)
 - Added experimental support for automatically excluding [generated files](https://docs.github.com/en/repositories/working-with-files/managing-files/customizing-how-changed-files-appear-on-github) from the analysis. This feature is not currently enabled for any analysis. In the future, it may be enabled by default for some GitHub-managed analyses. [#3318](https://github.com/github/codeql-action/pull/3318)
 - The changelog extracts that are included with releases of the CodeQL Action are now shorter to avoid duplicated information from appearing in Dependabot PRs. [#3403](https://github.com/github/codeql-action/pull/3403)

-## 3.31.10 - 12 Jan 2026
+## 4.31.10 - 12 Jan 2026

 - Update default CodeQL bundle version to 2.23.9. [#3393](https://github.com/github/codeql-action/pull/3393)

-## 3.31.9 - 16 Dec 2025
+## 4.31.9 - 16 Dec 2025

 No user facing changes.

-## 3.31.8 - 11 Dec 2025
+## 4.31.8 - 11 Dec 2025

 - Update default CodeQL bundle version to 2.23.8. [#3354](https://github.com/github/codeql-action/pull/3354)

-## 3.31.7 - 05 Dec 2025
+## 4.31.7 - 05 Dec 2025

 - Update default CodeQL bundle version to 2.23.7. [#3343](https://github.com/github/codeql-action/pull/3343)

-## 3.31.6 - 01 Dec 2025
+## 4.31.6 - 01 Dec 2025

 No user facing changes.

-## 3.31.5 - 24 Nov 2025
+## 4.31.5 - 24 Nov 2025

 - Update default CodeQL bundle version to 2.23.6. [#3321](https://github.com/github/codeql-action/pull/3321)

-## 3.31.4 - 18 Nov 2025
+## 4.31.4 - 18 Nov 2025

 No user facing changes.

-## 3.31.3 - 13 Nov 2025
+## 4.31.3 - 13 Nov 2025

 - CodeQL Action v3 will be deprecated in December 2026.  The Action now logs a warning for customers who are running v3 but could be running v4. For more information, see [Upcoming deprecation of CodeQL Action v3](https://github.blog/changelog/2025-10-28-upcoming-deprecation-of-codeql-action-v3/).
 - Update default CodeQL bundle version to 2.23.5. [#3288](https://github.com/github/codeql-action/pull/3288)

-## 3.31.2 - 30 Oct 2025
+## 4.31.2 - 30 Oct 2025

 No user facing changes.

-## 3.31.1 - 30 Oct 2025
+## 4.31.1 - 30 Oct 2025

 - The `add-snippets` input has been removed from the `analyze` action. This input has been deprecated since CodeQL Action 3.26.4 in August 2024 when this removal was announced.

-## 3.31.0 - 24 Oct 2025
+## 4.31.0 - 24 Oct 2025

 - Bump minimum CodeQL bundle version to 2.17.6. [#3223](https://github.com/github/codeql-action/pull/3223)
 - When SARIF files are uploaded by the `analyze` or `upload-sarif` actions, the CodeQL Action automatically performs post-processing steps to prepare the data for the upload. Previously, these post-processing steps were only performed before an upload took place. We are now changing this so that the post-processing steps will always be performed, even when the SARIF files are not uploaded. This does not change anything for the `upload-sarif` action. For `analyze`, this may affect Advanced Setup for CodeQL users who specify a value other than `always` for the `upload` input. [#3222](https://github.com/github/codeql-action/pull/3222)

-## 3.30.9 - 17 Oct 2025
+## 4.30.9 - 17 Oct 2025

 - Update default CodeQL bundle version to 2.23.3. [#3205](https://github.com/github/codeql-action/pull/3205)
 - Experimental: A new `setup-codeql` action has been added which is similar to `init`, except it only installs the CodeQL CLI and does not initialize a database. Do not use this in production as it is part of an internal experiment and subject to change at any time. [#3204](https://github.com/github/codeql-action/pull/3204)

-## 3.30.8 - 10 Oct 2025
+## 4.30.8 - 10 Oct 2025

 No user facing changes.

-## 3.30.7 - 06 Oct 2025
+## 4.30.7 - 06 Oct 2025

-No user facing changes.
+- [v4+ only] The CodeQL Action now runs on Node.js v24. [#3169](https://github.com/github/codeql-action/pull/3169)

 ## 3.30.6 - 02 Oct 2025

@@ -364,13 +398,17 @@ No user facing changes.
 ## 3.26.12 - 07 Oct 2024

 - _Upcoming breaking change_: Add a deprecation warning for customers using CodeQL version 2.14.5 and earlier. These versions of CodeQL were discontinued on 24 September 2024 alongside GitHub Enterprise Server 3.10, and will be unsupported by CodeQL Action versions 3.27.0 and later and versions 2.27.0 and later. [#2520](https://github.com/github/codeql-action/pull/2520)
+
  - If you are using one of these versions, please update to CodeQL CLI version 2.14.6 or later. For instance, if you have specified a custom version of the CLI using the 'tools' input to the 'init' Action, you can remove this input to use the default version.
+
  - Alternatively, if you want to continue using a version of the CodeQL CLI between 2.13.5 and 2.14.5, you can replace `github/codeql-action/*@v3` by `github/codeql-action/*@v3.26.11` and `github/codeql-action/*@v2` by `github/codeql-action/*@v2.26.11` in your code scanning workflow to ensure you continue using this version of the CodeQL Action.

 ## 3.26.11 - 03 Oct 2024

 - _Upcoming breaking change_: Add support for using `actions/download-artifact@v4` to programmatically consume CodeQL Action debug artifacts.
+
  Starting November 30, 2024, GitHub.com customers will [no longer be able to use `actions/download-artifact@v3`](https://github.blog/changelog/2024-04-16-deprecation-notice-v3-of-the-artifact-actions/). Therefore, to avoid breakage, customers who programmatically download the CodeQL Action debug artifacts should set the `CODEQL_ACTION_ARTIFACT_V4_UPGRADE` environment variable to `true` and bump `actions/download-artifact@v3` to `actions/download-artifact@v4` in their workflows. The CodeQL Action will enable this behavior by default in early November and workflows that have not yet bumped `actions/download-artifact@v3` to `actions/download-artifact@v4` will begin failing then.
+
  This change is currently unavailable for GitHub Enterprise Server customers, as `actions/upload-artifact@v4` and `actions/download-artifact@v4` are not yet compatible with GHES.
 - Update default CodeQL bundle version to 2.19.1. [#2519](https://github.com/github/codeql-action/pull/2519)

@@ -493,9 +531,12 @@ No user facing changes.
 ## 3.25.0 - 15 Apr 2024

 - The deprecated feature for extracting dependencies for a Python analysis has been removed. [#2224](https://github.com/github/codeql-action/pull/2224)
+
  As a result, the following inputs and environment variables are now ignored:
+
  - The `setup-python-dependencies` input to the `init` Action
  - The `CODEQL_ACTION_DISABLE_PYTHON_DEPENDENCY_INSTALLATION` environment variable
+
  We recommend removing any references to these from your workflows. For more information, see the release notes for CodeQL Action v3.23.0 and v2.23.0.
 - Automatically overwrite an existing database if found on the filesystem. [#2229](https://github.com/github/codeql-action/pull/2229)
 - Bump the minimum CodeQL bundle version to 2.12.6. [#2232](https://github.com/github/codeql-action/pull/2232)
@@ -69,12 +69,14 @@ Once the mergeback and backport pull request have been merged, the release is co

 ## Keeping the PR checks up to date (admin access required)

-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 [update-required-checks.sh](.github/workflows/script/update-required-checks.sh) script:
+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:

- If you run the script without an argument, it will retrieve the set of workflows that ran for the latest commit on `main`. Make sure that your local `main` branch is up to date before running the script.
- You can specify a commit SHA as argument to retrieve the set of workflows for that commit instead. You will likely want to use this if you have a PR that removes or adds PR checks.
+- 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.
+- 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.

-After running, go to the [branch protection rules settings page](https://github.com/github/codeql-action/settings/branches) and validate that the rules for `main`, `v3`, and any other currently supported major versions have been updated.
+After running, go to the [branch protection rules settings page](https://github.com/github/codeql-action/settings/branches) and validate that the rules for `main`, `v4`, and any other currently supported major versions have been updated.

 Note that any updates to checks on `main` need to be backported to all currently supported major version branches, in order to maintain the same set of names for required checks.

@@ -122,7 +124,7 @@ To deprecate an older version of the Action:
   - Implement an Actions warning for customers using the deprecated version.
 1. Wait for the deprecation period to pass.
 1. Upgrade the Actions warning for customers using the deprecated version to a non-fatal error, and mention that this version of the Action is no longer supported.
-1. Make a PR to bump the `OLDEST_SUPPORTED_MAJOR_VERSION` in [releases.ini](.github/releases.ini).  Once this PR is merged, the release process will no longer backport changes to the deprecated release version.
+1. Make a PR to bump the `OLDEST_SUPPORTED_MAJOR_VERSION` in [config.ts](pr-checks/config.ts).  Once this PR is merged, the release process will no longer backport changes to the deprecated release version.

 ## Resources

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

 | Minimum CodeQL Action | Minimum CodeQL Bundle Version | GitHub Environment | Notes |
 |-----------------------|-------------------------------|--------------------|-------|
+| `v4.33.0` | `2.24.3` | Enterprise Server 3.21 | |
 | `v4.31.10` | `2.23.9` | Enterprise Server 3.20 | |
 | `v3.29.11` | `2.22.4` | Enterprise Server 3.19 | |
 | `v3.28.21` | `2.21.3` | Enterprise Server 3.18 | |
@@ -94,6 +94,6 @@ outputs:
  sarif-id:
    description: The ID of the uploaded SARIF file.
 runs:
-  using: node20
+  using: node24
  main: "../lib/analyze-action.js"
  post: "../lib/analyze-action-post.js"
@@ -15,5 +15,5 @@ inputs:
      $GITHUB_WORKSPACE as its working directory.
    required: false
 runs:
-  using: node20
+  using: node24
  main: '../lib/autobuild-action.js'
@@ -1,4 +1,4 @@
-import { copyFile, rm } from "node:fs/promises";
+import { copyFile, rm, writeFile } from "node:fs/promises";
 import { dirname, join } from "node:path";
 import { fileURLToPath } from "node:url";

@@ -64,7 +64,11 @@ const onEndPlugin = {

 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: globSync([
+    `${SRC_DIR}/*-action.ts`,
+    `${SRC_DIR}/*-action-post.ts`,
+    "src/upload-lib.ts",
+  ]),
  bundle: true,
  format: "cjs",
  outdir: OUT_DIR,
@@ -74,7 +78,10 @@ const context = await esbuild.context({
  define: {
    __CODEQL_ACTION_VERSION__: JSON.stringify(pkg.version),
  },
+  metafile: true,
 });

-await context.rebuild();
+const result = await context.rebuild();
+await writeFile(join(__dirname, "meta.json"), JSON.stringify(result.metafile));
+
 await context.dispose();
@@ -7,7 +7,11 @@ import noAsyncForeach from "eslint-plugin-no-async-foreach";
 import jsdoc from "eslint-plugin-jsdoc";
 import tseslint from "typescript-eslint";
 import globals from "globals";
+import path from "path";
+import { fileURLToPath } from "url";

+const __filename = fileURLToPath(import.meta.url);
+const __dirname = path.dirname(__filename);
 const githubFlatConfigs = github.getFlatConfigs();

 export default [
@@ -43,7 +47,7 @@ export default [
    plugins: {
      "import-x": importX,
      "no-async-foreach": fixupPluginRules(noAsyncForeach),
-      "jsdoc": jsdoc,
+      jsdoc: jsdoc,
    },

    languageOptions: {
@@ -67,7 +71,13 @@ export default [

        typescript: {},
      },
-      "import/ignore": ["sinon", "uuid", "@octokit/plugin-retry", "del", "get-folder-size"],
+      "import/ignore": [
+        "sinon",
+        "uuid",
+        "@octokit/plugin-retry",
+        "del",
+        "get-folder-size",
+      ],
      "import-x/resolver-next": [
        createTypeScriptImportResolver(),
        createNodeResolver({
@@ -143,7 +153,7 @@ export default [
          // We don't currently require full JSDoc coverage, so this rule
          // should not error on missing @param annotations.
          disableMissingParamChecks: true,
-        }
+        },
      ],
    },
  },
@@ -162,9 +172,9 @@ export default [
      "@typescript-eslint/no-unused-vars": [
        "error",
        {
-          "args": "all",
-          "argsIgnorePattern": "^_",
-        }
+          args: "all",
+          argsIgnorePattern: "^_",
+        },
      ],
      "func-style": "off",
    },
@@ -183,6 +193,11 @@ export default [
      // The scripts in `pr-checks` are expected to output to the console.
      "no-console": "off",

+      "import/no-extraneous-dependencies": [
+        "error",
+        { packageDir: [__dirname, path.resolve(__dirname, "pr-checks")] },
+      ],
+
      "@typescript-eslint/no-floating-promises": [
        "error",
        {
@@ -170,6 +170,6 @@ outputs:
  codeql-version:
    description: The version of the CodeQL binary used for analysis
 runs:
-  using: node20
+  using: node24
  main: '../lib/init-action.js'
  post: '../lib/init-action-post.js'
@@ -1,6 +1,6 @@
 {
-  "bundleVersion": "codeql-bundle-v2.24.3",
-  "cliVersion": "2.24.3",
-  "priorBundleVersion": "codeql-bundle-v2.24.2",
-  "priorCliVersion": "2.24.2"
+  "bundleVersion": "codeql-bundle-v2.25.4",
+  "cliVersion": "2.25.4",
+  "priorBundleVersion": "codeql-bundle-v2.25.3",
+  "priorCliVersion": "2.25.3"
 }
@@ -1,6 +1,6 @@
 {
  "name": "codeql",
-  "version": "3.34.1",
+  "version": "4.35.5",
  "private": true,
  "description": "CodeQL action",
  "scripts": {
@@ -12,7 +12,7 @@
    "ava": "npm run transpile && ava --verbose",
    "test": "npm run ava -- src/",
    "test-debug": "npm run test -- --timeout=20m",
-    "transpile": "tsc --build --verbose"
+    "transpile": "tsc --build --verbose tsconfig.json"
  },
  "license": "MIT",
  "workspaces": [
@@ -29,47 +29,46 @@
    "@actions/http-client": "^3.0.0",
    "@actions/io": "^2.0.0",
    "@actions/tool-cache": "^3.0.1",
-    "@octokit/plugin-retry": "^8.0.0",
-    "@schemastore/package": "0.0.10",
+    "@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",
-    "jsonschema": "1.4.1",
+    "jsonschema": "1.5.0",
    "long": "^5.3.2",
-    "node-forge": "^1.3.3",
+    "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": "^2.0.3",
+    "@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": "^21.0.0",
+    "@types/sinon": "^21.0.1",
    "ava": "^7.0.0",
-    "esbuild": "^0.27.3",
-    "eslint": "^9.39.2",
-    "eslint-import-resolver-typescript": "^3.8.7",
+    "esbuild": "^0.28.0",
+    "eslint": "^9.39.4",
+    "eslint-import-resolver-typescript": "^4.4.4",
    "eslint-plugin-github": "^6.0.0",
-    "eslint-plugin-import-x": "^4.16.1",
-    "eslint-plugin-jsdoc": "^62.7.1",
+    "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",
-    "nock": "^14.0.11",
-    "sinon": "^21.0.2",
-    "typescript": "^5.9.3",
-    "typescript-eslint": "^8.57.0"
+    "globals": "^17.5.0",
+    "nock": "^14.0.12",
+    "sinon": "^21.1.2",
+    "typescript": "^6.0.3",
+    "typescript-eslint": "^8.59.1"
  },
  "overrides": {
    "@actions/tool-cache": {
@@ -91,6 +90,7 @@
      "semver": ">=6.3.1"
    },
    "brace-expansion@2.0.1": "2.0.2",
-    "glob": "^11.1.0"
+    "glob": "^11.1.0",
+    "undici": "^6.24.0"
  }
 }
@@ -0,0 +1,13 @@
+import * as githubUtils from "@actions/github/lib/utils";
+import { type Octokit } from "@octokit/core";
+import { type PaginateInterface } from "@octokit/plugin-paginate-rest";
+import { type Api } from "@octokit/plugin-rest-endpoint-methods";
+
+/** The type of the Octokit client. */
+export type ApiClient = Octokit & Api & { paginate: PaginateInterface };
+
+/** Constructs an `ApiClient` using `token` for authentication. */
+export function getApiClient(token: string): ApiClient {
+  const opts = githubUtils.getOctokitOptions(token);
+  return new githubUtils.GitHub(opts);
+}
@@ -0,0 +1,48 @@
+#!/usr/bin/env npx tsx
+
+import * as fs from "node:fs/promises";
+
+import { BUNDLE_METADATA_FILE } from "./config";
+
+interface InputInfo {
+  bytesInOutput: number;
+}
+
+type Inputs = Record<string, InputInfo>;
+
+interface Output {
+  bytes: number;
+  inputs: Inputs;
+}
+
+interface Metadata {
+  outputs: Record<string, Output>;
+}
+
+function toMB(bytes: number): string {
+  return `${(bytes / (1024 * 1024)).toFixed(2)}MB`;
+}
+
+async function main() {
+  const fileContents = await fs.readFile(BUNDLE_METADATA_FILE);
+  const metadata = JSON.parse(String(fileContents)) as Metadata;
+
+  for (const [outputFile, outputData] of Object.entries(
+    metadata.outputs,
+  ).reverse()) {
+    console.info(`${outputFile}: ${toMB(outputData.bytes)}`);
+
+    for (const [inputName, inputData] of Object.entries(outputData.inputs)) {
+      // Ignore any inputs that make up less than 5% of the output.
+      const percentage = (inputData.bytesInOutput / outputData.bytes) * 100.0;
+      if (percentage < 5.0) continue;
+
+      console.info(`  ${inputName}: ${toMB(inputData.bytesInOutput)}`);
+    }
+  }
+}
+
+// Only call `main` if this script was run directly.
+if (require.main === module) {
+  void main();
+}
@@ -5,12 +5,12 @@ versions:
 steps:
  - uses: ./../action/init
    with:
-      languages: C#,java-kotlin,swift,typescript
+      languages: C#,java-kotlin,typescript
      tools: ${{ steps.prepare-test.outputs.tools-url }}

  - name: "Check languages"
    run: |
-      expected_languages="csharp,java,swift,javascript"
+      expected_languages="csharp,java,javascript"
      actual_languages=$(jq -r '.languages | join(",")' "$RUNNER_TEMP"/config)

      if [ "$expected_languages" != "$actual_languages" ]; then
@@ -5,7 +5,7 @@ versions:
  - default
 steps:
  - name: Set up Ruby
-    uses: ruby/setup-ruby@09a7688d3b55cf0e976497ff046b70949eeaccfd # v1.288.0
+    uses: ruby/setup-ruby@c4e5b1316158f92e3d49443a9d58b31d25ac0f8f # v1.306.0
    with:
      ruby-version: 2.6
  - name: Install Code Scanning integration
@@ -16,7 +16,17 @@ steps:
    id: proxy
    uses: ./../action/start-proxy
    with:
-      registry_secrets: '[{ "type": "nuget_feed", "url": "https://api.nuget.org/v3/index.json" }]'
+      registry_secrets: |
+        [
+          {
+            "type": "maven_repository",
+            "url": "https://repo.maven.apache.org/maven2/"
+          },
+          {
+            "type": "maven_repository",
+            "url": "https://repo1.maven.org/maven2"
+          }
+        ]

  - name: Print proxy outputs
    run: |
@@ -27,3 +37,10 @@ steps:
  - name: Fail if proxy outputs are not set
    if: (!steps.proxy.outputs.proxy_host) || (!steps.proxy.outputs.proxy_port) || (!steps.proxy.outputs.proxy_ca_certificate) || (!steps.proxy.outputs.proxy_urls)
    run: exit 1
+
+  - name: Fail if proxy_urls does not contain all registries
+    if: |
+      join(fromJSON(steps.proxy.outputs.proxy_urls)[*].type, ',') != 'maven_repository,maven_repository'
+      || !contains(steps.proxy.outputs.proxy_urls, 'https://repo.maven.apache.org/maven2/')
+      || !contains(steps.proxy.outputs.proxy_urls, 'https://repo1.maven.org/maven2')
+    run: exit 1
@@ -0,0 +1,23 @@
+import path from "path";
+
+/** The oldest supported major version of the CodeQL Action. */
+export const OLDEST_SUPPORTED_MAJOR_VERSION = 3;
+
+/** The `pr-checks` directory. */
+export const PR_CHECKS_DIR = __dirname;
+
+/** The path of the file configuring which checks shouldn't be required. */
+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",
+);
@@ -0,0 +1,16 @@
+# PR checks to exclude from required checks
+contains:
+  - "https://"
+  - "Update"
+  - "ESLint"
+  - "update"
+  - "test-setup-python-scripts"
+is:
+  - "CodeQL"
+  - "Dependabot"
+  - "check-expected-release-files"
+  - "Agent"
+  - "Cleanup artifacts"
+  - "Prepare"
+  - "Upload results"
+  - "Label PR with size"
@@ -2,11 +2,15 @@
  "private": true,
  "description": "Dependencies for the sync.ts",
  "dependencies": {
-    "yaml": "^2.8.2"
+    "@actions/core": "^2.0.3",
+    "@actions/github": "^8.0.1",
+    "@octokit/core": "^7.0.6",
+    "@octokit/plugin-paginate-rest": ">=9.2.2",
+    "@octokit/plugin-rest-endpoint-methods": "^17.0.0",
+    "yaml": "^2.8.3"
  },
  "devDependencies": {
-    "@types/node": "^20.19.9",
-    "tsx": "^4.21.0",
-    "typescript": "^5.9.3"
+    "@types/node": "^20.19.39",
+    "tsx": "^4.21.0"
  }
 }
@@ -0,0 +1,61 @@
+#!/usr/bin/env npx tsx
+
+/*
+Tests for the release-branches.ts script
+*/
+
+import * as assert from "node:assert/strict";
+import { describe, it } from "node:test";
+
+import { computeBackportBranches } from "./release-branches";
+
+describe("computeBackportBranches", async () => {
+  await it("rejects invalid major versions", () => {
+    // The majorVersion is expected to be in vN format.
+    assert.throws(() => computeBackportBranches("3", "v4.28.0", 3));
+    assert.throws(() => computeBackportBranches("v3.1", "v4.28.0", 3));
+  });
+
+  await it("rejects invalid latest tags", () => {
+    // The latestTag is expected to be in vN.M.P format.
+    assert.throws(() => computeBackportBranches("v3", "v4", 3));
+    assert.throws(() => computeBackportBranches("v3", "4", 3));
+    assert.throws(() => computeBackportBranches("v3", "v4.28", 3));
+    assert.throws(() => computeBackportBranches("v3", "4.28", 3));
+    assert.throws(() => computeBackportBranches("v3", "4.28.0", 3));
+  });
+
+  await it("sets backport source branch based on major version", () => {
+    // Test that the backport source branch is releases/v{majorVersion}
+    const result = computeBackportBranches("v3", "v4.28.0", 3);
+    assert.equal(result.backportSourceBranch, "releases/v3");
+  });
+
+  await it("no backport targets when major version is the oldest supported", () => {
+    // When majorVersion equals the major version of latestTag and we do not support older major versions,
+    // then there are no older supported branches to backport to.
+    const result = computeBackportBranches("v3", "v3.28.0", 3);
+    assert.deepEqual(result.backportTargetBranches, []);
+  });
+
+  await it("backports to older supported major versions", () => {
+    const result = computeBackportBranches("v4", "v4.1.0", 3);
+    assert.equal(result.backportSourceBranch, "releases/v4");
+    assert.deepEqual(result.backportTargetBranches, ["releases/v3"]);
+  });
+
+  await it("backports to multiple older supported branches", () => {
+    const result = computeBackportBranches("v5", "v5.0.0", 3);
+    assert.equal(result.backportSourceBranch, "releases/v5");
+    assert.deepEqual(result.backportTargetBranches, [
+      "releases/v4",
+      "releases/v3",
+    ]);
+  });
+
+  await it("does not backport when major version is older than latest tag", () => {
+    const result = computeBackportBranches("v2", "v3.28.0", 2);
+    assert.equal(result.backportSourceBranch, "releases/v2");
+    assert.deepEqual(result.backportTargetBranches, []);
+  });
+});
@@ -0,0 +1,121 @@
+#!/usr/bin/env npx tsx
+
+import { parseArgs } from "node:util";
+
+import * as core from "@actions/core";
+
+import { OLDEST_SUPPORTED_MAJOR_VERSION } from "./config";
+
+/** The results of checking which release branches to backport to.  */
+export interface BackportInfo {
+  /** The source release branch. */
+  backportSourceBranch: string;
+  /**
+   * The computed release branches we should backport to.
+   * Will be empty if there are no branches we need to backport to.
+   */
+  backportTargetBranches: string[];
+}
+
+/**
+ * Compute the backport source and target branches for a release.
+ *
+ * @param majorVersion - The major version string (e.g. "v4").
+ * @param latestTag - The most recent tag published to the repository (e.g. "v4.32.6").
+ * @param oldestSupportedMajorVersion - The oldest supported major version number.
+ * @returns The names of the source branch and target branches.
+ */
+export function computeBackportBranches(
+  majorVersion: string,
+  latestTag: string,
+  oldestSupportedMajorVersion: number,
+): BackportInfo {
+  // Perform some sanity checks on the inputs.
+  // For `majorVersion`, we expect exactly `vN` for some `N`.
+  const majorVersionMatch = majorVersion.match(/^v(\d+)$/);
+  if (!majorVersionMatch) {
+    throw new Error("--major-version value must be in `vN` format.");
+  }
+
+  // For latestTag, we expect something starting with `vN.M.P`
+  const latestTagMatch = latestTag.match(/^v(\d+)\.\d+\.\d+/);
+  if (!latestTagMatch) {
+    throw new Error(
+      `--latest-tag value must be in 'vN.M.P' format, but '${latestTag}' is not.`,
+    );
+  }
+
+  const majorVersionNumber = Number.parseInt(majorVersionMatch[1]);
+  const latestTagMajor = Number.parseInt(latestTagMatch[1]);
+
+  // If this is a primary release, we backport to all supported branches,
+  // so we check whether the majorVersion taken from the package.json
+  // is greater than or equal to the latest tag pulled from the repo.
+  // For example...
+  //     'v1' >= 'v2' is False # we're operating from an older release branch and should not backport
+  //     'v2' >= 'v2' is True  # the normal case where we're updating the current version
+  //     'v3' >= 'v2' is True  # in this case we are making the first release of a new major version
+  const considerBackports = majorVersionNumber >= latestTagMajor;
+
+  const backportSourceBranch = `releases/v${majorVersionNumber}`;
+  const backportTargetBranches: string[] = [];
+
+  if (considerBackports) {
+    for (let i = majorVersionNumber - 1; i > 0; i--) {
+      const branchName = `releases/v${i}`;
+      if (i >= oldestSupportedMajorVersion) {
+        backportTargetBranches.push(branchName);
+      }
+    }
+  }
+
+  return { backportSourceBranch, backportTargetBranches };
+}
+
+async function main() {
+  const { values: options } = parseArgs({
+    options: {
+      // The major version of the release in `vN` format (e.g. `v4`).
+      "major-version": {
+        type: "string",
+      },
+      // The most recent tag published to the repository (e.g. `v4.28.0`).
+      "latest-tag": {
+        type: "string",
+      },
+    },
+    strict: true,
+  });
+
+  if (options["major-version"] === undefined) {
+    throw Error("--major-version is required");
+  }
+  if (options["latest-tag"] === undefined) {
+    throw Error("--latest-tag is required");
+  }
+
+  const majorVersion = options["major-version"];
+  const latestTag = options["latest-tag"];
+
+  console.log(`Major version: ${majorVersion}`);
+  console.log(`Latest tag: ${latestTag}`);
+
+  const result = computeBackportBranches(
+    majorVersion,
+    latestTag,
+    OLDEST_SUPPORTED_MAJOR_VERSION,
+  );
+
+  core.setOutput("backport_source_branch", result.backportSourceBranch);
+  core.setOutput(
+    "backport_target_branches",
+    JSON.stringify(result.backportTargetBranches),
+  );
+
+  process.exit(0);
+}
+
+// Only call `main` if this script was run directly.
+if (require.main === module) {
+  void main();
+}
@@ -0,0 +1,60 @@
+#!/usr/bin/env npx tsx
+
+/*
+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";
+
+const defaultOptions: Options = {
+  apply: false,
+  verbose: false,
+};
+
+const toCheckInfo = (name: string) =>
+  ({ context: name, app_id: -1 }) satisfies CheckInfo;
+
+const expectedPartialMatches = ["PR Check - Foo", "https://example.com"].map(
+  toCheckInfo,
+);
+
+const expectedExactMatches = ["CodeQL", "Update"].map(toCheckInfo);
+
+const testChecks = expectedExactMatches.concat(expectedPartialMatches);
+
+const emptyExclusions: Exclusions = {
+  is: [],
+  contains: [],
+};
+
+describe("removeExcluded", async () => {
+  await it("retains all checks if no exclusions are configured", () => {
+    const retained = removeExcluded(
+      defaultOptions,
+      emptyExclusions,
+      testChecks,
+    );
+    assert.deepEqual(retained, testChecks);
+  });
+
+  await it("removes exact matches", () => {
+    const retained = removeExcluded(
+      defaultOptions,
+      { ...emptyExclusions, is: ["CodeQL", "Update"] },
+      testChecks,
+    );
+    assert.deepEqual(retained, expectedPartialMatches);
+  });
+
+  await it("removes partial matches", () => {
+    const retained = removeExcluded(
+      defaultOptions,
+      { ...emptyExclusions, contains: ["https://", "PR Check"] },
+      testChecks,
+    );
+    assert.deepEqual(retained, expectedExactMatches);
+  });
+});
@@ -0,0 +1,287 @@
+#!/usr/bin/env npx tsx
+
+/** Update the required checks based on the current branch. */
+
+import * as fs from "fs";
+import { parseArgs } from "node:util";
+
+import * as yaml from "yaml";
+
+import { type ApiClient, getApiClient } from "./api-client";
+import {
+  OLDEST_SUPPORTED_MAJOR_VERSION,
+  PR_CHECK_EXCLUDED_FILE,
+} from "./config";
+
+/** Represents the command-line options. */
+export interface Options {
+  /** The token to use to authenticate to the GitHub API. */
+  token?: string;
+  /** The git ref to use the checks for. */
+  ref?: string;
+  /** Whether to actually apply the changes or not. */
+  apply: boolean;
+  /** Whether to output additional information. */
+  verbose: boolean;
+}
+
+/** Identifies the CodeQL Action repository. */
+const codeqlActionRepo = {
+  owner: "github",
+  repo: "codeql-action",
+};
+
+/** 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. */
+  contains: string[];
+  /** A list of check names that are excluded if their name is an exact match. */
+  is: string[];
+}
+
+/** Loads the configuration for which checks to exclude. */
+function loadExclusions(): Exclusions {
+  return yaml.parse(
+    fs.readFileSync(PR_CHECK_EXCLUDED_FILE, "utf-8"),
+  ) as Exclusions;
+}
+
+/**
+ * Represents information about a check run. We track the `app_id` that generated the check,
+ * because the API will require it in addition to the name in the future.
+ */
+export interface CheckInfo {
+  /** The display name of the check. */
+  context: string;
+  /** The ID of the app that generated the check. */
+  app_id: number;
+}
+
+/** Removes entries from `checkInfos` based on the configuration. */
+export function removeExcluded(
+  options: Options,
+  exclusions: Exclusions,
+  checkInfos: CheckInfo[],
+): CheckInfo[] {
+  if (options.verbose) {
+    console.log(exclusions);
+  }
+
+  return checkInfos.filter((checkInfo) => {
+    if (exclusions.is.includes(checkInfo.context)) {
+      console.info(
+        `Excluding '${checkInfo.context}' because it is an exact exclusion.`,
+      );
+      return false;
+    }
+
+    for (const containsStr of exclusions.contains) {
+      if (checkInfo.context.includes(containsStr)) {
+        console.info(
+          `Excluding '${checkInfo.context}' because it contains '${containsStr}'.`,
+        );
+        return false;
+      }
+    }
+
+    // Keep.
+    return true;
+  });
+}
+
+/** Gets a list of check run names for `ref`. */
+async function getChecksFor(
+  options: Options,
+  client: ApiClient,
+  ref: string,
+): Promise<CheckInfo[]> {
+  console.info(`Getting checks for '${ref}'`);
+
+  const response = await client.paginate(
+    "GET /repos/{owner}/{repo}/commits/{ref}/check-runs",
+    {
+      ...codeqlActionRepo,
+      ref,
+    },
+  );
+
+  if (response.length === 0) {
+    throw new Error(`No checks found for '${ref}'.`);
+  }
+
+  console.info(`Retrieved ${response.length} check runs.`);
+
+  const notSkipped = response.filter(
+    (checkRun) => checkRun.conclusion !== "skipped",
+  );
+  console.info(`Of those: ${notSkipped.length} were not skipped.`);
+
+  // We use the ID of the app that generated the check run when returned by the API,
+  // but default to -1 to tell the API that any check with the given name should be
+  // required.
+  const checkInfos = notSkipped.map((check) => ({
+    context: check.name,
+    app_id: check.app?.id || -1,
+  }));
+
+  // Load the configuration for which checks to exclude and apply it before
+  // returning the checks.
+  const exclusions = loadExclusions();
+  return removeExcluded(options, exclusions, checkInfos);
+}
+
+/** Gets the current list of release branches. */
+async function getReleaseBranches(client: ApiClient): Promise<string[]> {
+  const refs = await client.rest.git.listMatchingRefs({
+    ...codeqlActionRepo,
+    ref: "heads/releases/v",
+  });
+  return refs.data.map((ref) => ref.ref).sort();
+}
+
+/** Updates the required status checks for `branch` to `checks`. */
+async function patchBranchProtectionRule(
+  client: ApiClient,
+  branch: string,
+  checks: Set<string>,
+) {
+  await client.rest.repos.setStatusCheckContexts({
+    ...codeqlActionRepo,
+    branch,
+    contexts: Array.from(checks),
+  });
+}
+
+/** Sets `checkNames` as required checks for `branch`. */
+async function updateBranch(
+  options: Options,
+  client: ApiClient,
+  branch: string,
+  checkNames: Set<string>,
+) {
+  console.info(`Updating '${branch}'...`);
+
+  // Query the current set of required checks for this branch.
+  const currentContexts = await client.rest.repos.getAllStatusCheckContexts({
+    ...codeqlActionRepo,
+    branch,
+  });
+
+  // Identify which required checks we will remove and which ones we will add.
+  const currentCheckNames = new Set(currentContexts.data);
+  let additions = 0;
+  let removals = 0;
+  let unchanged = 0;
+
+  for (const currentCheck of currentCheckNames) {
+    if (!checkNames.has(currentCheck)) {
+      console.info(`- Removing '${currentCheck}' for branch '${branch}'`);
+      removals++;
+    } else {
+      unchanged++;
+    }
+  }
+  for (const newCheck of checkNames) {
+    if (!currentCheckNames.has(newCheck)) {
+      console.info(`+ Adding '${newCheck}' for branch '${branch}'`);
+      additions++;
+    }
+  }
+
+  console.info(
+    `For '${branch}': ${removals} removals; ${additions} additions; ${unchanged} unchanged`,
+  );
+
+  // Perform the update if there are changes and `--apply` was specified.
+  if (unchanged === checkNames.size && removals === 0 && additions === 0) {
+    console.info("Not applying changes because there is nothing to do.");
+  } else if (options.apply) {
+    await patchBranchProtectionRule(client, branch, checkNames);
+  } else {
+    console.info("Not applying changes because `--apply` was not specified.");
+  }
+}
+
+async function main(): Promise<void> {
+  const { values: options } = parseArgs({
+    options: {
+      // The token to use to authenticate to the API.
+      token: {
+        type: "string",
+      },
+      // The git ref for which to retrieve the check runs.
+      ref: {
+        type: "string",
+        default: "main",
+      },
+      // By default, we perform a dry-run. Setting `apply` to `true` actually applies the changes.
+      apply: {
+        type: "boolean",
+        default: false,
+      },
+      // Whether to output additional information.
+      verbose: {
+        type: "boolean",
+        default: false,
+      },
+    },
+    strict: true,
+  });
+
+  if (options.token === undefined) {
+    throw new Error("Missing --token");
+  }
+
+  console.info(
+    `Oldest supported major version is: ${OLDEST_SUPPORTED_MAJOR_VERSION}`,
+  );
+
+  // Initialise the API client.
+  const client = getApiClient(options.token);
+
+  // Find the check runs for the specified `ref` that we will later set as the required checks
+  // for the main and release branches.
+  const checkInfos = await getChecksFor(options, client, options.ref);
+  const checkNames = new Set(checkInfos.map((info) => info.context));
+
+  // Update the main branch.
+  await updateBranch(options, client, "main", checkNames);
+
+  // Retrieve the refs of the release branches.
+  const releaseBranches = await getReleaseBranches(client);
+  console.info(
+    `Found ${releaseBranches.length} release branches: ${releaseBranches.join(", ")}`,
+  );
+
+  for (const releaseBranchRef of releaseBranches) {
+    // Sanity check that the ref name is in the expected format and extract the major version.
+    const releaseBranchMatch = releaseBranchRef.match(
+      /^refs\/heads\/(releases\/v(\d+))/,
+    );
+    if (!releaseBranchMatch) {
+      console.warn(
+        `Branch ref '${releaseBranchRef}' not in the expected format.`,
+      );
+      continue;
+    }
+    const releaseBranch = releaseBranchMatch[1];
+    const releaseBranchMajor = Number.parseInt(releaseBranchMatch[2]);
+
+    // Update the required checks for this major version if it is still supported.
+    if (releaseBranchMajor < OLDEST_SUPPORTED_MAJOR_VERSION) {
+      console.info(
+        `Skipping '${releaseBranch}' since it is older than v${OLDEST_SUPPORTED_MAJOR_VERSION}`,
+      );
+      continue;
+    } else {
+      await updateBranch(options, client, releaseBranch, checkNames);
+    }
+  }
+
+  process.exit(0);
+}
+
+// Only call `main` if this script was run directly.
+if (require.main === module) {
+  void main();
+}
@@ -5,7 +5,7 @@ import * as path from "path";

 import * as yaml from "yaml";

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

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

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

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

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

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

    if (
@@ -3,6 +3,7 @@
  "compilerOptions": {
    /* Basic Options */
    "lib": ["esnext"],
+    "module": "preserve",
    "rootDir": "..",
    "sourceMap": false,
    "noEmit": true,
@@ -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();
@@ -21,5 +21,5 @@ outputs:
  environment:
    description: The inferred build environment configuration.
 runs:
-  using: node20
+  using: node24
  main: '../lib/resolve-environment-action.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 }}
@@ -35,5 +54,5 @@ outputs:
  codeql-version:
    description: The version of the CodeQL binary that was installed.
 runs:
-  using: node20
+  using: node24
  main: '../lib/setup-codeql-action.js'
@@ -53,6 +53,12 @@ export function getTemporaryDirectory(): string {
    : getRequiredEnvParam("RUNNER_TEMP");
 }

+const PR_DIFF_RANGE_JSON_FILENAME = "pr-diff-range.json";
+
+export function getDiffRangesJsonFilePath(): string {
+  return path.join(getTemporaryDirectory(), PR_DIFF_RANGE_JSON_FILENAME);
+}
+
 export function getActionVersion(): string {
  return __CODEQL_ACTION_VERSION__;
 }
@@ -28,12 +28,11 @@ import {
  DependencyCacheUploadStatusReport,
  uploadDependencyCaches,
 } from "./dependency-caching";
-import { getDiffInformedAnalysisBranches } from "./diff-informed-analysis-utils";
 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";
+import { cleanupAndUploadOverlayBaseDatabaseToCache } from "./overlay/caching";
 import { getRepositoryNwo } from "./repository";
 import * as statusReport from "./status-report";
 import {
@@ -136,9 +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
@@ -170,7 +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) {
@@ -183,7 +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.",
    );
@@ -206,7 +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) {
@@ -305,14 +308,8 @@ async function run(startedAt: Date) {
      logger,
    );

-    const branches = await getDiffInformedAnalysisBranches(
-      codeql,
-      features,
-      logger,
-    );
-    const diffRangePackDir = branches
-      ? await setupDiffInformedQueryRun(branches, logger)
-      : undefined;
+    // Setup diff informed analysis if needed (based on whether init created the file)
+    const diffRangePackDir = await setupDiffInformedQueryRun(logger);

    await warnIfGoInstalledAfterInit(config, logger);
    await runAutobuildIfLegacyGoWorkflow(config, logger);
@@ -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),
@@ -5,11 +5,7 @@ import { performance } from "perf_hooks";
 import * as io from "@actions/io";
 import * as yaml from "js-yaml";

-import {
-  getTemporaryDirectory,
-  getRequiredInput,
-  PullRequestBranches,
-} from "./actions-util";
+import { getTemporaryDirectory, getRequiredInput } from "./actions-util";
 import * as analyses from "./analyses";
 import { setupCppAutobuild } from "./autobuild";
 import { type CodeQL } from "./codeql";
@@ -21,14 +17,13 @@ import {
 import { addDiagnostic, makeDiagnostic } from "./diagnostics";
 import {
  DiffThunkRange,
-  writeDiffRangesJsonFile,
-  getPullRequestEditedDiffRanges,
+  readDiffRangesJsonFile,
 } 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";
+import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import type * as sarif from "./sarif";
 import { DatabaseCreationTimings, EventReport } from "./status-report";
 import { endTracingForCluster } from "./tracer-config";
@@ -46,7 +41,7 @@ export class CodeQLAnalysisError extends Error {
  }
 }

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

 type RunQueriesDurationStatusReport = {
  /**
@@ -55,12 +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
@@ -120,12 +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);
@@ -136,14 +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))
        ) {
@@ -237,32 +232,28 @@ async function finalizeDatabaseCreation(
 * the diff range information, or `undefined` if the feature is disabled.
 */
 export async function setupDiffInformedQueryRun(
-  branches: PullRequestBranches,
  logger: Logger,
 ): Promise<string | undefined> {
  return await withGroupAsync(
    "Generating diff range extension pack",
    async () => {
-      logger.info(
-        `Calculating diff ranges for ${branches.base}...${branches.head}`,
-      );
-      const diffRanges = await getPullRequestEditedDiffRanges(branches, logger);
+      const diffRanges = readDiffRangesJsonFile(logger);
+      if (diffRanges === undefined) {
+        logger.info(
+          "No precomputed diff ranges found; skipping diff-informed analysis stage.",
+        );
+        return undefined;
+      }
+
      const checkoutPath = getRequiredInput("checkout_path");
      const packDir = writeDiffRangeDataExtensionPack(
        logger,
        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;
    },
  );
@@ -316,18 +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
@@ -368,10 +354,6 @@ dataExtensions:
    `Wrote pr-diff-range extension pack to ${extensionFilePath}:\n${extensionContents}`,
  );

-  // Write the diff ranges to a JSON file, for action-side alert filtering by the
-  // upload-lib module.
-  writeDiffRangesJsonFile(logger, ranges);
-
  return diffRangeDir;
 }

@@ -704,7 +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"}
@@ -141,7 +141,12 @@ test("scanArtifactsForTokens handles files without tokens", async (t) => {
  }
 });

-if (os.platform() !== "win32") {
+// This test is slow (extracts and scans a zip artifact), so by default we only run it in CI. Set
+// RUN_SLOW_TESTS=1 to run it locally.
+if (
+  os.platform() !== "win32" &&
+  (process.env.CI === "true" || process.env.RUN_SLOW_TESTS === "1")
+) {
  test("scanArtifactsForTokens finds token in debug artifacts", async (t) => {
    t.timeout(15000); // 15 seconds
    const messages: LoggedMessage[] = [];
@@ -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: [],
@@ -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();
@@ -299,6 +299,20 @@ test("wrapCliConfigurationError - swift build failed", (t) => {
  t.true(wrappedError instanceof ConfigurationError);
 });

+test("wrapCliConfigurationError - swift incompatible os", (t) => {
+  const commandError = new CommandInvocationError(
+    "codeql",
+    ["swift/tools/autobuild.sh"],
+    1,
+    "2026-04-01 18:35:00 EST ERRO [extractor/main] [incompatible-os] Currently, Swift analysis is only supported on macOS. (IncompatibleOs.cpp:26)",
+  );
+  const cliError = new CliError(commandError);
+
+  const wrappedError = wrapCliConfigurationError(cliError);
+
+  t.true(wrappedError instanceof ConfigurationError);
+});
+
 test("wrapCliConfigurationError - pack cannot be found", (t) => {
  const commandError = new CommandInvocationError(
    "codeql",
@@ -144,6 +144,7 @@ export enum CliConfigErrorCategory {
  OutOfMemoryOrDisk = "OutOfMemoryOrDisk",
  PackCannotBeFound = "PackCannotBeFound",
  PackMissingAuth = "PackMissingAuth",
+  SwiftIncompatibleOs = "SwiftIncompatibleOs",
  SwiftBuildFailed = "SwiftBuildFailed",
  UnsupportedBuildMode = "UnsupportedBuildMode",
 }
@@ -281,6 +282,12 @@ const cliErrorsConfig: Record<CliConfigErrorCategory, CliErrorConfiguration> = {
      ),
    ],
  },
+  [CliConfigErrorCategory.SwiftIncompatibleOs]: {
+    cliErrorMessageCandidates: [
+      new RegExp("\\[incompatible-os\\]"),
+      new RegExp("Swift analysis is only supported on macOS"),
+    ],
+  },
  [CliConfigErrorCategory.UnsupportedBuildMode]: {
    cliErrorMessageCandidates: [
      new RegExp(
@@ -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:
@@ -24,11 +24,8 @@ import {
 import { isAnalyzingDefaultBranch } from "./git-utils";
 import { Language } from "./languages";
 import { Logger } from "./logging";
-import {
-  OverlayDatabaseMode,
-  writeBaseDatabaseOidsFile,
-  writeOverlayChangesFile,
-} from "./overlay";
+import { writeBaseDatabaseOidsFile, writeOverlayChangesFile } from "./overlay";
+import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import * as setupCodeql from "./setup-codeql";
 import { ZstdAvailability } from "./tar";
 import { ToolsDownloadStatusReport } from "./tools-download";
@@ -285,17 +282,17 @@ const CODEQL_MINIMUM_VERSION = "2.17.6";
 /**
 * This version will shortly become the oldest version of CodeQL that the Action will run with.
 */
-const CODEQL_NEXT_MINIMUM_VERSION = "2.17.6";
+const CODEQL_NEXT_MINIMUM_VERSION = "2.19.4";

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

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

 /** The CLI verbosity level to use for extraction in debug mode. */
 const EXTRACTION_DEBUG_MODE_VERBOSITY = "progress++";
@@ -308,6 +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
@@ -320,6 +319,8 @@ export async function setupCodeQL(
  tempDir: string,
  variant: util.GitHubVariant,
  defaultCliVersion: CodeQLDefaultVersionInfo,
+  rawLanguages: string[] | undefined,
+  useOverlayAwareDefaultCliVersion: boolean,
  features: FeatureEnablement,
  logger: Logger,
  checkVersion: boolean,
@@ -343,6 +344,8 @@ export async function setupCodeQL(
      tempDir,
      variant,
      defaultCliVersion,
+      rawLanguages,
+      useOverlayAwareDefaultCliVersion,
      features,
      logger,
    );
@@ -18,10 +18,11 @@ 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, OverlayDatabaseMode } from "./overlay";
+import { CODEQL_OVERLAY_MINIMUM_VERSION } from "./overlay";
 import { OverlayDisabledReason } from "./overlay/diagnostics";
+import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import * as overlayStatus from "./overlay/status";
 import { parseRepositoryNwo } from "./repository";
 import {
@@ -33,6 +34,7 @@ import {
  LoggedMessage,
  mockCodeQLVersion,
  createTestConfig,
+  makeMacro,
 } from "./testing-utils";
 import {
  GitHubVariant,
@@ -214,7 +216,7 @@ 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,
@@ -267,7 +269,7 @@ test.serial(

      const expectedConfig = createTestConfig({
        analysisKinds: [AnalysisKind.CodeQuality],
-        languages: [KnownLanguage.javascript],
+        languages: [BuiltInLanguage.javascript],
        codeQLCmd: codeql.getPath(),
        computedConfig,
        dbLocation: path.resolve(tempDir, "codeql_databases"),
@@ -517,7 +519,7 @@ 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,
@@ -891,10 +893,10 @@ 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],
@@ -943,12 +945,12 @@ 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,
  },
 ]) {
@@ -968,7 +970,7 @@ for (const { displayName, language, feature } of [
    const messages: LoggedMessage[] = [];
    const buildMode = await configUtils.parseBuildModeInput(
      "none",
-      [KnownLanguage.python],
+      [BuiltInLanguage.python],
      createFeatures([feature]),
      getRecordingLogger(messages),
    );
@@ -1004,6 +1006,7 @@ interface OverlayDatabaseModeTestSetup {
  codeqlVersion: string;
  gitRoot: string | undefined;
  gitVersion: GitVersionInfo | undefined;
+  hasSubmodules: boolean;
  codeScanningConfig: UserConfig;
  diskUsage: DiskUsage | undefined;
  memoryFlagValue: number;
@@ -1017,13 +1020,11 @@ 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(
-    gitUtils.GIT_MINIMUM_VERSION_FOR_OVERLAY,
-    gitUtils.GIT_MINIMUM_VERSION_FOR_OVERLAY,
-  ),
+  gitVersion: new GitVersionInfo("2.39.0", "2.39.0"),
+  hasSubmodules: false,
  codeScanningConfig: {},
  diskUsage: {
    numAvailableBytes: 50_000_000_000,
@@ -1034,10 +1035,9 @@ const defaultOverlayDatabaseModeTestSetup: OverlayDatabaseModeTestSetup = {
  repositoryProperties: {},
 };

-const checkOverlayEnablementMacro = test.macro({
+const checkOverlayEnablementMacro = makeMacro({
  exec: async (
    t: ExecutionContext,
-    _title: string,
    setupOverrides: Partial<OverlayDatabaseModeTestSetup>,
    expected:
      | {
@@ -1091,7 +1091,7 @@ 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
@@ -1099,6 +1099,9 @@ const checkOverlayEnablementMacro = test.macro({
          sinon.stub(gitUtils, "getGitRoot").resolves(setup.gitRoot);
        }

+        // Mock submodule detection
+        sinon.stub(gitUtils, "hasSubmodules").returns(setup.hasSubmodules);
+
        // Mock default branch detection
        sinon
          .stub(gitUtils, "isAnalyzingDefaultBranch")
@@ -1128,11 +1131,10 @@ const checkOverlayEnablementMacro = test.macro({
      }
    });
  },
-  title: (_, title) => `checkOverlayEnablement: ${title}`,
+  title: (title) => `checkOverlayEnablement: ${title}`,
 });

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Environment variable override - Overlay",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -1143,8 +1145,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Environment variable override - OverlayBase",
  {
    overlayDatabaseEnvVar: "overlay-base",
@@ -1155,8 +1156,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Environment variable override - None",
  {
    overlayDatabaseEnvVar: "none",
@@ -1166,8 +1166,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Ignore invalid environment variable",
  {
    overlayDatabaseEnvVar: "invalid-mode",
@@ -1177,11 +1176,10 @@ 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],
  },
  {
@@ -1189,11 +1187,10 @@ 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,
  },
@@ -1203,15 +1200,14 @@ 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,
  },
  {
@@ -1220,11 +1216,10 @@ 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,
@@ -1237,11 +1232,10 @@ 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,
@@ -1257,11 +1251,10 @@ 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,
@@ -1274,11 +1267,10 @@ 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,
@@ -1296,11 +1288,10 @@ 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,
@@ -1317,11 +1308,10 @@ 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,
@@ -1339,11 +1329,10 @@ 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,
@@ -1359,11 +1348,10 @@ 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,
@@ -1376,11 +1364,10 @@ 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,
@@ -1395,11 +1382,10 @@ 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,
@@ -1414,11 +1400,10 @@ 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,
@@ -1432,11 +1417,10 @@ 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,
@@ -1450,18 +1434,17 @@ 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,
  },
  {
@@ -1469,18 +1452,17 @@ 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,
  },
  {
@@ -1488,18 +1470,17 @@ 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,
  },
  {
@@ -1507,18 +1488,17 @@ 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,
  },
  {
@@ -1526,11 +1506,10 @@ 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,
  },
@@ -1539,11 +1518,10 @@ 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,
  },
@@ -1552,11 +1530,10 @@ 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,
  },
@@ -1565,11 +1542,10 @@ 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,
  },
@@ -1579,15 +1555,14 @@ 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,
  },
  {
@@ -1596,11 +1571,10 @@ 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,
@@ -1613,11 +1587,10 @@ 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,
@@ -1633,11 +1606,10 @@ 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,
@@ -1655,11 +1627,10 @@ 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,
@@ -1672,11 +1643,10 @@ 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,
@@ -1689,11 +1659,10 @@ 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,
@@ -1708,11 +1677,10 @@ 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,
@@ -1727,18 +1695,17 @@ 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,
  },
  {
@@ -1746,18 +1713,17 @@ 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,
  },
  {
@@ -1765,18 +1731,17 @@ 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,
  },
  {
@@ -1784,18 +1749,17 @@ 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,
  },
  {
@@ -1803,11 +1767,10 @@ 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,
  },
@@ -1816,11 +1779,10 @@ 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,
  },
@@ -1829,11 +1791,10 @@ 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,
  },
@@ -1842,8 +1803,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay PR analysis by env",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -1854,8 +1814,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Overlay PR analysis by env on a runner with low disk space",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -1867,11 +1826,10 @@ 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,
  },
@@ -1881,34 +1839,31 @@ 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",
@@ -1919,8 +1874,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Fallback due to missing git root",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -1931,35 +1885,47 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
-  "Fallback due to old git version",
+checkOverlayEnablementMacro.serial(
+  "Fallback due to old git version with submodules",
  {
    overlayDatabaseEnvVar: "overlay",
-    gitVersion: new GitVersionInfo("2.30.0", "2.30.0"), // Version below required 2.38.0
+    gitVersion: new GitVersionInfo("2.34.1", "2.34.1"), // Above 2.11.0 but below 2.36.0
+    hasSubmodules: true,
  },
  {
    disabledReason: OverlayDisabledReason.IncompatibleGit,
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
-  "Fallback when git version cannot be determined",
+checkOverlayEnablementMacro.serial(
+  "Fallback when git version cannot be determined and repo has submodules",
  {
    overlayDatabaseEnvVar: "overlay",
    gitVersion: undefined,
+    hasSubmodules: true,
  },
  {
    disabledReason: OverlayDisabledReason.IncompatibleGit,
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
+  "Overlay enabled when git version cannot be determined and repo has no submodules",
+  {
+    overlayDatabaseEnvVar: "overlay",
+    gitVersion: undefined,
+    hasSubmodules: false,
+  },
+  {
+    overlayDatabaseMode: OverlayDatabaseMode.Overlay,
+    useOverlayDatabaseCaching: false,
+  },
+);
+
+checkOverlayEnablementMacro.serial(
  "No overlay when disabled via repository property",
  {
-    languages: [KnownLanguage.javascript],
+    languages: [BuiltInLanguage.javascript],
    features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
    isPullRequest: true,
    repositoryProperties: {
@@ -1971,11 +1937,10 @@ 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: {
@@ -1988,8 +1953,7 @@ test.serial(
  },
 );

-test.serial(
-  checkOverlayEnablementMacro,
+checkOverlayEnablementMacro.serial(
  "Environment variable override takes precedence over repository property",
  {
    overlayDatabaseEnvVar: "overlay",
@@ -2004,9 +1968,8 @@ 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],
@@ -2023,11 +1986,10 @@ 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,
  },
@@ -43,17 +43,19 @@ import {
  getGeneratedFiles,
  getGitRoot,
  getGitVersionOrThrow,
-  GIT_MINIMUM_VERSION_FOR_OVERLAY,
+  GIT_MINIMUM_VERSION_FOR_OVERLAY_WITH_SUBMODULES,
  GitVersionInfo,
+  hasSubmodules,
  isAnalyzingDefaultBranch,
 } from "./git-utils";
-import { KnownLanguage, Language } from "./languages";
+import { BuiltInLanguage, Language } from "./languages";
 import { Logger } from "./logging";
-import { CODEQL_OVERLAY_MINIMUM_VERSION, OverlayDatabaseMode } from "./overlay";
+import { CODEQL_OVERLAY_MINIMUM_VERSION } from "./overlay";
 import {
  addOverlayDisablementDiagnostics,
  OverlayDisabledReason,
 } from "./overlay/diagnostics";
+import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import { shouldSkipOverlayAnalysis } from "./overlay/status";
 import { RepositoryNwo } from "./repository";
 import { ToolsFeature } from "./tools-features";
@@ -272,10 +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;
    }
@@ -405,6 +407,7 @@ export async function getLanguages(
  return languages;
 }

+/** Parses the `languages` input into a list of languages without checking if they are supported by CodeQL. */
 export function getRawLanguagesNoAutodetect(
  languagesInput: string | undefined,
 ): string[] {
@@ -945,7 +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.
@@ -969,7 +972,8 @@ async function validateOverlayDatabaseMode(
    );
    return new Failure(OverlayDisabledReason.IncompatibleCodeQl);
  }
-  if ((await getGitRoot(sourceRoot)) === undefined) {
+  const gitRoot = await getGitRoot(sourceRoot);
+  if (gitRoot === undefined) {
    logger.warning(
      `Cannot build an ${overlayDatabaseMode} database because ` +
        `the source root "${sourceRoot}" is not inside a git repository. ` +
@@ -977,21 +981,26 @@ async function validateOverlayDatabaseMode(
    );
    return new Failure(OverlayDisabledReason.NoGitRoot);
  }
-  if (gitVersion === undefined) {
-    logger.warning(
-      `Cannot build an ${overlayDatabaseMode} database because ` +
-        "the Git version could not be determined. " +
-        "Falling back to creating a normal full database instead.",
-    );
-    return new Failure(OverlayDisabledReason.IncompatibleGit);
-  }
-  if (!gitVersion.isAtLeast(GIT_MINIMUM_VERSION_FOR_OVERLAY)) {
-    logger.warning(
-      `Cannot build an ${overlayDatabaseMode} database because ` +
-        `the installed Git version is older than ${GIT_MINIMUM_VERSION_FOR_OVERLAY}. ` +
-        "Falling back to creating a normal full database instead.",
-    );
-    return new Failure(OverlayDisabledReason.IncompatibleGit);
+  if (hasSubmodules(gitRoot)) {
+    if (gitVersion === undefined) {
+      logger.warning(
+        `Cannot build an ${overlayDatabaseMode} database because ` +
+          "the repository has submodules and the Git version could not be determined. " +
+          "Falling back to creating a normal full database instead.",
+      );
+      return new Failure(OverlayDisabledReason.IncompatibleGit);
+    }
+    if (
+      !gitVersion.isAtLeast(GIT_MINIMUM_VERSION_FOR_OVERLAY_WITH_SUBMODULES)
+    ) {
+      logger.warning(
+        `Cannot build an ${overlayDatabaseMode} database because ` +
+          "the repository has submodules and the installed Git version is older " +
+          `than ${GIT_MINIMUM_VERSION_FOR_OVERLAY_WITH_SUBMODULES}. ` +
+          "Falling back to creating a normal full database instead.",
+      );
+      return new Failure(OverlayDisabledReason.IncompatibleGit);
+    }
  }

  return new Success({
@@ -1028,13 +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 {
@@ -1531,7 +1540,7 @@ export async function parseBuildModeInput(
  }

  if (
-    languages.includes(KnownLanguage.csharp) &&
+    languages.includes(BuiltInLanguage.csharp) &&
    (await features.getValue(Feature.DisableCsharpBuildless))
  ) {
    logger.warning(
@@ -1541,7 +1550,7 @@ 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,
  });
 }
@@ -12,7 +12,7 @@ import { Config } from "./config-utils";
 import { Feature, FeatureEnablement } from "./feature-flags";
 import * as gitUtils from "./git-utils";
 import { Logger, withGroupAsync } from "./logging";
-import { OverlayDatabaseMode } from "./overlay";
+import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import { RepositoryNwo } from "./repository";
 import * as util from "./util";
 import { asHTTPError, bundleDb, CleanupLevel, parseGitHubUrl } from "./util";
@@ -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-v2.24.3",
-  "cliVersion": "2.24.3",
-  "priorBundleVersion": "codeql-bundle-v2.24.2",
-  "priorCliVersion": "2.24.2"
+  "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));
@@ -16,6 +16,7 @@ import {
  mockCodeQLVersion,
  mockFeatureFlagApiEndpoint,
  setupActionsVars,
+  makeMacro,
 } from "./testing-utils";
 import { GitHubVariant, withTmpDir } from "./util";
 import type { GitHubVersion } from "./util";
@@ -42,10 +43,9 @@ 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,
  ) => {
@@ -94,18 +94,16 @@ const testShouldPerformDiffInformedAnalysis = test.macro({
      getPullRequestBranchesStub.restore();
    });
  },
-  title: (_, title) => `shouldPerformDiffInformedAnalysis: ${title}`,
+  title: (title) => `shouldPerformDiffInformedAnalysis: ${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 +111,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false when CODEQL_ACTION_DIFF_INFORMED_QUERIES is set to false",
  {
    featureEnabled: true,
@@ -123,8 +120,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns true when CODEQL_ACTION_DIFF_INFORMED_QUERIES is set to true",
  {
    featureEnabled: false,
@@ -133,8 +129,7 @@ test.serial(
  true,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false for CodeQL version 2.20.0",
  {
    codeQLVersion: "2.20.0",
@@ -142,8 +137,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false for invalid GHES version",
  {
    gitHubVersion: {
@@ -154,8 +148,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false for GHES version 3.18.5",
  {
    gitHubVersion: {
@@ -166,8 +159,7 @@ test.serial(
  false,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns true for GHES version 3.19.0",
  {
    gitHubVersion: {
@@ -178,8 +170,7 @@ test.serial(
  true,
 );

-test.serial(
-  testShouldPerformDiffInformedAnalysis,
+testShouldPerformDiffInformedAnalysis.serial(
  "returns false when not a pull request",
  {
    pullRequestBranches: undefined,
@@ -1,5 +1,4 @@
 import * as fs from "fs";
-import * as path from "path";

 import * as actionsUtil from "./actions-util";
 import type { PullRequestBranches } from "./actions-util";
@@ -77,16 +76,12 @@ export interface DiffThunkRange {
  endLine: number;
 }

-function getDiffRangesJsonFilePath(): string {
-  return path.join(actionsUtil.getTemporaryDirectory(), "pr-diff-range.json");
-}
-
 export function writeDiffRangesJsonFile(
  logger: Logger,
  ranges: DiffThunkRange[],
 ): void {
  const jsonContents = JSON.stringify(ranges, null, 2);
-  const jsonFilePath = getDiffRangesJsonFilePath();
+  const jsonFilePath = actionsUtil.getDiffRangesJsonFilePath();
  fs.writeFileSync(jsonFilePath, jsonContents);
  logger.debug(
    `Wrote pr-diff-range JSON file to ${jsonFilePath}:\n${jsonContents}`,
@@ -96,7 +91,7 @@ export function writeDiffRangesJsonFile(
 export function readDiffRangesJsonFile(
  logger: Logger,
 ): DiffThunkRange[] | undefined {
-  const jsonFilePath = getDiffRangesJsonFilePath();
+  const jsonFilePath = actionsUtil.getDiffRangesJsonFilePath();
  if (!fs.existsSync(jsonFilePath)) {
    logger.debug(`Diff ranges JSON file does not exist at ${jsonFilePath}`);
    return undefined;
@@ -105,7 +100,14 @@ export function readDiffRangesJsonFile(
  logger.debug(
    `Read pr-diff-range JSON file from ${jsonFilePath}:\n${jsonContents}`,
  );
-  return JSON.parse(jsonContents) as DiffThunkRange[];
+  try {
+    return JSON.parse(jsonContents) as DiffThunkRange[];
+  } catch (e) {
+    logger.warning(
+      `Failed to parse diff ranges JSON file at ${jsonFilePath}: ${e}`,
+    );
+    return undefined;
+  }
 }

 /**
@@ -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/",
@@ -451,12 +451,16 @@ test.serial(`selects CLI from defaults.json on GHES`, async (t) => {
  await withTmpDir(async (tmpDir) => {
    const features = setUpFeatureFlagTests(tmpDir);

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

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

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

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

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

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

@@ -72,6 +95,19 @@ 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.
@@ -85,7 +121,6 @@ export enum Feature {
  OverlayAnalysisStatusCheck = "overlay_analysis_status_check",
  /** Controls whether overlay build failures on the default branch are stored in the Actions cache. */
  OverlayAnalysisStatusSave = "overlay_analysis_status_save",
-  PythonDefaultIsToNotExtractStdlib = "python_default_is_to_not_extract_stdlib",
  QaTelemetryEnabled = "qa_telemetry_enabled",
  /** Note that this currently only disables baseline file coverage information. */
  SkipFileCoverageOnPrs = "skip_file_coverage_on_prs",
@@ -278,6 +313,16 @@ 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",
@@ -298,12 +343,6 @@ export const featureConfig = {
    envVar: "CODEQL_ACTION_OVERLAY_ANALYSIS_SKIP_RESOURCE_CHECKS",
    minimumVersion: undefined,
  },
-  [Feature.PythonDefaultIsToNotExtractStdlib]: {
-    defaultValue: false,
-    envVar: "CODEQL_ACTION_DISABLE_PYTHON_STANDARD_LIBRARY_EXTRACTION",
-    minimumVersion: undefined,
-    toolsFeature: ToolsFeature.PythonDefaultIsToNotExtractStdlib,
-  },
  [Feature.QaTelemetryEnabled]: {
    defaultValue: false,
    envVar: "CODEQL_ACTION_QA_TELEMETRY",
@@ -353,8 +392,12 @@ 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>;
@@ -378,12 +421,11 @@ 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],
    };
  }

@@ -393,7 +435,7 @@ 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;
  }

  /**
@@ -525,13 +567,13 @@ 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);
  }

  /**
@@ -607,16 +649,22 @@ 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
@@ -632,8 +680,7 @@ 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;
@@ -641,17 +688,14 @@ 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,
    };
  }
@@ -343,75 +343,142 @@ test.serial("decodeGitFilePath quoted strings", async (t) => {
  );
 });

-test.serial("getFileOidsUnderPath returns correct file mapping", async (t) => {
-  const runGitCommandStub = sinon
-    .stub(gitUtils as any, "runGitCommand")
-    .resolves(
-      "30d998ded095371488be3a729eb61d86ed721a18_lib/git-utils.js\n" +
-        "d89514599a9a99f22b4085766d40af7b99974827_lib/git-utils.js.map\n" +
-        "a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96_src/git-utils.ts",
-    );
+test.serial(
+  "getFileOidsUnderPath uses --recurse-submodules when submodules exist",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      fs.writeFileSync(path.join(tmpDir, ".gitmodules"), "");
+      const runGitCommandStub = sinon
+        .stub(gitUtils as any, "runGitCommand")
+        .callsFake(async (_cwd: any, args: any) => {
+          if (args[0] === "rev-parse") {
+            return `${tmpDir}\n`;
+          }
+          return (
+            "100644 30d998ded095371488be3a729eb61d86ed721a18 0\tlib/git-utils.js\n" +
+            "100644 d89514599a9a99f22b4085766d40af7b99974827 0\tlib/git-utils.js.map\n" +
+            "100644 a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96 0\tsrc/git-utils.ts"
+          );
+        });

-  const result = await gitUtils.getFileOidsUnderPath("/fake/path");
+      const result = await gitUtils.getFileOidsUnderPath("/fake/path");

-  t.deepEqual(result, {
-    "lib/git-utils.js": "30d998ded095371488be3a729eb61d86ed721a18",
-    "lib/git-utils.js.map": "d89514599a9a99f22b4085766d40af7b99974827",
-    "src/git-utils.ts": "a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96",
-  });
+      t.deepEqual(result, {
+        "lib/git-utils.js": "30d998ded095371488be3a729eb61d86ed721a18",
+        "lib/git-utils.js.map": "d89514599a9a99f22b4085766d40af7b99974827",
+        "src/git-utils.ts": "a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96",
+      });

-  t.deepEqual(runGitCommandStub.firstCall.args, [
-    "/fake/path",
-    ["ls-files", "--recurse-submodules", "--format=%(objectname)_%(path)"],
-    "Cannot list Git OIDs of tracked files.",
-  ]);
-});
+      // Second call (after getGitRoot) should include --recurse-submodules
+      t.deepEqual(runGitCommandStub.secondCall.args[1], [
+        "ls-files",
+        "--recurse-submodules",
+        "--stage",
+      ]);
+    });
+  },
+);
+
+test.serial(
+  "getFileOidsUnderPath omits --recurse-submodules when no submodules exist",
+  async (t) => {
+    await withTmpDir(async (tmpDir) => {
+      const runGitCommandStub = sinon
+        .stub(gitUtils as any, "runGitCommand")
+        .callsFake(async (_cwd: any, args: any) => {
+          if (args[0] === "rev-parse") {
+            return `${tmpDir}\n`;
+          }
+          return (
+            "100644 30d998ded095371488be3a729eb61d86ed721a18 0\tlib/git-utils.js\n" +
+            "100644 a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96 0\tsrc/git-utils.ts"
+          );
+        });
+
+      const result = await gitUtils.getFileOidsUnderPath("/fake/path");
+
+      t.deepEqual(result, {
+        "lib/git-utils.js": "30d998ded095371488be3a729eb61d86ed721a18",
+        "src/git-utils.ts": "a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96",
+      });
+
+      // Second call (after getGitRoot) should NOT include --recurse-submodules
+      t.deepEqual(runGitCommandStub.secondCall.args[1], [
+        "ls-files",
+        "--stage",
+      ]);
+    });
+  },
+);

 test.serial("getFileOidsUnderPath handles quoted paths", async (t) => {
-  sinon
-    .stub(gitUtils as any, "runGitCommand")
-    .resolves(
-      "30d998ded095371488be3a729eb61d86ed721a18_lib/normal-file.js\n" +
-        'd89514599a9a99f22b4085766d40af7b99974827_"lib/file with spaces.js"\n' +
-        'a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96_"lib/file\\twith\\ttabs.js"',
-    );
+  await withTmpDir(async (tmpDir) => {
+    sinon
+      .stub(gitUtils as any, "runGitCommand")
+      .callsFake(async (_cwd: any, args: any) => {
+        if (args[0] === "rev-parse") {
+          return `${tmpDir}\n`;
+        }
+        return (
+          "100644 30d998ded095371488be3a729eb61d86ed721a18 0\tlib/normal-file.js\n" +
+          '100644 d89514599a9a99f22b4085766d40af7b99974827 0\t"lib/file with spaces.js"\n' +
+          '100644 a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96 0\t"lib/file\\twith\\ttabs.js"'
+        );
+      });

-  const result = await gitUtils.getFileOidsUnderPath("/fake/path");
+    const result = await gitUtils.getFileOidsUnderPath("/fake/path");

-  t.deepEqual(result, {
-    "lib/normal-file.js": "30d998ded095371488be3a729eb61d86ed721a18",
-    "lib/file with spaces.js": "d89514599a9a99f22b4085766d40af7b99974827",
-    "lib/file\twith\ttabs.js": "a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96",
+    t.deepEqual(result, {
+      "lib/normal-file.js": "30d998ded095371488be3a729eb61d86ed721a18",
+      "lib/file with spaces.js": "d89514599a9a99f22b4085766d40af7b99974827",
+      "lib/file\twith\ttabs.js": "a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96",
+    });
  });
 });

 test.serial("getFileOidsUnderPath handles empty output", async (t) => {
-  sinon.stub(gitUtils as any, "runGitCommand").resolves("");
+  await withTmpDir(async (tmpDir) => {
+    sinon
+      .stub(gitUtils as any, "runGitCommand")
+      .callsFake(async (_cwd: any, args: any) => {
+        if (args[0] === "rev-parse") {
+          return `${tmpDir}\n`;
+        }
+        return "";
+      });

-  const result = await gitUtils.getFileOidsUnderPath("/fake/path");
-  t.deepEqual(result, {});
+    const result = await gitUtils.getFileOidsUnderPath("/fake/path");
+    t.deepEqual(result, {});
+  });
 });

 test.serial(
  "getFileOidsUnderPath throws on unexpected output format",
  async (t) => {
-    sinon
-      .stub(gitUtils as any, "runGitCommand")
-      .resolves(
-        "30d998ded095371488be3a729eb61d86ed721a18_lib/git-utils.js\n" +
-          "invalid-line-format\n" +
-          "a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96_src/git-utils.ts",
-      );
+    await withTmpDir(async (tmpDir) => {
+      sinon
+        .stub(gitUtils as any, "runGitCommand")
+        .callsFake(async (_cwd: any, args: any) => {
+          if (args[0] === "rev-parse") {
+            return `${tmpDir}\n`;
+          }
+          return (
+            "100644 30d998ded095371488be3a729eb61d86ed721a18 0\tlib/git-utils.js\n" +
+            "invalid-line-format\n" +
+            "100644 a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96 0\tsrc/git-utils.ts"
+          );
+        });

-    await t.throwsAsync(
-      async () => {
-        await gitUtils.getFileOidsUnderPath("/fake/path");
-      },
-      {
-        instanceOf: Error,
-        message: 'Unexpected "git ls-files" output: invalid-line-format',
-      },
-    );
+      await t.throwsAsync(
+        async () => {
+          await gitUtils.getFileOidsUnderPath("/fake/path");
+        },
+        {
+          instanceOf: Error,
+          message: 'Unexpected "git ls-files" output: invalid-line-format',
+        },
+      );
+    });
  },
 );

@@ -1,4 +1,6 @@
+import * as fs from "fs";
 import * as os from "os";
+import * as path from "path";

 import * as core from "@actions/core";
 import { ExecOptions } from "@actions/exec";
@@ -14,10 +16,11 @@ import {
 import { ConfigurationError, getRequiredEnvParam } from "./util";

 /**
- * Minimum Git version required for overlay analysis. The `git ls-files --format`
- * option, which is used by `getFileOidsUnderPath`, was introduced in Git 2.38.0.
+ * Minimum Git version required for overlay analysis in repositories that
+ * contain submodules. Support for using the `git ls-files
+ * --recurse-submodules` option with `--stage` was added in Git 2.36.0.
 */
-export const GIT_MINIMUM_VERSION_FOR_OVERLAY = "2.38.0";
+export const GIT_MINIMUM_VERSION_FOR_OVERLAY_WITH_SUBMODULES = "2.36.0";

 /**
 * Git version information
@@ -244,6 +247,16 @@ export const getGitRoot = async function (
  }
 };

+/**
+ * Returns true if the Git repository has submodules registered (i.e. a
+ * `.gitmodules` file exists at the repository root).
+ *
+ * @param gitRoot The root of the Git repository.
+ */
+export function hasSubmodules(gitRoot: string): boolean {
+  return fs.existsSync(path.join(gitRoot, ".gitmodules"));
+}
+
 /**
 * Returns the Git OIDs of all tracked files (in the index and in the working
 * tree) that are under the given base path, including files in active
@@ -252,31 +265,45 @@ export const getGitRoot = async function (
 *
 * @param basePath A path into the Git repository.
 * @returns a map from file paths (relative to `basePath`) to Git OIDs.
- * @throws {Error} if "git ls-tree" produces unexpected output.
+ * @throws {Error} if "git ls-files" produces unexpected output.
 */
 export const getFileOidsUnderPath = async function (
  basePath: string,
 ): Promise<{ [key: string]: string }> {
  // Without the --full-name flag, the path is relative to the current working
  // directory of the git command, which is basePath.
+  //
+  // We use --stage rather than --format here because --format was only
+  // introduced in Git 2.38.0, which would limit overlay rollout.
+  //
+  // We only pass --recurse-submodules when the repository actually has
+  // submodules, because the combination of --recurse-submodules and --stage is
+  // only supported since Git 2.36.0.
+  const gitRoot = await getGitRoot(basePath);
+  const mayHaveSubmodules =
+    gitRoot === undefined ? true : hasSubmodules(gitRoot);
+  const args = mayHaveSubmodules
+    ? ["ls-files", "--recurse-submodules", "--stage"]
+    : ["ls-files", "--stage"];
  const stdout = await runGitCommand(
    basePath,
-    ["ls-files", "--recurse-submodules", "--format=%(objectname)_%(path)"],
+    args,
    "Cannot list Git OIDs of tracked files.",
  );

  const fileOidMap: { [key: string]: string } = {};
-  // With --format=%(objectname)_%(path), the output is a list of lines like:
-  // 30d998ded095371488be3a729eb61d86ed721a18_lib/git-utils.js
-  // d89514599a9a99f22b4085766d40af7b99974827_lib/git-utils.js.map
-  const regex = /^([0-9a-f]{40})_(.+)$/;
+  // With --stage, the output is a list of lines like:
+  // 100644 4c51bc1d9e86cd86e01b0f340cb8ce095c33b283 0\tsrc/git-utils.test.ts
+  // 100644 6b792ea543ce75d7a8a03df591e3c85311ecb64f 0\tsrc/git-utils.ts
+  // The fields are: <mode> <oid> <stage>\t<path>
+  const regex = /^[0-9]+ ([0-9a-f]{40}) [0-9]+\t(.+)$/;
  for (const line of stdout.split("\n")) {
    if (line) {
      const match = line.match(regex);
      if (match) {
        const oid = match[1];
-        const path = decodeGitFilePath(match[2]);
-        fileOidMap[path] = oid;
+        const filePath = decodeGitFilePath(match[2]);
+        fileOidMap[filePath] = oid;
      } else {
        throw new Error(`Unexpected "git ls-files" output: ${line}`);
      }
@@ -12,13 +12,14 @@ import { EnvVar } from "./environment";
 import { Feature } from "./feature-flags";
 import * as initActionPostHelper from "./init-action-post-helper";
 import { getRunnerLogger } from "./logging";
-import { OverlayDatabaseMode } from "./overlay";
+import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import * as overlayStatus from "./overlay/status";
 import { parseRepositoryNwo } from "./repository";
 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],
@@ -21,7 +21,7 @@ import * as dependencyCaching from "./dependency-caching";
 import { EnvVar } from "./environment";
 import { Feature, FeatureEnablement } from "./feature-flags";
 import { Logger } from "./logging";
-import { OverlayDatabaseMode } from "./overlay";
+import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import {
  createOverlayStatus,
  OverlayStatus,
@@ -37,6 +37,11 @@ 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 {
@@ -53,13 +58,13 @@ import {
  initConfig,
  runDatabaseInitCluster,
 } from "./init";
-import { JavaEnvVars, KnownLanguage } from "./languages";
-import { getActionsLogger, Logger } from "./logging";
+import { JavaEnvVars, BuiltInLanguage } from "./languages";
+import { getActionsLogger, Logger, withGroupAsync } from "./logging";
 import {
  downloadOverlayBaseDatabaseFromCache,
  OverlayBaseDatabaseDownloadStats,
-  OverlayDatabaseMode,
-} from "./overlay";
+} from "./overlay/caching";
+import { OverlayDatabaseMode } from "./overlay/overlay-database-mode";
 import { getRepositoryNwo, RepositoryNwo } from "./repository";
 import { ToolsSource } from "./setup-codeql";
 import {
@@ -293,16 +298,23 @@ 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?.includes(
+      AnalysisKind.CodeScanning,
+    );
    const initCodeQLResult = await initCodeQL(
      getOptionalInput("tools"),
      apiDetails,
      getTemporaryDirectory(),
      gitHubVersion.type,
      codeQLDefaultVersionInfo,
+      rawLanguages,
+      useOverlayAwareDefaultCliVersion,
      features,
      logger,
    );
@@ -325,7 +337,7 @@ 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";
@@ -384,6 +396,15 @@ async function run(startedAt: Date) {
      logger,
    });

+    if (
+      config.languages.includes(BuiltInLanguage.swift) &&
+      process.platform !== "darwin"
+    ) {
+      throw new ConfigurationError(
+        `Swift analysis is only supported on macOS runner images. Please migrate to a macOS runner.`,
+      );
+    }
+
    if (repositoryPropertiesResult.isFailure()) {
      addNoLanguageDiagnostic(
        config,
@@ -413,6 +434,7 @@ 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);
@@ -450,18 +472,23 @@ 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) {
@@ -494,16 +521,7 @@ async function run(startedAt: Date) {
    }

    if (
-      config.languages.includes(KnownLanguage.swift) &&
-      process.platform === "linux"
-    ) {
-      logger.warning(
-        `Swift analysis on Ubuntu runner images is no longer supported. Please migrate to a macOS runner if this affects you.`,
-      );
-    }
-
-    if (
-      config.languages.includes(KnownLanguage.go) &&
+      config.languages.includes(BuiltInLanguage.go) &&
      process.platform === "linux"
    ) {
      try {
@@ -561,7 +579,7 @@ 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",
@@ -639,27 +657,6 @@ async function run(startedAt: Date) {
      );
    }

-    if (
-      await codeql.supportsFeature(
-        ToolsFeature.PythonDefaultIsToNotExtractStdlib,
-      )
-    ) {
-      if (process.env["CODEQL_EXTRACTOR_PYTHON_EXTRACT_STDLIB"]) {
-        logger.debug(
-          "CODEQL_EXTRACTOR_PYTHON_EXTRACT_STDLIB is already set, so the Action will not override it.",
-        );
-      } else if (
-        !(await features.getValue(
-          Feature.PythonDefaultIsToNotExtractStdlib,
-          codeql,
-        ))
-      ) {
-        // We are in a situation where the feature flag is not rolled out,
-        // so we need to suppress the new default CLI behavior.
-        core.exportVariable("CODEQL_EXTRACTOR_PYTHON_EXTRACT_STDLIB", "true");
-      }
-    }
-
    // If we are doing a Java `build-mode: none` analysis, then set the environment variable that
    // enables the option in the Java extractor to minimize dependency jars. We also only do this if
    // dependency caching is enabled, since the option is intended to reduce the size of dependency
@@ -676,7 +673,7 @@ 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,
@@ -833,6 +830,42 @@ 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,
@@ -15,13 +15,14 @@ import {
  getFileCoverageInformationEnabled,
  logFileCoverageOnPrsDeprecationWarning,
 } from "./init";
-import { KnownLanguage } from "./languages";
+import { BuiltInLanguage } from "./languages";
 import {
  createFeatures,
  LoggedMessage,
  createTestConfig,
  getRecordingLogger,
  setupTests,
+  makeMacro,
 } from "./testing-utils";
 import { ConfigurationError, withTmpDir } from "./util";

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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