Move conversion of PR diff-range paths to absolute paths

Bump the npm-minor group with 4 updates

.github/workflows/codeql.yml

@@ -81,7 +81,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04,ubuntu-24.04,windows-2022,windows-2025,macos-13,macos-14,macos-15]
+        os: [ubuntu-22.04,ubuntu-24.04,windows-2022,windows-2025,macos-14,macos-15]
         tools: ${{ fromJson(needs.check-codeql-versions.outputs.versions) }}
     runs-on: ${{ matrix.os }}
 

.github/workflows/publish-immutable-action.yml

@@ -1,8 +1,10 @@
 name: 'Publish Immutable Action Version'
 
 on:
-  release:
-    types: [published]
+  push:
+    tags:
+      # Match version tags, but not the major version tags.
+      - 'v[0-9]+.**'
 
 defaults:
   run:
@@ -17,23 +19,9 @@ jobs:
       packages: write
 
     steps:
-      - name: Check release name
-        id: check
-        env:
-          RELEASE_NAME: ${{ github.event.release.name }}
-        run: |
-          echo "Release name: ${{ github.event.release.name }}"
-          if [[ $RELEASE_NAME == v* ]]; then
-            echo "This is a CodeQL Action release. Create an Immutable Action"
-            echo "is-action-release=true" >> $GITHUB_OUTPUT
-          else
-            echo "This is a CodeQL Bundle release. Do not create an Immutable Action"
-            echo "is-action-release=false" >> $GITHUB_OUTPUT
-          fi
-      - name: Checking out
-        if: steps.check.outputs.is-action-release == 'true'
+      - name: Checkout repository
         uses: actions/checkout@v5
-      - name: Publish
-        if: steps.check.outputs.is-action-release == 'true'
+
+      - name: Publish immutable release
         id: publish
         uses: actions/publish-immutable-action@v0.0.4

.github/workflows/script/bundle_changelog.py

@@ -0,0 +1,18 @@
+import os
+import re
+
+# Get the PR number from the PR URL.
+pr_number = os.environ['PR_URL'].split('/')[-1]
+changelog_note = f"- Update default CodeQL bundle version to {os.environ['CLI_VERSION']}. [#{pr_number}]({os.environ['PR_URL']})"
+
+# If the "[UNRELEASED]" section starts with "no user facing changes", remove that line.
+with open('CHANGELOG.md', 'r') as f:
+    changelog = f.read()
+
+changelog = changelog.replace('## [UNRELEASED]\n\nNo user facing changes.', '## [UNRELEASED]\n')
+
+# Add the changelog note to the bottom of the "[UNRELEASED]" section.
+changelog = re.sub(r'\n## (\d+\.\d+\.\d+)', f'{changelog_note}\n\n## \\1', changelog, count=1)
+
+with open('CHANGELOG.md', 'w') as f:
+    f.write(changelog)

.github/workflows/script/update-required-checks.sh

@@ -29,7 +29,7 @@ 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") | not)] | unique | sort')"
+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" | not)] | unique | sort')"
 
 echo "$CHECKS" | jq
 

.github/workflows/update-bundle.yml

@@ -40,6 +40,11 @@ jobs:
           git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
           git config --global user.name "github-actions[bot]"
 
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.12'
+
       - name: Set up Node.js
         uses: actions/setup-node@v6
         with:
@@ -78,28 +83,8 @@ jobs:
           echo "PR_URL=$pr_url" | tee -a "$GITHUB_ENV"
 
       - name: Create changelog note
-        shell: python
         run: |
-          import os
-          import re
-
-          # Get the PR number from the PR URL.
-          pr_number = os.environ['PR_URL'].split('/')[-1]
-          changelog_note = f"- Update default CodeQL bundle version to {os.environ['CLI_VERSION']}. [#{pr_number}]({os.environ['PR_URL']})"
-
-          # If the "[UNRELEASED]" section starts with "no user facing changes", remove that line.
-          # Use perl to avoid having to escape the newline character.
-
-          with open('CHANGELOG.md', 'r') as f:
-              changelog = f.read()
-
-          changelog = changelog.replace('## [UNRELEASED]\n\nNo user facing changes.', '## [UNRELEASED]\n')
-
-          # Add the changelog note to the bottom of the "[UNRELEASED]" section.
-          changelog = re.sub(r'\n## (\d+\.\d+\.\d+)', f'{changelog_note}\n\n## \\1', changelog, count=1)
-
-          with open('CHANGELOG.md', 'w') as f:
-              f.write(changelog)
+          python .github/workflows/script/bundle_changelog.py
 
       - name: Push changelog note
         run: |

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 See the [releases page](https://github.com/github/codeql-action/releases) for the relevant changes to the CodeQL CLI and language packs.
 
+## [UNRELEASED]
+
+- 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/).
+
 ## 4.31.2 - 30 Oct 2025
 
 No user facing changes.

eslint.config.mjs

@@ -12,6 +12,7 @@ import filenames from "eslint-plugin-filenames";
 import github from "eslint-plugin-github";
 import _import from "eslint-plugin-import";
 import noAsyncForeach from "eslint-plugin-no-async-foreach";
+import jsdoc from "eslint-plugin-jsdoc";
 import globals from "globals";
 
 const __filename = fileURLToPath(import.meta.url);
@@ -52,6 +53,7 @@ export default [
       github: fixupPluginRules(github),
       import: fixupPluginRules(_import),
       "no-async-foreach": noAsyncForeach,
+      "jsdoc": jsdoc,
     },
 
     languageOptions: {
@@ -133,6 +135,16 @@ export default [
       "@typescript-eslint/no-shadow": "error",
       "@typescript-eslint/prefer-optional-chain": "error",
       "one-var": ["error", "never"],
+
+      // Check param names to ensure that we don't have outdated JSDocs.
+      "jsdoc/check-param-names": [
+        "error",
+        {
+          // We don't currently require full JSDoc coverage, so this rule
+          // should not error on missing @param annotations.
+          disableMissingParamChecks: true,
+        }
+      ],
     },
   },
   {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "codeql",
-  "version": "4.31.2",
+  "version": "4.31.3",
   "private": true,
   "description": "CodeQL action",
   "scripts": {
@@ -31,11 +31,11 @@
     "@actions/exec": "^1.1.1",
     "@actions/github": "^6.0.0",
     "@actions/glob": "^0.5.0",
-    "@actions/http-client": "^2.2.3",
-    "@actions/io": "^1.1.3",
+    "@actions/http-client": "^3.0.0",
+    "@actions/io": "^2.0.0",
     "@actions/tool-cache": "^2.0.2",
     "@octokit/plugin-retry": "^6.0.0",
-    "@octokit/request-error": "^7.0.1",
+    "@octokit/request-error": "^7.0.2",
     "@schemastore/package": "0.0.10",
     "archiver": "^7.0.1",
     "fast-deep-equal": "^3.1.3",
@@ -45,33 +45,34 @@
     "jsonschema": "1.4.1",
     "long": "^5.3.2",
     "node-forge": "^1.3.1",
-    "octokit": "^5.0.4",
+    "octokit": "^5.0.5",
     "semver": "^7.7.3",
     "uuid": "^13.0.0"
   },
   "devDependencies": {
     "@ava/typescript": "6.0.0",
-    "@eslint/compat": "^1.4.0",
+    "@eslint/compat": "^1.4.1",
     "@eslint/eslintrc": "^3.3.1",
-    "@eslint/js": "^9.38.0",
+    "@eslint/js": "^9.39.1",
     "@microsoft/eslint-formatter-sarif": "^3.1.0",
-    "@octokit/types": "^15.0.1",
-    "@types/archiver": "^6.0.4",
+    "@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-forge": "^1.3.14",
     "@types/semver": "^7.7.1",
     "@types/sinon": "^17.0.4",
-    "@typescript-eslint/eslint-plugin": "^8.46.2",
+    "@typescript-eslint/eslint-plugin": "^8.46.4",
     "@typescript-eslint/parser": "^8.41.0",
     "ava": "^6.4.1",
-    "esbuild": "^0.25.11",
+    "esbuild": "^0.27.0",
     "eslint": "^8.57.1",
     "eslint-import-resolver-typescript": "^3.8.7",
     "eslint-plugin-filenames": "^1.3.2",
     "eslint-plugin-github": "^5.1.8",
     "eslint-plugin-import": "2.29.1",
+    "eslint-plugin-jsdoc": "^61.1.12",
     "eslint-plugin-no-async-foreach": "^0.1.1",
     "glob": "^11.0.3",
     "nock": "^14.0.10",

src/analyze.test.ts

@@ -4,12 +4,14 @@ import * as path from "path";
 import test from "ava";
 import * as sinon from "sinon";
 
+import * as actionsUtil from "./actions-util";
 import { CodeQuality, CodeScanning } from "./analyses";
 import {
   runQueries,
   defaultSuites,
   resolveQuerySuiteAlias,
   addSarifExtension,
+  diffRangeExtensionPackContents,
 } from "./analyze";
 import { createStubCodeQL } from "./codeql";
 import { Feature } from "./feature-flags";
@@ -158,3 +160,23 @@ test("addSarifExtension", (t) => {
     );
   }
 });
+
+test("diffRangeExtensionPackContents", (t) => {
+  sinon
+    .stub(actionsUtil, "getRequiredInput")
+    .withArgs("checkout_path")
+    .returns("/checkout/path");
+  const output = diffRangeExtensionPackContents([
+    {
+      path: "main.js",
+      startLine: 10,
+      endLine: 20,
+    },
+  ]);
+
+  const expected = fs.readFileSync(
+    `${__dirname}/../src/testdata/pr-diff-range.yml`,
+    "utf8",
+  );
+  t.deepEqual(output, expected);
+});

src/analyze.ts

@@ -5,7 +5,11 @@ import { performance } from "perf_hooks";
 import * as io from "@actions/io";
 import * as yaml from "js-yaml";
 
-import { getTemporaryDirectory, PullRequestBranches } from "./actions-util";
+import {
+  getTemporaryDirectory,
+  getRequiredInput,
+  PullRequestBranches,
+} from "./actions-util";
 import * as analyses from "./analyses";
 import { setupCppAutobuild } from "./autobuild";
 import { type CodeQL } from "./codeql";
@@ -38,89 +42,26 @@ export class CodeQLAnalysisError extends Error {
   }
 }
 
-export interface QueriesStatusReport {
-  /**
-   * Time taken in ms to run queries for actions (or undefined if this language was not analyzed).
-   *
-   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
-   * taken to run _all_ the queries.
-   */
-  analyze_builtin_queries_actions_duration_ms?: number;
-  /**
-   * Time taken in ms to run queries for cpp (or undefined if this language was not analyzed).
-   *
-   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
-   * taken to run _all_ the queries.
-   */
-  analyze_builtin_queries_cpp_duration_ms?: number;
-  /**
-   * Time taken in ms to run queries for csharp (or undefined if this language was not analyzed).
-   *
-   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
-   * taken to run _all_ the queries.
-   */
-  analyze_builtin_queries_csharp_duration_ms?: number;
-  /**
-   * Time taken in ms to run queries for go (or undefined if this language was not analyzed).
-   *
-   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
-   * taken to run _all_ the queries.
-   */
-  analyze_builtin_queries_go_duration_ms?: number;
-  /**
-   * Time taken in ms to run queries for java (or undefined if this language was not analyzed).
-   *
-   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
-   * taken to run _all_ the queries.
-   */
-  analyze_builtin_queries_java_duration_ms?: number;
-  /**
-   * Time taken in ms to run queries for javascript (or undefined if this language was not analyzed).
-   *
-   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
-   * taken to run _all_ the queries.
-   */
-  analyze_builtin_queries_javascript_duration_ms?: number;
-  /**
-   * Time taken in ms to run queries for python (or undefined if this language was not analyzed).
-   *
-   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
-   * taken to run _all_ the queries.
-   */
-  analyze_builtin_queries_python_duration_ms?: number;
-  /**
-   * Time taken in ms to run queries for ruby (or undefined if this language was not analyzed).
-   *
-   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
-   * taken to run _all_ the queries.
-   */
-  analyze_builtin_queries_ruby_duration_ms?: number;
-  /** Time taken in ms to run queries for swift (or undefined if this language was not analyzed).
-   *
-   * The "builtin" designation is now outdated with the move to CLI config parsing: this is the time
-   * taken to run _all_ the queries.
-   */
-  analyze_builtin_queries_swift_duration_ms?: number;
+type KnownLanguageKey = keyof typeof KnownLanguage;
 
-  /** Time taken in ms to interpret results for actions (or undefined if this language was not analyzed). */
-  interpret_results_actions_duration_ms?: number;
-  /** Time taken in ms to interpret results for cpp (or undefined if this language was not analyzed). */
-  interpret_results_cpp_duration_ms?: number;
-  /** Time taken in ms to interpret results for csharp (or undefined if this language was not analyzed). */
-  interpret_results_csharp_duration_ms?: number;
-  /** Time taken in ms to interpret results for go (or undefined if this language was not analyzed). */
-  interpret_results_go_duration_ms?: number;
-  /** Time taken in ms to interpret results for java (or undefined if this language was not analyzed). */
-  interpret_results_java_duration_ms?: number;
-  /** Time taken in ms to interpret results for javascript (or undefined if this language was not analyzed). */
-  interpret_results_javascript_duration_ms?: number;
-  /** Time taken in ms to interpret results for python (or undefined if this language was not analyzed). */
-  interpret_results_python_duration_ms?: number;
-  /** Time taken in ms to interpret results for ruby (or undefined if this language was not analyzed). */
-  interpret_results_ruby_duration_ms?: number;
-  /** Time taken in ms to interpret results for swift (or undefined if this language was not analyzed). */
-  interpret_results_swift_duration_ms?: number;
+type RunQueriesDurationStatusReport = {
+  /**
+   * Time taken in ms to run queries for the language (or undefined if this language was not analyzed).
+   *
+   * 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;
+};
 
+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;
+};
+
+export interface QueriesStatusReport
+  extends RunQueriesDurationStatusReport,
+    InterpretResultsDurationStatusReport {
   /**
    * Whether the analysis is diff-informed (in the sense that the action generates a diff-range data
    * extension for the analysis, regardless of whether the data extension is actually used by queries).
@@ -307,6 +248,45 @@ export async function setupDiffInformedQueryRun(
   );
 }
 
+export function diffRangeExtensionPackContents(
+  ranges: DiffThunkRange[],
+): string {
+  const header = `
+extensions:
+  - addsTo:
+      pack: codeql/util
+      extensible: restrictAlertsTo
+      checkPresence: false
+    data:
+`;
+
+  let data = ranges
+    .map((range) => {
+      // Diff-informed queries expect the file path to be absolute. CodeQL always
+      // uses forward slashes as the path separator, so on Windows we need to
+      // replace any backslashes with forward slashes.
+      const filename = path
+        .join(getRequiredInput("checkout_path"), range.path)
+        .replaceAll(path.sep, "/");
+
+      // Using yaml.dump() with `forceQuotes: true` ensures that all special
+      // characters are escaped, and that the path is always rendered as a
+      // quoted string on a single line.
+      return (
+        `      - [${yaml.dump(filename, { forceQuotes: true }).trim()}, ` +
+        `${range.startLine}, ${range.endLine}]\n`
+      );
+    })
+    .join("");
+  if (!data) {
+    // Ensure that the data extension is not empty, so that a pull request with
+    // no edited lines would exclude (instead of accepting) all alerts.
+    data = '      - ["", 0, 0]\n';
+  }
+
+  return header + data;
+}
+
 /**
  * Create an extension pack in the temporary directory that contains the file
  * line ranges that were added or modified in the pull request.
@@ -355,32 +335,7 @@ dataExtensions:
 `,
   );
 
-  const header = `
-extensions:
-  - addsTo:
-      pack: codeql/util
-      extensible: restrictAlertsTo
-      checkPresence: false
-    data:
-`;
-
-  let data = ranges
-    .map(
-      (range) =>
-        // Using yaml.dump() with `forceQuotes: true` ensures that all special
-        // characters are escaped, and that the path is always rendered as a
-        // quoted string on a single line.
-        `      - [${yaml.dump(range.path, { forceQuotes: true }).trim()}, ` +
-        `${range.startLine}, ${range.endLine}]\n`,
-    )
-    .join("");
-  if (!data) {
-    // Ensure that the data extension is not empty, so that a pull request with
-    // no edited lines would exclude (instead of accepting) all alerts.
-    data = '      - ["", 0, 0]\n';
-  }
-
-  const extensionContents = header + data;
+  const extensionContents = diffRangeExtensionPackContents(ranges);
   const extensionFilePath = path.join(diffRangeDir, "pr-diff-range.yml");
   fs.writeFileSync(extensionFilePath, extensionContents);
   logger.debug(

src/codeql.ts

@@ -1071,8 +1071,11 @@ export async function getCodeQLForCmd(
 /**
  * Gets the options for `path` of `options` as an array of extra option strings.
  *
- * @param ignoringOptions Options that should be ignored, for example because they have already
- *                        been passed and it is an error to pass them more than once.
+ * @param paths The CLI command components to get extra options for.
+ * @param args Additional arguments for this function.
+ * @param args.ignoringOptions
+ *   Options that should be ignored, for example because they have already
+ *   been passed and it is an error to pass them more than once.
  */
 function getExtraOptionsFromEnv(
   paths: string[],
@@ -1154,8 +1157,9 @@ async function runCli(
 /**
  * Writes the code scanning configuration that is to be used by the CLI.
  *
- * @param codeql The CodeQL object to use.
- * @param config The CodeQL Action state to use.
+ * @param config The CodeQL Action state to write.
+ * @param logger The logger to use.
+ *
  * @returns The path to the generated user configuration file.
  */
 async function writeCodeScanningConfigFile(

src/config-utils.test.ts

@@ -873,71 +873,62 @@ const mockRepositoryNwo = parseRepositoryNwo("owner/repo");
     expectedLanguages: ["javascript"],
   },
 ].forEach((args) => {
-  for (const resolveSupportedLanguagesUsingCli of [true, false]) {
-    test(`getLanguages${resolveSupportedLanguagesUsingCli ? " (supported languages via CLI)" : ""}: ${args.name}`, async (t) => {
-      const features = createFeatures(
-        resolveSupportedLanguagesUsingCli
-          ? [Feature.ResolveSupportedLanguagesUsingCli]
-          : [],
-      );
-      const mockRequest = mockLanguagesInRepo(args.languagesInRepository);
-      const stubExtractorEntry = {
-        extractor_root: "",
-      };
-      const codeQL = createStubCodeQL({
-        betterResolveLanguages: (options) =>
-          Promise.resolve({
-            aliases: {
-              "c#": KnownLanguage.csharp,
-              c: KnownLanguage.cpp,
-              kotlin: KnownLanguage.java,
-              typescript: KnownLanguage.javascript,
-            },
-            extractors: {
-              cpp: [stubExtractorEntry],
-              csharp: [stubExtractorEntry],
-              java: [stubExtractorEntry],
-              javascript: [stubExtractorEntry],
-              python: [stubExtractorEntry],
-              ...(options?.filterToLanguagesWithQueries
-                ? {}
-                : {
-                    html: [stubExtractorEntry],
-                  }),
-            },
-          }),
-      });
-
-      if (args.expectedLanguages) {
-        // happy path
-        const actualLanguages = await configUtils.getLanguages(
-          codeQL,
-          args.languagesInput,
-          mockRepositoryNwo,
-          ".",
-          features,
-          mockLogger,
-        );
-
-        t.deepEqual(actualLanguages.sort(), args.expectedLanguages.sort());
-      } else {
-        // there is an error
-        await t.throwsAsync(
-          async () =>
-            await configUtils.getLanguages(
-              codeQL,
-              args.languagesInput,
-              mockRepositoryNwo,
-              ".",
-              features,
-              mockLogger,
-            ),
-          { message: args.expectedError },
-        );
-      }
-      t.deepEqual(mockRequest.called, args.expectedApiCall);
+  test(`getLanguages: ${args.name}`, async (t) => {
+    const mockRequest = mockLanguagesInRepo(args.languagesInRepository);
+    const stubExtractorEntry = {
+      extractor_root: "",
+    };
+    const codeQL = createStubCodeQL({
+      betterResolveLanguages: (options) =>
+        Promise.resolve({
+          aliases: {
+            "c#": KnownLanguage.csharp,
+            c: KnownLanguage.cpp,
+            kotlin: KnownLanguage.java,
+            typescript: KnownLanguage.javascript,
+          },
+          extractors: {
+            cpp: [stubExtractorEntry],
+            csharp: [stubExtractorEntry],
+            java: [stubExtractorEntry],
+            javascript: [stubExtractorEntry],
+            python: [stubExtractorEntry],
+            ...(options?.filterToLanguagesWithQueries
+              ? {}
+              : {
+                  html: [stubExtractorEntry],
+                }),
+          },
+        }),
     });
-  }
+
+    if (args.expectedLanguages) {
+      // happy path
+      const actualLanguages = await configUtils.getLanguages(
+        codeQL,
+        args.languagesInput,
+        mockRepositoryNwo,
+        ".",
+        mockLogger,
+      );
+
+      t.deepEqual(actualLanguages.sort(), args.expectedLanguages.sort());
+    } else {
+      // there is an error
+      await t.throwsAsync(
+        async () =>
+          await configUtils.getLanguages(
+            codeQL,
+            args.languagesInput,
+            mockRepositoryNwo,
+            ".",
+            mockLogger,
+          ),
+        { message: args.expectedError },
+      );
+    }
+    t.deepEqual(mockRequest.called, args.expectedApiCall);
+  });
 });
 
 for (const { displayName, language, feature } of [

src/config-utils.ts

@@ -34,6 +34,7 @@ import {
   OverlayDatabaseMode,
 } from "./overlay-database-utils";
 import { RepositoryNwo } from "./repository";
+import { ToolsFeature } from "./tools-features";
 import { downloadTrapCaches } from "./trap-caching";
 import {
   GitHubVersion,
@@ -177,12 +178,10 @@ export interface Config {
 
 export async function getSupportedLanguageMap(
   codeql: CodeQL,
-  features: FeatureEnablement,
   logger: Logger,
 ): Promise<Record<string, string>> {
-  const resolveSupportedLanguagesUsingCli = await features.getValue(
-    Feature.ResolveSupportedLanguagesUsingCli,
-    codeql,
+  const resolveSupportedLanguagesUsingCli = await codeql.supportsFeature(
+    ToolsFeature.BuiltinExtractorsSpecifyDefaultQueries,
   );
   const resolveResult = await codeql.betterResolveLanguages({
     filterToLanguagesWithQueries: resolveSupportedLanguagesUsingCli,
@@ -283,7 +282,6 @@ export async function getLanguages(
   languagesInput: string | undefined,
   repository: RepositoryNwo,
   sourceRoot: string,
-  features: FeatureEnablement,
   logger: Logger,
 ): Promise<Language[]> {
   // Obtain languages without filtering them.
@@ -294,7 +292,7 @@ export async function getLanguages(
     logger,
   );
 
-  const languageMap = await getSupportedLanguageMap(codeql, features, logger);
+  const languageMap = await getSupportedLanguageMap(codeql, logger);
   const languagesSet = new Set<Language>();
   const unknownLanguages: string[] = [];
 
@@ -431,7 +429,6 @@ export async function initActionState(
     languagesInput,
     repository,
     sourceRoot,
-    features,
     logger,
   );
 
@@ -1036,7 +1033,6 @@ export async function getConfig(
  * pack.
  *
  * @param registriesInput The value of the `registries` input.
- * @param codeQL a codeQL object, used only for checking the version of CodeQL.
  * @param tempDir a temporary directory to store the generated qlconfig.yml file.
  * @param logger a logger object.
  * @returns The path to the generated `qlconfig.yml` file and the auth tokens to

src/config/db-config.ts

@@ -160,7 +160,6 @@ const PACK_IDENTIFIER_PATTERN = (function () {
  * Version and path are optional.
  *
  * @param packStr the package specification to verify.
- * @param configFile Config file to use for error reporting
  */
 export function parsePacksSpecification(packStr: string): Pack {
   if (typeof packStr !== "string") {

src/diff-informed-analysis-utils.test.ts

@@ -188,10 +188,6 @@ test(
 );
 
 function runGetDiffRanges(changes: number, patch: string[] | undefined): any {
-  sinon
-    .stub(actionsUtil, "getRequiredInput")
-    .withArgs("checkout_path")
-    .returns("/checkout/path");
   return exportedForTesting.getDiffRanges(
     {
       filename: "test.txt",
@@ -211,7 +207,7 @@ test("getDiffRanges: file diff too large", async (t) => {
   const diffRanges = runGetDiffRanges(1000000, undefined);
   t.deepEqual(diffRanges, [
     {
-      path: "/checkout/path/test.txt",
+      path: "test.txt",
       startLine: 0,
       endLine: 0,
     },
@@ -232,7 +228,7 @@ test("getDiffRanges: diff thunk with single addition range", async (t) => {
   ]);
   t.deepEqual(diffRanges, [
     {
-      path: "/checkout/path/test.txt",
+      path: "test.txt",
       startLine: 53,
       endLine: 54,
     },
@@ -268,7 +264,7 @@ test("getDiffRanges: diff thunk with single update range", async (t) => {
   ]);
   t.deepEqual(diffRanges, [
     {
-      path: "/checkout/path/test.txt",
+      path: "test.txt",
       startLine: 53,
       endLine: 53,
     },
@@ -290,12 +286,12 @@ test("getDiffRanges: diff thunk with addition ranges", async (t) => {
   ]);
   t.deepEqual(diffRanges, [
     {
-      path: "/checkout/path/test.txt",
+      path: "test.txt",
       startLine: 53,
       endLine: 53,
     },
     {
-      path: "/checkout/path/test.txt",
+      path: "test.txt",
       startLine: 55,
       endLine: 55,
     },
@@ -322,12 +318,12 @@ test("getDiffRanges: diff thunk with mixed ranges", async (t) => {
   ]);
   t.deepEqual(diffRanges, [
     {
-      path: "/checkout/path/test.txt",
+      path: "test.txt",
       startLine: 54,
       endLine: 54,
     },
     {
-      path: "/checkout/path/test.txt",
+      path: "test.txt",
       startLine: 57,
       endLine: 58,
     },
@@ -357,12 +353,12 @@ test("getDiffRanges: multiple diff thunks", async (t) => {
   ]);
   t.deepEqual(diffRanges, [
     {
-      path: "/checkout/path/test.txt",
+      path: "test.txt",
       startLine: 53,
       endLine: 54,
     },
     {
-      path: "/checkout/path/test.txt",
+      path: "test.txt",
       startLine: 153,
       endLine: 154,
     },
@@ -373,7 +369,7 @@ test("getDiffRanges: no diff context lines", async (t) => {
   const diffRanges = runGetDiffRanges(2, ["@@ -30 +50,2 @@", "+1", "+2"]);
   t.deepEqual(diffRanges, [
     {
-      path: "/checkout/path/test.txt",
+      path: "test.txt",
       startLine: 50,
       endLine: 51,
     },

src/diff-informed-analysis-utils.ts

@@ -191,13 +191,6 @@ function getDiffRanges(
   fileDiff: FileDiff,
   logger: Logger,
 ): DiffThunkRange[] | undefined {
-  // Diff-informed queries expect the file path to be absolute. CodeQL always
-  // uses forward slashes as the path separator, so on Windows we need to
-  // replace any backslashes with forward slashes.
-  const filename = path
-    .join(actionsUtil.getRequiredInput("checkout_path"), fileDiff.filename)
-    .replaceAll(path.sep, "/");
-
   if (fileDiff.patch === undefined) {
     if (fileDiff.changes === 0) {
       // There are situations where a changed file legitimately has no diff.
@@ -212,7 +205,7 @@ function getDiffRanges(
     // to a special diff range that covers the entire file.
     return [
       {
-        path: filename,
+        path: fileDiff.filename,
         startLine: 0,
         endLine: 0,
       },
@@ -247,7 +240,7 @@ function getDiffRanges(
       // Any line that does not start with a "+" or "-" terminates the current
       // range of added lines.
       diffRanges.push({
-        path: filename,
+        path: fileDiff.filename,
         startLine: additionRangeStartLine,
         endLine: currentLine - 1,
       });

src/feature-flags.ts

@@ -76,7 +76,6 @@ export enum Feature {
   OverlayAnalysisSwift = "overlay_analysis_swift",
   PythonDefaultIsToNotExtractStdlib = "python_default_is_to_not_extract_stdlib",
   QaTelemetryEnabled = "qa_telemetry_enabled",
-  ResolveSupportedLanguagesUsingCli = "resolve_supported_languages_using_cli",
   UseRepositoryProperties = "use_repository_properties",
   ValidateDbConfig = "validate_db_config",
 }
@@ -161,12 +160,6 @@ export const featureConfig: Record<
     legacyApi: true,
     minimumVersion: undefined,
   },
-  [Feature.ResolveSupportedLanguagesUsingCli]: {
-    defaultValue: false,
-    envVar: "CODEQL_ACTION_RESOLVE_SUPPORTED_LANGUAGES_USING_CLI",
-    minimumVersion: undefined,
-    toolsFeature: ToolsFeature.BuiltinExtractorsSpecifyDefaultQueries,
-  },
   [Feature.OverlayAnalysis]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_OVERLAY_ANALYSIS",

src/status-report.ts

@@ -252,7 +252,7 @@ export interface EventReport {
  *
  * @param actionName The name of the action, e.g. 'init', 'finish', 'upload-sarif'
  * @param status The status. Must be 'success', 'failure', or 'starting'
- * @param startedAt The time this action started executing.
+ * @param actionStartedAt The time this action started executing.
  * @param cause  Cause of failure (only supply if status is 'failure')
  * @param exception Exception (only supply if status is 'failure')
  * @returns undefined if an exception was thrown.

src/testdata/pr-diff-range.yml

@@ -0,0 +1,8 @@
+
+extensions:
+  - addsTo:
+      pack: codeql/util
+      extensible: restrictAlertsTo
+      checkPresence: false
+    data:
+      - ['/checkout/path/main.js', 10, 20]

src/testdata/valid-sarif-diff-filtered.sarif

@@ -0,0 +1,178 @@
+{
+  "$schema": "https://raw.githubusercontent.com/oasis-tcs/sarif-spec/master/Schemata/sarif-schema-2.1.0.json",
+  "version": "2.1.0",
+  "runs": [{
+      "tool": {
+        "driver": {
+          "name": "LGTM.com",
+          "organization": "Semmle",
+          "version": "1.24.0-SNAPSHOT",
+          "rules": [{
+            "id": "js/unused-local-variable",
+            "name": "js/unused-local-variable",
+            "shortDescription": {
+              "text": "Unused variable, import, function or class"
+            },
+            "fullDescription": {
+              "text": "Unused variables, imports, functions or classes may be a symptom of a bug and should be examined carefully."
+            },
+            "defaultConfiguration": {
+              "level": "note"
+            },
+            "properties": {
+              "tags": ["maintainability"],
+              "kind": "problem",
+              "precision": "very-high",
+              "name": "Unused variable, import, function or class",
+              "description": "Unused variables, imports, functions or classes may be a symptom of a bug\n              and should be examined carefully.",
+              "id": "js/unused-local-variable",
+              "problem.severity": "recommendation"
+            }
+          }]
+        }
+      },
+      "results": [{
+        "ruleId": "js/unused-local-variable",
+        "ruleIndex": 0,
+        "message": {
+          "text": "Unused variable foo."
+        },
+        "locations": [{
+          "physicalLocation": {
+            "artifactLocation": {
+              "uri": "main.js",
+              "uriBaseId": "%SRCROOT%",
+              "index": 0
+            },
+            "region": {
+              "startLine": 2,
+              "startColumn": 7,
+              "endColumn": 10
+            }
+          }
+        }],
+        "partialFingerprints": {
+          "primaryLocationLineHash": "39fa2ee980eb94b0:1",
+          "primaryLocationStartColumnFingerprint": "4"
+        }
+      }],
+      "columnKind": "utf16CodeUnits",
+      "properties": {
+        "semmle.formatSpecifier": "2.1.0",
+        "semmle.sourceLanguage": "java"
+      }
+    },
+    {
+      "tool" : {
+        "driver" : {
+          "name" : "CodeQL command-line toolchain",
+          "organization" : "GitHub",
+          "semanticVersion" : "2.0.0",
+          "rules" : [ {
+            "id" : "js/unused-local-variable",
+            "name" : "js/unused-local-variable",
+            "shortDescription" : {
+              "text" : "Unused variable, import, function or class"
+            },
+            "fullDescription" : {
+              "text" : "Unused variables, imports, functions or classes may be a symptom of a bug and should be examined carefully."
+            },
+            "defaultConfiguration" : {
+              "level": "note"
+            },
+            "properties" : {
+              "tags" : [ "maintainability" ],
+              "kind" : "problem",
+              "precision" : "very-high",
+              "name" : "Unused variable, import, function or class",
+              "description" : "Unused variables, imports, functions or classes may be a symptom of a bug\n              and should be examined carefully.",
+              "id" : "js/unused-local-variable",
+              "problem.severity" : "recommendation"
+            }
+          },
+          {
+            "id": "js/inconsistent-use-of-new",
+            "name": "js/inconsistent-use-of-new",
+            "shortDescription": {
+              "text": "Inconsistent use of 'new'"
+            },
+            "fullDescription": {
+              "text": "If a function is intended to be a constructor, it should always be invoked with 'new'. Otherwise, it should always be invoked as a normal function, that is, without 'new'."
+            },
+            "defaultConfiguration": {
+              "level": "note"
+            },
+            "properties": {
+              "tags": [
+                "reliability",
+                "correctness",
+                "language-features"
+              ],
+              "kind": "problem",
+              "precision": "very-high",
+              "problem.severity": "warning"
+            }
+          } ]
+        }
+      },
+      "artifacts" : [ {
+        "location" : {
+          "uri" : "main.js",
+          "uriBaseId" : "%SRCROOT%",
+          "index" : 0
+        }
+      },
+      {
+        "location": {
+          "uri": "src/promiseUtils.js",
+          "uriBaseId": "%SRCROOT%",
+          "index": 1
+        }
+      },
+      {
+        "location": {
+          "uri": "src/LiveQueryClient.js",
+          "uriBaseId": "%SRCROOT%",
+          "index": 2
+        }
+      },
+      {
+        "location": {
+          "uri": "src/ParseObject.js",
+          "uriBaseId": "%SRCROOT%",
+          "index": 3
+        }
+      } ],
+      "results" : [ {
+        "ruleId" : "js/unused-local-variable",
+        "ruleIndex" : 0,
+        "message" : {
+          "text" : "Unused variable foo."
+        },
+        "locations" : [ {
+          "physicalLocation" : {
+            "artifactLocation" : {
+              "uri" : "main.js",
+              "uriBaseId" : "%SRCROOT%",
+              "index" : 0
+            },
+            "region" : {
+              "startLine" : 2,
+              "startColumn" : 7,
+              "endColumn" : 10
+            }
+          }
+        } ],
+        "partialFingerprints" : {
+          "primaryLocationLineHash" : "39fa2ee980eb94b0:1",
+          "primaryLocationStartColumnFingerprint" : "4"
+        }
+      }],
+      "newlineSequences" : [ "\r\n", "\n", "
", "
" ],
+      "columnKind" : "utf16CodeUnits",
+      "properties" : {
+        "semmle.formatSpecifier" : "sarif-latest"
+      }
+    }
+  ]
+}

src/upload-lib.test.ts

@@ -9,10 +9,16 @@ import * as sinon from "sinon";
 import * as analyses from "./analyses";
 import { AnalysisKind, CodeQuality, CodeScanning } from "./analyses";
 import * as api from "./api-client";
+import * as diffUtils from "./diff-informed-analysis-utils";
 import { getRunnerLogger, Logger } from "./logging";
 import { setupTests } from "./testing-utils";
 import * as uploadLib from "./upload-lib";
-import { GitHubVariant, initializeEnvironment, withTmpDir } from "./util";
+import {
+  GitHubVariant,
+  initializeEnvironment,
+  SarifFile,
+  withTmpDir,
+} from "./util";
 
 setupTests(test);
 
@@ -960,3 +966,30 @@ for (const analysis of [CodeScanning, CodeQuality]) {
     });
   });
 }
+
+function runFilterAlertsByDiffRange(
+  input: SarifFile,
+  diffRanges: diffUtils.DiffThunkRange[],
+): SarifFile {
+  sinon.stub(diffUtils, "readDiffRangesJsonFile").returns(diffRanges);
+  return uploadLib.filterAlertsByDiffRange(getRunnerLogger(true), input);
+}
+
+test("filterAlertsByDiffRange filters out alerts outside diff-range", (t) => {
+  const input = uploadLib.readSarifFile(
+    `${__dirname}/../src/testdata/valid-sarif.sarif`,
+  );
+  const actualOutput = runFilterAlertsByDiffRange(input, [
+    {
+      path: "main.js",
+      startLine: 1,
+      endLine: 3,
+    },
+  ]);
+
+  const expectedOutput = uploadLib.readSarifFile(
+    `${__dirname}/../src/testdata/valid-sarif-diff-filtered.sarif`,
+  );
+
+  t.deepEqual(actualOutput, expectedOutput);
+});

src/upload-lib.ts

@@ -738,7 +738,7 @@ export async function postProcessSarifFiles(
  * @param logger The logger to use.
  * @param pathInput The input provided for `post-processed-sarif-path`.
  * @param uploadTarget The upload target.
- * @param processingResults The results of post-processing SARIF files.
+ * @param postProcessingResults The results of post-processing SARIF files.
  */
 export async function writePostProcessedFiles(
   logger: Logger,
@@ -1134,14 +1134,15 @@ export class InvalidSarifUploadError extends Error {
   }
 }
 
-function filterAlertsByDiffRange(logger: Logger, sarif: SarifFile): SarifFile {
+export function filterAlertsByDiffRange(
+  logger: Logger,
+  sarif: SarifFile,
+): SarifFile {
   const diffRanges = readDiffRangesJsonFile(logger);
   if (!diffRanges?.length) {
     return sarif;
   }
 
-  const checkoutPath = actionsUtil.getRequiredInput("checkout_path");
-
   for (const run of sarif.runs) {
     if (run.results) {
       run.results = run.results.filter((result) => {
@@ -1156,11 +1157,6 @@ function filterAlertsByDiffRange(logger: Logger, sarif: SarifFile): SarifFile {
           if (!locationUri || locationStartLine === undefined) {
             return false;
           }
-          // CodeQL always uses forward slashes as the path separator, so on Windows we
-          // need to replace any backslashes with forward slashes.
-          const locationPath = path
-            .join(checkoutPath, locationUri)
-            .replaceAll(path.sep, "/");
           // Alert filtering here replicates the same behavior as the restrictAlertsTo
           // extensible predicate in CodeQL. See the restrictAlertsTo documentation
           // https://codeql.github.com/codeql-standard-libraries/csharp/codeql/util/AlertFiltering.qll/predicate.AlertFiltering$restrictAlertsTo.3.html
@@ -1168,7 +1164,7 @@ function filterAlertsByDiffRange(logger: Logger, sarif: SarifFile): SarifFile {
           // of an alert location.
           return diffRanges.some(
             (range) =>
-              range.path === locationPath &&
+              range.path === locationUri &&
               ((range.startLine <= locationStartLine &&
                 range.endLine >= locationStartLine) ||
                 (range.startLine === 0 && range.endLine === 0)),

src/util.test.ts

@@ -447,13 +447,21 @@ const CHECK_ACTION_VERSION_TESTS: Array<[string, util.GitHubVersion, boolean]> =
     ["2.2.1", { type: util.GitHubVariant.DOTCOM }, true],
     ["2.2.1", { type: util.GitHubVariant.GHE_DOTCOM }, true],
     ["2.2.1", { type: util.GitHubVariant.GHES, version: "3.10" }, false],
-    ["2.2.1", { type: util.GitHubVariant.GHES, version: "3.11" }, true],
-    ["2.2.1", { type: util.GitHubVariant.GHES, version: "3.12" }, true],
-    ["3.2.1", { type: util.GitHubVariant.DOTCOM }, false],
-    ["3.2.1", { type: util.GitHubVariant.GHE_DOTCOM }, false],
+    ["2.2.1", { type: util.GitHubVariant.GHES, version: "3.11" }, false],
+    ["2.2.1", { type: util.GitHubVariant.GHES, version: "3.12" }, false],
+    ["3.2.1", { type: util.GitHubVariant.DOTCOM }, true],
+    ["3.2.1", { type: util.GitHubVariant.GHE_DOTCOM }, true],
     ["3.2.1", { type: util.GitHubVariant.GHES, version: "3.10" }, false],
     ["3.2.1", { type: util.GitHubVariant.GHES, version: "3.11" }, false],
     ["3.2.1", { type: util.GitHubVariant.GHES, version: "3.12" }, false],
+    ["3.2.1", { type: util.GitHubVariant.GHES, version: "3.19" }, false],
+    ["3.2.1", { type: util.GitHubVariant.GHES, version: "3.20" }, true],
+    ["3.2.1", { type: util.GitHubVariant.GHES, version: "3.21" }, true],
+    ["4.2.1", { type: util.GitHubVariant.DOTCOM }, false],
+    ["4.2.1", { type: util.GitHubVariant.GHE_DOTCOM }, false],
+    ["4.2.1", { type: util.GitHubVariant.GHES, version: "3.19" }, false],
+    ["4.2.1", { type: util.GitHubVariant.GHES, version: "3.20" }, false],
+    ["4.2.1", { type: util.GitHubVariant.GHES, version: "3.21" }, false],
   ];
 
 for (const [
@@ -480,9 +488,7 @@ for (const [
     if (shouldReportError) {
       t.true(
         warningSpy.calledOnceWithExactly(
-          sinon.match(
-            "CodeQL Action major versions v1 and v2 have been deprecated.",
-          ),
+          sinon.match("CodeQL Action v3 will be deprecated in December 2026."),
         ),
       );
     } else {

src/util.ts

@@ -1114,38 +1114,38 @@ export async function checkDiskUsage(
 }
 
 /**
- * Prompt the customer to upgrade to CodeQL Action v3, if appropriate.
+ * Prompt the customer to upgrade to CodeQL Action v4, if appropriate.
  *
- * Check whether a customer is running v1 or v2. If they are, and we can determine that the GitHub
- * instance supports v3, then log an error prompting the customer to upgrade to v3.
+ * Check whether a customer is running v3. If they are, and we can determine that the GitHub
+ * instance supports v4, then log an error prompting the customer to upgrade to v4.
  */
 export function checkActionVersion(
   version: string,
   githubVersion: GitHubVersion,
 ) {
   if (
-    !semver.satisfies(version, ">=3") && // do not log error if the customer is already running v3
+    !semver.satisfies(version, ">=4") && // do not log error if the customer is already running v4
     !process.env[EnvVar.LOG_VERSION_DEPRECATION] // do not log error if we have already
   ) {
-    // Only error for versions of GHES that are compatible with CodeQL Action version 3.
+    // Only error for versions of GHES that are compatible with CodeQL Action version 4.
     //
-    // GHES 3.11 shipped without the v3 tag, but it also shipped without this warning message code.
-    // Therefore users who are seeing this warning message code have pulled in a new version of the
-    // Action, and with it the v3 tag.
+    // GHES 3.20 is the first version to ship with the v4 tag and this warning message code.
+    // Therefore, users who are seeing this warning message code are running on GHES 3.20 or newer,
+    // and should update to CodeQL Action v4.
     if (
       githubVersion.type === GitHubVariant.DOTCOM ||
       githubVersion.type === GitHubVariant.GHE_DOTCOM ||
       (githubVersion.type === GitHubVariant.GHES &&
         semver.satisfies(
           semver.coerce(githubVersion.version) ?? "0.0.0",
-          ">=3.11",
+          ">=3.20",
         ))
     ) {
       core.error(
-        "CodeQL Action major versions v1 and v2 have been deprecated. " +
-          "Please update all occurrences of the CodeQL Action in your workflow files to v3. " +
+        "CodeQL Action v3 will be deprecated in December 2026. " +
+          "Please update all occurrences of the CodeQL Action in your workflow files to v4. " +
           "For more information, see " +
-          "https://github.blog/changelog/2025-01-10-code-scanning-codeql-action-v2-is-now-deprecated/",
+          "https://github.blog/changelog/2025-10-28-upcoming-deprecation-of-codeql-action-v3/",
       );
       // set LOG_VERSION_DEPRECATION env var to prevent the warning from being logged multiple times
       core.exportVariable(EnvVar.LOG_VERSION_DEPRECATION, "true");