Merge pull request #2819 from github/update-v3.28.13-e0ea14102

Merge main into releases/v3
Update changelog for v3.28.13
2026-10-25 00:13:42 +03:00 · 2025-03-24 06:42:41 -07:00 · 2025-03-24 13:18:07 +00:00 · 2025-03-21 16:04:38 -07:00 · 2025-03-21 14:18:25 -07:00 · 2025-03-21 12:30:26 -07:00
36 changed files with 907 additions and 92 deletions
@@ -46,7 +46,7 @@ jobs:
          use-all-platform-bundle: 'false'
          setup-kotlin: 'true'
      - name: Set up Ruby
-        uses: ruby/setup-ruby@277ba2a127aba66d45bad0fa2dc56f80dbfedffa # v1.222.0
+        uses: ruby/setup-ruby@922ebc4c5262cd14e07bb0e1db020984b6c064fe # v1.226.0
        with:
          ruby-version: 2.6
      - name: Install Code Scanning integration
@@ -2,10 +2,15 @@

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

-## [UNRELEASED]
+## 3.28.13 - 24 Mar 2025

 No user facing changes.

+## 3.28.12 - 19 Mar 2025
+
+- Dependency caching should now cache more dependencies for Java `build-mode: none` extractions. This should speed up workflows and avoid inconsistent alerts in some cases.
+- Update default CodeQL bundle version to 2.20.7. [#2810](https://github.com/github/codeql-action/pull/2810)
+
 ## 3.28.11 - 07 Mar 2025

 - Update default CodeQL bundle version to 2.20.6. [#2793](https://github.com/github/codeql-action/pull/2793)
@@ -3,7 +3,7 @@ all: lint sync

 # Lint source typescript
 lint:
-    npm run lint -- --fix
+    npm run lint-fix

 # Sync generated files (javascript and PR checks)
 sync: build update-pr-checks
@@ -15,3 +15,16 @@ update-pr-checks:
 # Transpile typescript code into javascript
 build:
    npm run build
+
+# Build then run all the tests
+test: build
+    npm run test
+
+# Run the tests for a single file
+test_file filename: build
+    npx ava --verbose {{filename}}
+
+[doc("Refresh the .js build artefacts in the lib directory")]
+[confirm]
+refresh-lib:
+    rm -rf lib && npm run build
@@ -38,12 +38,14 @@ Object.defineProperty(exports, "__esModule", { value: true });
 * It will run after the all steps in this job, in reverse order in relation to
 * other `post:` hooks.
 */
+const fs = __importStar(require("fs"));
 const core = __importStar(require("@actions/core"));
 const actionsUtil = __importStar(require("./actions-util"));
 const api_client_1 = require("./api-client");
 const codeql_1 = require("./codeql");
 const config_utils_1 = require("./config-utils");
 const debugArtifacts = __importStar(require("./debug-artifacts"));
+const dependency_caching_1 = require("./dependency-caching");
 const environment_1 = require("./environment");
 const logging_1 = require("./logging");
 const util_1 = require("./util");
@@ -63,6 +65,18 @@ async function runWrapper() {
                await debugArtifacts.uploadCombinedSarifArtifacts(logger, config.gitHubVersion.type, version.version);
            }
        }
+        // If we analysed Java in build-mode: none, we may have downloaded dependencies
+        // to the temp directory. Clean these up so they don't persist unnecessarily
+        // long on self-hosted runners.
+        const javaTempDependencyDir = (0, dependency_caching_1.getJavaTempDependencyDir)();
+        if (fs.existsSync(javaTempDependencyDir)) {
+            try {
+                fs.rmSync(javaTempDependencyDir, { recursive: true });
+            }
+            catch (error) {
+                logger.info(`Failed to remove temporary Java dependencies directory: ${(0, util_1.getErrorMessage)(error)}`);
+            }
+        }
    }
    catch (error) {
        core.setFailed(`analyze post-action step failed: ${(0, util_1.getErrorMessage)(error)}`);
@@ -1 +1 @@
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+{"version":3,"file":"analyze-action-post.js","sourceRoot":"","sources":["../src/analyze-action-post.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA;;;;GAIG;AACH,uCAAyB;AAEzB,oDAAsC;AAEtC,4DAA8C;AAC9C,6CAAgD;AAChD,qCAAqC;AACrC,iDAA2C;AAC3C,kEAAoD;AACpD,6DAAgE;AAChE,+CAAuC;AACvC,uCAA6C;AAC7C,iCAAoE;AAEpE,KAAK,UAAU,UAAU;IACvB,IAAI,CAAC;QACH,WAAW,CAAC,aAAa,EAAE,CAAC;QAC5B,MAAM,MAAM,GAAG,IAAA,0BAAgB,GAAE,CAAC;QAClC,MAAM,aAAa,GAAG,MAAM,IAAA,6BAAgB,GAAE,CAAC;QAC/C,IAAA,gCAAyB,EAAC,aAAa,EAAE,MAAM,CAAC,CAAC;QAEjD,kFAAkF;QAClF,wFAAwF;QACxF,IAAI,OAAO,CAAC,GAAG,CAAC,oBAAM,CAAC,mBAAmB,CAAC,KAAK,MAAM,EAAE,CAAC;YACvD,MAAM,MAAM,GAAG,MAAM,IAAA,wBAAS,EAC5B,WAAW,CAAC,qBAAqB,EAAE,EACnC,MAAM,CACP,CAAC;YACF,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;gBACzB,MAAM,MAAM,GAAG,MAAM,IAAA,kBAAS,EAAC,MAAM,CAAC,SAAS,CAAC,CAAC;gBACjD,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,UAAU,EAAE,CAAC;gBAC1C,MAAM,cAAc,CAAC,4BAA4B,CAC/C,MAAM,EACN,MAAM,CAAC,aAAa,CAAC,IAAI,EACzB,OAAO,CAAC,OAAO,CAChB,CAAC;YACJ,CAAC;QACH,CAAC;QAED,+EAA+E;QAC/E,4EAA4E;QAC5E,+BAA+B;QAC/B,MAAM,qBAAqB,GAAG,IAAA,6CAAwB,GAAE,CAAC;QACzD,IAAI,EAAE,CAAC,UAAU,CAAC,qBAAqB,CAAC,EAAE,CAAC;YACzC,IAAI,CAAC;gBACH,EAAE,CAAC,MAAM,CAAC,qBAAqB,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;YACxD,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,MAAM,CAAC,IAAI,CACT,2DAA2D,IAAA,sBAAe,EAAC,KAAK,CAAC,EAAE,CACpF,CAAC;YACJ,CAAC;QACH,CAAC;IACH,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,IAAI,CAAC,SAAS,CACZ,oCAAoC,IAAA,sBAAe,EAAC,KAAK,CAAC,EAAE,CAC7D,CAAC;IACJ,CAAC;AACH,CAAC;AAED,KAAK,UAAU,EAAE,CAAC"}
@@ -41,7 +41,6 @@ const fs = __importStar(require("fs"));
 const path_1 = __importDefault(require("path"));
 const perf_hooks_1 = require("perf_hooks");
 const core = __importStar(require("@actions/core"));
-const github = __importStar(require("@actions/github"));
 const actionsUtil = __importStar(require("./actions-util"));
 const analyze_1 = require("./analyze");
 const api_client_1 = require("./api-client");
@@ -194,9 +193,7 @@ async function run() {
        util.checkActionVersion(actionsUtil.getActionVersion(), gitHubVersion);
        const features = new feature_flags_1.Features(gitHubVersion, repositoryNwo, actionsUtil.getTemporaryDirectory(), logger);
        const memory = util.getMemoryFlag(actionsUtil.getOptionalInput("ram") || process.env["CODEQL_RAM"], logger);
-        const pull_request = github.context.payload.pull_request;
-        const diffRangePackDir = pull_request &&
-            (await (0, analyze_1.setupDiffInformedQueryRun)(pull_request.base.ref, pull_request.head.label, codeql, logger, features));
+        const diffRangePackDir = await (0, analyze_1.setupDiffInformedQueryRun)(codeql, logger, features);
        await (0, analyze_1.warnIfGoInstalledAfterInit)(config, logger);
        await runAutobuildIfLegacyGoWorkflow(config, logger);
        dbCreationTimings = await (0, analyze_1.runFinalize)(outputDir, threads, memory, codeql, config, logger);
@@ -1 +1 @@
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truncated
@@ -47,6 +47,7 @@ exports.runCleanup = runCleanup;
 const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const perf_hooks_1 = require("perf_hooks");
+const github = __importStar(require("@actions/github"));
 const io = __importStar(require("@actions/io"));
 const del_1 = __importDefault(require("del"));
 const yaml = __importStar(require("js-yaml"));
@@ -54,6 +55,7 @@ const actionsUtil = __importStar(require("./actions-util"));
 const api_client_1 = require("./api-client");
 const autobuild_1 = require("./autobuild");
 const codeql_1 = require("./codeql");
+const dependency_caching_1 = require("./dependency-caching");
 const diagnostics_1 = require("./diagnostics");
 const diff_filtering_utils_1 = require("./diff-filtering-utils");
 const environment_1 = require("./environment");
@@ -102,6 +104,14 @@ async function runExtraction(codeql, config, logger) {
                    config.buildMode === util_1.BuildMode.Autobuild) {
                    await (0, autobuild_1.setupCppAutobuild)(codeql, logger);
                }
+                // The Java `build-mode: none` extractor places dependencies (.jar files) in the
+                // database scratch directory by default. For dependency caching purposes, we want
+                // 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 === languages_1.Language.java && config.buildMode === util_1.BuildMode.None) {
+                    process.env["CODEQL_EXTRACTOR_JAVA_OPTION_BUILDLESS_DEPENDENCY_DIR"] =
+                        (0, dependency_caching_1.getJavaTempDependencyDir)();
+                }
                await codeql.extractUsingBuildMode(config, language);
            }
            else {
@@ -149,24 +159,50 @@ async function finalizeDatabaseCreation(codeql, config, threadsFlag, memoryFlag,
        trap_import_duration_ms: Math.round(trapImportTime),
    };
 }
+function getPullRequestBranches() {
+    const pullRequest = github.context.payload.pull_request;
+    if (pullRequest) {
+        return {
+            base: pullRequest.base.ref,
+            // We use the head label instead of the head ref here, because the head
+            // ref lacks owner information and by itself does not uniquely identify
+            // the head branch (which may be in a forked repository).
+            head: pullRequest.head.label,
+        };
+    }
+    // PR analysis under Default Setup does not have the pull_request context,
+    // but it should set CODE_SCANNING_REF and CODE_SCANNING_BASE_BRANCH.
+    const codeScanningRef = process.env.CODE_SCANNING_REF;
+    const codeScanningBaseBranch = process.env.CODE_SCANNING_BASE_BRANCH;
+    if (codeScanningRef && codeScanningBaseBranch) {
+        return {
+            base: codeScanningBaseBranch,
+            // PR analysis under Default Setup analyzes the PR head commit instead of
+            // the merge commit, so we can use the provided ref directly.
+            head: codeScanningRef,
+        };
+    }
+    return undefined;
+}
 /**
 * Set up the diff-informed analysis feature.
 *
- * @param baseRef The base branch name, used for calculating the diff range.
- * @param headLabel The label that uniquely identifies the head branch across
- * repositories, used for calculating the diff range.
- * @param codeql
- * @param logger
- * @param features
 * @returns Absolute path to the directory containing the extension pack for
 * the diff range information, or `undefined` if the feature is disabled.
 */
-async function setupDiffInformedQueryRun(baseRef, headLabel, codeql, logger, features) {
+async function setupDiffInformedQueryRun(codeql, logger, features) {
    if (!(await features.getValue(feature_flags_1.Feature.DiffInformedQueries, codeql))) {
        return undefined;
    }
+    const branches = getPullRequestBranches();
+    if (!branches) {
+        logger.info("Not performing diff-informed analysis " +
+            "because we are not analyzing a pull request.");
+        return undefined;
+    }
    return await (0, logging_1.withGroupAsync)("Generating diff range extension pack", async () => {
-        const diffRanges = await getPullRequestEditedDiffRanges(baseRef, headLabel, logger);
+        logger.info(`Calculating diff ranges for ${branches.base}...${branches.head}`);
+        const diffRanges = await getPullRequestEditedDiffRanges(branches, logger);
        const packDir = writeDiffRangeDataExtensionPack(logger, diffRanges);
        if (packDir === undefined) {
            logger.warning("Cannot create diff range extension pack for diff-informed queries; " +
@@ -181,17 +217,15 @@ async function setupDiffInformedQueryRun(baseRef, headLabel, codeql, logger, fea
 /**
 * Return the file line ranges that were added or modified in the pull request.
 *
- * @param baseRef The base branch name, used for calculating the diff range.
- * @param headLabel The label that uniquely identifies the head branch across
- * repositories, used for calculating the diff range.
+ * @param branches The base and head branches of the pull request.
 * @param logger
 * @returns An array of tuples, where each tuple contains the absolute path of a
 * file, the start line and the end line (both 1-based and inclusive) of an
 * added or modified range in that file. Returns `undefined` if the action was
 * not triggered by a pull request or if there was an error.
 */
-async function getPullRequestEditedDiffRanges(baseRef, headLabel, logger) {
-    const fileDiffs = await getFileDiffsWithBasehead(baseRef, headLabel, logger);
+async function getPullRequestEditedDiffRanges(branches, logger) {
+    const fileDiffs = await getFileDiffsWithBasehead(branches, logger);
    if (fileDiffs === undefined) {
        return undefined;
    }
@@ -214,11 +248,11 @@ async function getPullRequestEditedDiffRanges(baseRef, headLabel, logger) {
    }
    return results;
 }
-async function getFileDiffsWithBasehead(baseRef, headLabel, logger) {
+async function getFileDiffsWithBasehead(branches, logger) {
    const ownerRepo = util.getRequiredEnvParam("GITHUB_REPOSITORY").split("/");
    const owner = ownerRepo[0];
    const repo = ownerRepo[1];
-    const basehead = `${baseRef}...${headLabel}`;
+    const basehead = `${branches.base}...${branches.head}`;
    try {
        const response = await (0, api_client_1.getApiClient)().rest.repos.compareCommitsWithBasehead({
            owner,
@@ -334,6 +368,14 @@ function writeDiffRangeDataExtensionPack(logger, ranges) {
    if (ranges === undefined) {
        return undefined;
    }
+    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
+        // interprets an empty data extension differently, as an indication that
+        // all alerts should be included. So we need to specifically set the diff
+        // range to a non-empty list that cannot match any alert location.
+        ranges = [{ path: "", startLine: 0, endLine: 0 }];
+    }
    const diffRangeDir = path.join(actionsUtil.getTemporaryDirectory(), "pr-diff-range");
    fs.mkdirSync(diffRangeDir);
    fs.writeFileSync(path.join(diffRangeDir, "qlpack.yml"), `
@@ -1 +1 @@
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@@ -292,7 +292,8 @@ async function getCodeQLForCmd(cmd, checkVersion) {
                ? "--force-overwrite"
                : "--overwrite";
            if (overlayDatabaseMode === overlay_database_utils_1.OverlayDatabaseMode.Overlay) {
-                extraArgs.push("--overlay");
+                const overlayChangesFile = await (0, overlay_database_utils_1.writeOverlayChangesFile)(config, sourceRoot, logger);
+                extraArgs.push(`--overlay-changes=${overlayChangesFile}`);
            }
            else if (overlayDatabaseMode === overlay_database_utils_1.OverlayDatabaseMode.OverlayBase) {
                extraArgs.push("--overlay-base");
@@ -314,6 +315,9 @@ async function getCodeQLForCmd(cmd, checkVersion) {
                    ignoringOptions: ["--overwrite"],
                }),
            ], { stdin: externalRepositoryToken });
+            if (overlayDatabaseMode === overlay_database_utils_1.OverlayDatabaseMode.OverlayBase) {
+                await (0, overlay_database_utils_1.writeBaseDatabaseOidsFile)(config, sourceRoot);
+            }
        },
        async runAutobuild(config, language) {
            applyAutobuildAzurePipelinesTimeoutFix();
@@ -1 +1 @@
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@@ -1,6 +1,6 @@
 {
-    "bundleVersion": "codeql-bundle-v2.20.6",
-    "cliVersion": "2.20.6",
-    "priorBundleVersion": "codeql-bundle-v2.20.5",
-    "priorCliVersion": "2.20.5"
+    "bundleVersion": "codeql-bundle-v2.20.7",
+    "cliVersion": "2.20.7",
+    "priorBundleVersion": "codeql-bundle-v2.20.6",
+    "priorCliVersion": "2.20.6"
 }
@@ -33,17 +33,27 @@ var __importStar = (this && this.__importStar) || (function () {
    };
 })();
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.getJavaTempDependencyDir = getJavaTempDependencyDir;
 exports.downloadDependencyCaches = downloadDependencyCaches;
 exports.uploadDependencyCaches = uploadDependencyCaches;
 const os = __importStar(require("os"));
 const path_1 = require("path");
 const actionsCache = __importStar(require("@actions/cache"));
 const glob = __importStar(require("@actions/glob"));
+const actions_util_1 = require("./actions-util");
 const caching_utils_1 = require("./caching-utils");
 const environment_1 = require("./environment");
 const util_1 = require("./util");
 const CODEQL_DEPENDENCY_CACHE_PREFIX = "codeql-dependencies";
 const CODEQL_DEPENDENCY_CACHE_VERSION = 1;
+/**
+ * Returns a path to a directory intended to be used to store .jar files
+ * for the Java `build-mode: none` extractor.
+ * @returns The path to the directory that should be used by the `build-mode: none` extractor.
+ */
+function getJavaTempDependencyDir() {
+    return (0, path_1.join)((0, actions_util_1.getTemporaryDirectory)(), "codeql_java", "repository");
+}
 /**
 * Default caching configurations per language.
 */
@@ -54,6 +64,8 @@ const CODEQL_DEFAULT_CACHE_CONFIG = {
            (0, path_1.join)(os.homedir(), ".m2", "repository"),
            // Gradle
            (0, path_1.join)(os.homedir(), ".gradle", "caches"),
+            // CodeQL Java build-mode: none
+            getJavaTempDependencyDir(),
        ],
        hash: [
            // Maven
@@ -1 +1 @@
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@@ -33,7 +33,7 @@ var __importStar = (this && this.__importStar) || (function () {
    };
 })();
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getGitRoot = exports.decodeGitFilePath = exports.gitRepack = exports.gitFetch = exports.deepenGitHistory = exports.determineBaseBranchHeadCommitOid = exports.getCommitOid = void 0;
+exports.getFileOidsUnderPath = exports.getGitRoot = exports.decodeGitFilePath = exports.gitRepack = exports.gitFetch = exports.deepenGitHistory = exports.determineBaseBranchHeadCommitOid = exports.getCommitOid = exports.runGitCommand = void 0;
 exports.getRef = getRef;
 exports.isAnalyzingDefaultBranch = isAnalyzingDefaultBranch;
 const core = __importStar(require("@actions/core"));
@@ -41,7 +41,7 @@ const toolrunner = __importStar(require("@actions/exec/lib/toolrunner"));
 const io = __importStar(require("@actions/io"));
 const actions_util_1 = require("./actions-util");
 const util_1 = require("./util");
-async function runGitCommand(checkoutPath, args, customErrorMessage) {
+const runGitCommand = async function (workingDirectory, args, customErrorMessage) {
    let stdout = "";
    let stderr = "";
    core.debug(`Running git command: git ${args.join(" ")}`);
@@ -56,7 +56,7 @@ async function runGitCommand(checkoutPath, args, customErrorMessage) {
                    stderr += data.toString();
                },
            },
-            cwd: checkoutPath,
+            cwd: workingDirectory,
        }).exec();
        return stdout;
    }
@@ -69,7 +69,8 @@ async function runGitCommand(checkoutPath, args, customErrorMessage) {
        core.info(`git call failed. ${customErrorMessage} Error: ${reason}`);
        throw error;
    }
-}
+};
+exports.runGitCommand = runGitCommand;
 /**
 * Gets the SHA of the commit that is currently checked out.
 */
@@ -82,7 +83,7 @@ const getCommitOid = async function (checkoutPath, ref = "HEAD") {
    // Even if this does go wrong, it's not a huge problem for the alerts to
    // reported on the merge commit.
    try {
-        const stdout = await runGitCommand(checkoutPath, ["rev-parse", ref], "Continuing with commit SHA from user input or environment.");
+        const stdout = await (0, exports.runGitCommand)(checkoutPath, ["rev-parse", ref], "Continuing with commit SHA from user input or environment.");
        return stdout.trim();
    }
    catch {
@@ -106,7 +107,7 @@ const determineBaseBranchHeadCommitOid = async function (checkoutPathOverride) {
        let commitOid = "";
        let baseOid = "";
        let headOid = "";
-        const stdout = await runGitCommand(checkoutPath, ["show", "-s", "--format=raw", mergeSha], "Will calculate the base branch SHA on the server.");
+        const stdout = await (0, exports.runGitCommand)(checkoutPath, ["show", "-s", "--format=raw", mergeSha], "Will calculate the base branch SHA on the server.");
        for (const data of stdout.split("\n")) {
            if (data.startsWith("commit ") && commitOid === "") {
                commitOid = data.substring(7);
@@ -141,7 +142,7 @@ exports.determineBaseBranchHeadCommitOid = determineBaseBranchHeadCommitOid;
 */
 const deepenGitHistory = async function () {
    try {
-        await runGitCommand((0, actions_util_1.getOptionalInput)("checkout_path"), [
+        await (0, exports.runGitCommand)((0, actions_util_1.getOptionalInput)("checkout_path"), [
            "fetch",
            "origin",
            "HEAD",
@@ -163,7 +164,7 @@ exports.deepenGitHistory = deepenGitHistory;
 */
 const gitFetch = async function (branch, extraFlags) {
    try {
-        await runGitCommand((0, actions_util_1.getOptionalInput)("checkout_path"), ["fetch", "--no-tags", ...extraFlags, "origin", `${branch}:${branch}`], `Cannot fetch ${branch}.`);
+        await (0, exports.runGitCommand)((0, actions_util_1.getOptionalInput)("checkout_path"), ["fetch", "--no-tags", ...extraFlags, "origin", `${branch}:${branch}`], `Cannot fetch ${branch}.`);
    }
    catch {
        // Errors are already logged by runGitCommand()
@@ -178,7 +179,7 @@ exports.gitFetch = gitFetch;
 */
 const gitRepack = async function (flags) {
    try {
-        await runGitCommand((0, actions_util_1.getOptionalInput)("checkout_path"), ["repack", ...flags], "Cannot repack the repository.");
+        await (0, exports.runGitCommand)((0, actions_util_1.getOptionalInput)("checkout_path"), ["repack", ...flags], "Cannot repack the repository.");
    }
    catch {
        // Errors are already logged by runGitCommand()
@@ -238,7 +239,7 @@ exports.decodeGitFilePath = decodeGitFilePath;
 */
 const getGitRoot = async function (sourceRoot) {
    try {
-        const stdout = await runGitCommand(sourceRoot, ["rev-parse", "--show-toplevel"], `Cannot find Git repository root from the source root ${sourceRoot}.`);
+        const stdout = await (0, exports.runGitCommand)(sourceRoot, ["rev-parse", "--show-toplevel"], `Cannot find Git repository root from the source root ${sourceRoot}.`);
        return stdout.trim();
    }
    catch {
@@ -247,6 +248,41 @@ const getGitRoot = async function (sourceRoot) {
    }
 };
 exports.getGitRoot = getGitRoot;
+/**
+ * Returns the Git OIDs of all tracked files (in the index and in the working
+ * tree) that are under the given base path, including files in active
+ * submodules. Untracked files and files not under the given base path are
+ * ignored.
+ *
+ * @param basePath A path into the Git repository.
+ * @returns a map from file paths (relative to `basePath`) to Git OIDs.
+ * @throws {Error} if "git ls-tree" produces unexpected output.
+ */
+const getFileOidsUnderPath = async function (basePath) {
+    // Without the --full-name flag, the path is relative to the current working
+    // directory of the git command, which is basePath.
+    const stdout = await (0, exports.runGitCommand)(basePath, ["ls-files", "--recurse-submodules", "--format=%(objectname)_%(path)"], "Cannot list Git OIDs of tracked files.");
+    const fileOidMap = {};
+    // With --format=%(objectname)_%(path), the output is a list of lines like:
+    // 30d998ded095371488be3a729eb61d86ed721a18_lib/git-utils.js
+    // d89514599a9a99f22b4085766d40af7b99974827_lib/git-utils.js.map
+    const regex = /^([0-9a-f]{40})_(.+)$/;
+    for (const line of stdout.split("\n")) {
+        if (line) {
+            const match = line.match(regex);
+            if (match) {
+                const oid = match[1];
+                const path = (0, exports.decodeGitFilePath)(match[2]);
+                fileOidMap[path] = oid;
+            }
+            else {
+                throw new Error(`Unexpected "git ls-files" output: ${line}`);
+            }
+        }
+    }
+    return fileOidMap;
+};
+exports.getFileOidsUnderPath = getFileOidsUnderPath;
 function getRefFromEnv() {
    // To workaround a limitation of Actions dynamic workflows not setting
    // the GITHUB_REF in some cases, we accept also the ref within the
@@ -1 +1 @@
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Line truncated
@@ -265,4 +265,75 @@ const util_1 = require("./util");
    t.deepEqual(gitUtils.decodeGitFilePath('"foo\\vbar"'), "foo\vbar");
    t.deepEqual(gitUtils.decodeGitFilePath('"\\a\\b\\f\\n\\r\\t\\v"'), "\x07\b\f\n\r\t\v");
 });
+(0, ava_1.default)("getFileOidsUnderPath returns correct file mapping", async (t) => {
+    const runGitCommandStub = sinon
+        .stub(gitUtils, "runGitCommand")
+        .resolves("30d998ded095371488be3a729eb61d86ed721a18_lib/git-utils.js\n" +
+        "d89514599a9a99f22b4085766d40af7b99974827_lib/git-utils.js.map\n" +
+        "a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96_src/git-utils.ts");
+    try {
+        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(runGitCommandStub.firstCall.args, [
+            "/fake/path",
+            ["ls-files", "--recurse-submodules", "--format=%(objectname)_%(path)"],
+            "Cannot list Git OIDs of tracked files.",
+        ]);
+    }
+    finally {
+        runGitCommandStub.restore();
+    }
+});
+(0, ava_1.default)("getFileOidsUnderPath handles quoted paths", async (t) => {
+    const runGitCommandStub = sinon
+        .stub(gitUtils, "runGitCommand")
+        .resolves("30d998ded095371488be3a729eb61d86ed721a18_lib/normal-file.js\n" +
+        'd89514599a9a99f22b4085766d40af7b99974827_"lib/file with spaces.js"\n' +
+        'a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96_"lib/file\\twith\\ttabs.js"');
+    try {
+        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",
+        });
+    }
+    finally {
+        runGitCommandStub.restore();
+    }
+});
+(0, ava_1.default)("getFileOidsUnderPath handles empty output", async (t) => {
+    const runGitCommandStub = sinon
+        .stub(gitUtils, "runGitCommand")
+        .resolves("");
+    try {
+        const result = await gitUtils.getFileOidsUnderPath("/fake/path");
+        t.deepEqual(result, {});
+    }
+    finally {
+        runGitCommandStub.restore();
+    }
+});
+(0, ava_1.default)("getFileOidsUnderPath throws on unexpected output format", async (t) => {
+    const runGitCommandStub = sinon
+        .stub(gitUtils, "runGitCommand")
+        .resolves("30d998ded095371488be3a729eb61d86ed721a18_lib/git-utils.js\n" +
+        "invalid-line-format\n" +
+        "a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96_src/git-utils.ts");
+    try {
+        await t.throwsAsync(async () => {
+            await gitUtils.getFileOidsUnderPath("/fake/path");
+        }, {
+            instanceOf: Error,
+            message: 'Unexpected "git ls-files" output: invalid-line-format',
+        });
+    }
+    finally {
+        runGitCommandStub.restore();
+    }
+});
 //# sourceMappingURL=git-utils.test.js.map
@@ -1 +1 @@
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truncated
@@ -1,6 +1,45 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.CODEQL_OVERLAY_MINIMUM_VERSION = exports.OverlayDatabaseMode = void 0;
+exports.writeBaseDatabaseOidsFile = writeBaseDatabaseOidsFile;
+exports.writeOverlayChangesFile = writeOverlayChangesFile;
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const actions_util_1 = require("./actions-util");
+const git_utils_1 = require("./git-utils");
 var OverlayDatabaseMode;
 (function (OverlayDatabaseMode) {
    OverlayDatabaseMode["Overlay"] = "overlay";
@@ -8,4 +47,83 @@ var OverlayDatabaseMode;
    OverlayDatabaseMode["None"] = "none";
 })(OverlayDatabaseMode || (exports.OverlayDatabaseMode = OverlayDatabaseMode = {}));
 exports.CODEQL_OVERLAY_MINIMUM_VERSION = "2.20.5";
+/**
+ * Writes a JSON file containing Git OIDs for all tracked files (represented
+ * by path relative to the source root) under the source root. The file is
+ * written into the database location specified in the config.
+ *
+ * @param config The configuration object containing the database location
+ * @param sourceRoot The root directory containing the source files to process
+ * @throws {Error} If the Git repository root cannot be determined
+ */
+async function writeBaseDatabaseOidsFile(config, sourceRoot) {
+    const gitFileOids = await (0, git_utils_1.getFileOidsUnderPath)(sourceRoot);
+    const gitFileOidsJson = JSON.stringify(gitFileOids);
+    const baseDatabaseOidsFilePath = getBaseDatabaseOidsFilePath(config);
+    await fs.promises.writeFile(baseDatabaseOidsFilePath, gitFileOidsJson);
+}
+/**
+ * Reads and parses the JSON file containing the base database Git OIDs.
+ * This file contains the mapping of file paths to their corresponding Git OIDs
+ * that was previously written by writeBaseDatabaseOidsFile().
+ *
+ * @param config The configuration object containing the database location
+ * @param logger The logger instance to use for error reporting
+ * @returns An object mapping file paths (relative to source root) to their Git OIDs
+ * @throws {Error} If the file cannot be read or parsed
+ */
+async function readBaseDatabaseOidsFile(config, logger) {
+    const baseDatabaseOidsFilePath = getBaseDatabaseOidsFilePath(config);
+    try {
+        const contents = await fs.promises.readFile(baseDatabaseOidsFilePath, "utf-8");
+        return JSON.parse(contents);
+    }
+    catch (e) {
+        logger.error("Failed to read overlay-base file OIDs from " +
+            `${baseDatabaseOidsFilePath}: ${e.message || e}`);
+        throw e;
+    }
+}
+function getBaseDatabaseOidsFilePath(config) {
+    return path.join(config.dbLocation, "base-database-oids.json");
+}
+/**
+ * Writes a JSON file containing the source-root-relative paths of files under
+ * `sourceRoot` that have changed (added, removed, or modified) from the overlay
+ * base database.
+ *
+ * This function uses the Git index to determine which files have changed, so it
+ * requires the following preconditions, both when this function is called and
+ * when the overlay-base database was initialized:
+ *
+ * - It requires that `sourceRoot` is inside a Git repository.
+ * - It assumes that all changes in the working tree are staged in the index.
+ * - It assumes that all files of interest are tracked by Git, e.g. not covered
+ *   by `.gitignore`.
+ */
+async function writeOverlayChangesFile(config, sourceRoot, logger) {
+    const baseFileOids = await readBaseDatabaseOidsFile(config, logger);
+    const overlayFileOids = await (0, git_utils_1.getFileOidsUnderPath)(sourceRoot);
+    const changedFiles = computeChangedFiles(baseFileOids, overlayFileOids);
+    logger.info(`Found ${changedFiles.length} changed file(s) under ${sourceRoot}.`);
+    const changedFilesJson = JSON.stringify({ changes: changedFiles });
+    const overlayChangesFile = path.join((0, actions_util_1.getTemporaryDirectory)(), "overlay-changes.json");
+    logger.debug(`Writing overlay changed files to ${overlayChangesFile}: ${changedFilesJson}`);
+    await fs.promises.writeFile(overlayChangesFile, changedFilesJson);
+    return overlayChangesFile;
+}
+function computeChangedFiles(baseFileOids, overlayFileOids) {
+    const changes = [];
+    for (const [file, oid] of Object.entries(overlayFileOids)) {
+        if (!(file in baseFileOids) || baseFileOids[file] !== oid) {
+            changes.push(file);
+        }
+    }
+    for (const file of Object.keys(baseFileOids)) {
+        if (!(file in overlayFileOids)) {
+            changes.push(file);
+        }
+    }
+    return changes;
+}
 //# sourceMappingURL=overlay-database-utils.js.map
@@ -1 +1 @@
-{"version":3,"file":"overlay-database-utils.js","sourceRoot":"","sources":["../src/overlay-database-utils.ts"],"names":[],"mappings":";;;AAAA,IAAY,mBAIX;AAJD,WAAY,mBAAmB;IAC7B,0CAAmB,CAAA;IACnB,mDAA4B,CAAA;IAC5B,oCAAa,CAAA;AACf,CAAC,EAJW,mBAAmB,mCAAnB,mBAAmB,QAI9B;AAEY,QAAA,8BAA8B,GAAG,QAAQ,CAAC"}
+{"version":3,"file":"overlay-database-utils.js","sourceRoot":"","sources":["../src/overlay-database-utils.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAyBA,8DAQC;AAkDD,0DAsBC;AAzGD,uCAAyB;AACzB,2CAA6B;AAE7B,iDAAuD;AAEvD,2CAAmD;AAGnD,IAAY,mBAIX;AAJD,WAAY,mBAAmB;IAC7B,0CAAmB,CAAA;IACnB,mDAA4B,CAAA;IAC5B,oCAAa,CAAA;AACf,CAAC,EAJW,mBAAmB,mCAAnB,mBAAmB,QAI9B;AAEY,QAAA,8BAA8B,GAAG,QAAQ,CAAC;AAEvD;;;;;;;;GAQG;AACI,KAAK,UAAU,yBAAyB,CAC7C,MAAc,EACd,UAAkB;IAElB,MAAM,WAAW,GAAG,MAAM,IAAA,gCAAoB,EAAC,UAAU,CAAC,CAAC;IAC3D,MAAM,eAAe,GAAG,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,CAAC;IACpD,MAAM,wBAAwB,GAAG,2BAA2B,CAAC,MAAM,CAAC,CAAC;IACrE,MAAM,EAAE,CAAC,QAAQ,CAAC,SAAS,CAAC,wBAAwB,EAAE,eAAe,CAAC,CAAC;AACzE,CAAC;AAED;;;;;;;;;GASG;AACH,KAAK,UAAU,wBAAwB,CACrC,MAAc,EACd,MAAc;IAEd,MAAM,wBAAwB,GAAG,2BAA2B,CAAC,MAAM,CAAC,CAAC;IACrE,IAAI,CAAC;QACH,MAAM,QAAQ,GAAG,MAAM,EAAE,CAAC,QAAQ,CAAC,QAAQ,CACzC,wBAAwB,EACxB,OAAO,CACR,CAAC;QACF,OAAO,IAAI,CAAC,KAAK,CAAC,QAAQ,CAA8B,CAAC;IAC3D,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,MAAM,CAAC,KAAK,CACV,6CAA6C;YAC3C,GAAG,wBAAwB,KAAM,CAAS,CAAC,OAAO,IAAI,CAAC,EAAE,CAC5D,CAAC;QACF,MAAM,CAAC,CAAC;IACV,CAAC;AACH,CAAC;AAED,SAAS,2BAA2B,CAAC,MAAc;IACjD,OAAO,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,EAAE,yBAAyB,CAAC,CAAC;AACjE,CAAC;AAED;;;;;;;;;;;;;GAaG;AACI,KAAK,UAAU,uBAAuB,CAC3C,MAAc,EACd,UAAkB,EAClB,MAAc;IAEd,MAAM,YAAY,GAAG,MAAM,wBAAwB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACpE,MAAM,eAAe,GAAG,MAAM,IAAA,gCAAoB,EAAC,UAAU,CAAC,CAAC;IAC/D,MAAM,YAAY,GAAG,mBAAmB,CAAC,YAAY,EAAE,eAAe,CAAC,CAAC;IACxE,MAAM,CAAC,IAAI,CACT,SAAS,YAAY,CAAC,MAAM,0BAA0B,UAAU,GAAG,CACpE,CAAC;IAEF,MAAM,gBAAgB,GAAG,IAAI,CAAC,SAAS,CAAC,EAAE,OAAO,EAAE,YAAY,EAAE,CAAC,CAAC;IACnE,MAAM,kBAAkB,GAAG,IAAI,CAAC,IAAI,CAClC,IAAA,oCAAqB,GAAE,EACvB,sBAAsB,CACvB,CAAC;IACF,MAAM,CAAC,KAAK,CACV,oCAAoC,kBAAkB,KAAK,gBAAgB,EAAE,CAC9E,CAAC;IACF,MAAM,EAAE,CAAC,QAAQ,CAAC,SAAS,CAAC,kBAAkB,EAAE,gBAAgB,CAAC,CAAC;IAClE,OAAO,kBAAkB,CAAC;AAC5B,CAAC;AAED,SAAS,mBAAmB,CAC1B,YAAuC,EACvC,eAA0C;IAE1C,MAAM,OAAO,GAAa,EAAE,CAAC;IAC7B,KAAK,MAAM,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,eAAe,CAAC,EAAE,CAAC;QAC1D,IAAI,CAAC,CAAC,IAAI,IAAI,YAAY,CAAC,IAAI,YAAY,CAAC,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;YAC1D,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACrB,CAAC;IACH,CAAC;IACD,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,EAAE,CAAC;QAC7C,IAAI,CAAC,CAAC,IAAI,IAAI,eAAe,CAAC,EAAE,CAAC;YAC/B,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACrB,CAAC;IACH,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}
@@ -0,0 +1,94 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const ava_1 = __importDefault(require("ava"));
+const sinon = __importStar(require("sinon"));
+const actionsUtil = __importStar(require("./actions-util"));
+const gitUtils = __importStar(require("./git-utils"));
+const logging_1 = require("./logging");
+const overlay_database_utils_1 = require("./overlay-database-utils");
+const testing_utils_1 = require("./testing-utils");
+const util_1 = require("./util");
+(0, testing_utils_1.setupTests)(ava_1.default);
+(0, ava_1.default)("writeOverlayChangesFile generates correct changes file", async (t) => {
+    await (0, util_1.withTmpDir)(async (tmpDir) => {
+        const dbLocation = path.join(tmpDir, "db");
+        await fs.promises.mkdir(dbLocation, { recursive: true });
+        const sourceRoot = path.join(tmpDir, "src");
+        await fs.promises.mkdir(sourceRoot, { recursive: true });
+        const tempDir = path.join(tmpDir, "temp");
+        await fs.promises.mkdir(tempDir, { recursive: true });
+        const logger = (0, logging_1.getRunnerLogger)(true);
+        const config = (0, testing_utils_1.createTestConfig)({ dbLocation });
+        // Mock the getFileOidsUnderPath function to return base OIDs
+        const baseOids = {
+            "unchanged.js": "aaa111",
+            "modified.js": "bbb222",
+            "deleted.js": "ccc333",
+        };
+        const getFileOidsStubForBase = sinon
+            .stub(gitUtils, "getFileOidsUnderPath")
+            .resolves(baseOids);
+        // Write the base database OIDs file
+        await (0, overlay_database_utils_1.writeBaseDatabaseOidsFile)(config, sourceRoot);
+        getFileOidsStubForBase.restore();
+        // Mock the getFileOidsUnderPath function to return overlay OIDs
+        const currentOids = {
+            "unchanged.js": "aaa111",
+            "modified.js": "ddd444", // Changed OID
+            "added.js": "eee555", // New file
+        };
+        const getFileOidsStubForOverlay = sinon
+            .stub(gitUtils, "getFileOidsUnderPath")
+            .resolves(currentOids);
+        // Write the overlay changes file, which uses the mocked overlay OIDs
+        // and the base database OIDs file
+        const getTempDirStub = sinon
+            .stub(actionsUtil, "getTemporaryDirectory")
+            .returns(tempDir);
+        const changesFilePath = await (0, overlay_database_utils_1.writeOverlayChangesFile)(config, sourceRoot, logger);
+        getFileOidsStubForOverlay.restore();
+        getTempDirStub.restore();
+        const fileContent = await fs.promises.readFile(changesFilePath, "utf-8");
+        const parsedContent = JSON.parse(fileContent);
+        t.deepEqual(parsedContent.changes.sort(), ["added.js", "deleted.js", "modified.js"], "Should identify added, deleted, and modified files");
+    });
+});
+//# sourceMappingURL=overlay-database-utils.test.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"overlay-database-utils.test.js","sourceRoot":"","sources":["../src/overlay-database-utils.test.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uCAAyB;AACzB,2CAA6B;AAE7B,8CAAuB;AACvB,6CAA+B;AAE/B,4DAA8C;AAC9C,sDAAwC;AACxC,uCAA4C;AAC5C,qEAGkC;AAClC,mDAA+D;AAC/D,iCAAoC;AAEpC,IAAA,0BAAU,EAAC,aAAI,CAAC,CAAC;AAEjB,IAAA,aAAI,EAAC,wDAAwD,EAAE,KAAK,EAAE,CAAC,EAAE,EAAE;IACzE,MAAM,IAAA,iBAAU,EAAC,KAAK,EAAE,MAAM,EAAE,EAAE;QAChC,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC;QAC3C,MAAM,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,UAAU,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QACzD,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;QAC5C,MAAM,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,UAAU,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QACzD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QAC1C,MAAM,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QAEtD,MAAM,MAAM,GAAG,IAAA,yBAAe,EAAC,IAAI,CAAC,CAAC;QACrC,MAAM,MAAM,GAAG,IAAA,gCAAgB,EAAC,EAAE,UAAU,EAAE,CAAC,CAAC;QAEhD,6DAA6D;QAC7D,MAAM,QAAQ,GAAG;YACf,cAAc,EAAE,QAAQ;YACxB,aAAa,EAAE,QAAQ;YACvB,YAAY,EAAE,QAAQ;SACvB,CAAC;QACF,MAAM,sBAAsB,GAAG,KAAK;aACjC,IAAI,CAAC,QAAQ,EAAE,sBAAsB,CAAC;aACtC,QAAQ,CAAC,QAAQ,CAAC,CAAC;QAEtB,oCAAoC;QACpC,MAAM,IAAA,kDAAyB,EAAC,MAAM,EAAE,UAAU,CAAC,CAAC;QACpD,sBAAsB,CAAC,OAAO,EAAE,CAAC;QAEjC,gEAAgE;QAChE,MAAM,WAAW,GAAG;YAClB,cAAc,EAAE,QAAQ;YACxB,aAAa,EAAE,QAAQ,EAAE,cAAc;YACvC,UAAU,EAAE,QAAQ,EAAE,WAAW;SAClC,CAAC;QACF,MAAM,yBAAyB,GAAG,KAAK;aACpC,IAAI,CAAC,QAAQ,EAAE,sBAAsB,CAAC;aACtC,QAAQ,CAAC,WAAW,CAAC,CAAC;QAEzB,qEAAqE;QACrE,kCAAkC;QAClC,MAAM,cAAc,GAAG,KAAK;aACzB,IAAI,CAAC,WAAW,EAAE,uBAAuB,CAAC;aAC1C,OAAO,CAAC,OAAO,CAAC,CAAC;QACpB,MAAM,eAAe,GAAG,MAAM,IAAA,gDAAuB,EACnD,MAAM,EACN,UAAU,EACV,MAAM,CACP,CAAC;QACF,yBAAyB,CAAC,OAAO,EAAE,CAAC;QACpC,cAAc,CAAC,OAAO,EAAE,CAAC;QAEzB,MAAM,WAAW,GAAG,MAAM,EAAE,CAAC,QAAQ,CAAC,QAAQ,CAAC,eAAe,EAAE,OAAO,CAAC,CAAC;QACzE,MAAM,aAAa,GAAG,IAAI,CAAC,KAAK,CAAC,WAAW,CAA0B,CAAC;QAEvE,CAAC,CAAC,SAAS,CACT,aAAa,CAAC,OAAO,CAAC,IAAI,EAAE,EAC5B,CAAC,UAAU,EAAE,YAAY,EAAE,aAAa,CAAC,EACzC,oDAAoD,CACrD,CAAC;IACJ,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}
@@ -1,6 +1,6 @@
 {
  "name": "codeql",
-  "version": "3.28.12",
+  "version": "3.28.13",
  "lockfileVersion": 3,
  "requires": true,
  "packages": {
@@ -1,12 +1,12 @@
 {
  "name": "codeql",
-  "version": "3.28.12",
+  "version": "3.28.13",
  "lockfileVersion": 3,
  "requires": true,
  "packages": {
    "": {
      "name": "codeql",
-      "version": "3.28.12",
+      "version": "3.28.13",
      "license": "MIT",
      "dependencies": {
        "@actions/artifact": "^2.3.1",
@@ -1,6 +1,6 @@
 {
  "name": "codeql",
-  "version": "3.28.12",
+  "version": "3.28.13",
  "private": true,
  "description": "CodeQL action",
  "scripts": {
@@ -5,7 +5,7 @@ operatingSystems: ["ubuntu"]
 versions: ["default"]
 steps:
  - name: Set up Ruby
-    uses: ruby/setup-ruby@277ba2a127aba66d45bad0fa2dc56f80dbfedffa # v1.222.0
+    uses: ruby/setup-ruby@922ebc4c5262cd14e07bb0e1db020984b6c064fe # v1.226.0
    with:
      ruby-version: 2.6
  - name: Install Code Scanning integration
@@ -3,6 +3,8 @@
 * It will run after the all steps in this job, in reverse order in relation to
 * other `post:` hooks.
 */
+import * as fs from "fs";
+
 import * as core from "@actions/core";

 import * as actionsUtil from "./actions-util";
@@ -10,6 +12,7 @@ import { getGitHubVersion } from "./api-client";
 import { getCodeQL } from "./codeql";
 import { getConfig } from "./config-utils";
 import * as debugArtifacts from "./debug-artifacts";
+import { getJavaTempDependencyDir } from "./dependency-caching";
 import { EnvVar } from "./environment";
 import { getActionsLogger } from "./logging";
 import { checkGitHubVersionInRange, getErrorMessage } from "./util";
@@ -38,6 +41,20 @@ async function runWrapper() {
        );
      }
    }
+
+    // If we analysed Java in build-mode: none, we may have downloaded dependencies
+    // to the temp directory. Clean these up so they don't persist unnecessarily
+    // long on self-hosted runners.
+    const javaTempDependencyDir = getJavaTempDependencyDir();
+    if (fs.existsSync(javaTempDependencyDir)) {
+      try {
+        fs.rmSync(javaTempDependencyDir, { recursive: true });
+      } catch (error) {
+        logger.info(
+          `Failed to remove temporary Java dependencies directory: ${getErrorMessage(error)}`,
+        );
+      }
+    }
  } catch (error) {
    core.setFailed(
      `analyze post-action step failed: ${getErrorMessage(error)}`,
@@ -3,7 +3,6 @@ import path from "path";
 import { performance } from "perf_hooks";

 import * as core from "@actions/core";
-import * as github from "@actions/github";

 import * as actionsUtil from "./actions-util";
 import {
@@ -272,16 +271,11 @@ async function run() {
      logger,
    );

-    const pull_request = github.context.payload.pull_request;
-    const diffRangePackDir =
-      pull_request &&
-      (await setupDiffInformedQueryRun(
-        pull_request.base.ref as string,
-        pull_request.head.label as string,
-        codeql,
-        logger,
-        features,
-      ));
+    const diffRangePackDir = await setupDiffInformedQueryRun(
+      codeql,
+      logger,
+      features,
+    );

    await warnIfGoInstalledAfterInit(config, logger);
    await runAutobuildIfLegacyGoWorkflow(config, logger);
@@ -2,6 +2,7 @@ import * as fs from "fs";
 import * as path from "path";
 import { performance } from "perf_hooks";

+import * as github from "@actions/github";
 import * as io from "@actions/io";
 import del from "del";
 import * as yaml from "js-yaml";
@@ -11,6 +12,7 @@ import { getApiClient } from "./api-client";
 import { setupCppAutobuild } from "./autobuild";
 import { CodeQL, getCodeQL } from "./codeql";
 import * as configUtils from "./config-utils";
+import { getJavaTempDependencyDir } from "./dependency-caching";
 import { addDiagnostic, makeDiagnostic } from "./diagnostics";
 import {
  DiffThunkRange,
@@ -166,6 +168,16 @@ export async function runExtraction(
        ) {
          await setupCppAutobuild(codeql, logger);
        }
+
+        // The Java `build-mode: none` extractor places dependencies (.jar files) in the
+        // database scratch directory by default. For dependency caching purposes, we want
+        // 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 === Language.java && config.buildMode === BuildMode.None) {
+          process.env["CODEQL_EXTRACTOR_JAVA_OPTION_BUILDLESS_DEPENDENCY_DIR"] =
+            getJavaTempDependencyDir();
+        }
+
        await codeql.extractUsingBuildMode(config, language);
      } else {
        await codeql.extractScannedLanguage(config, language);
@@ -242,21 +254,45 @@ async function finalizeDatabaseCreation(
  };
 }

+interface PullRequestBranches {
+  base: string;
+  head: string;
+}
+
+function getPullRequestBranches(): PullRequestBranches | undefined {
+  const pullRequest = github.context.payload.pull_request;
+  if (pullRequest) {
+    return {
+      base: pullRequest.base.ref,
+      // We use the head label instead of the head ref here, because the head
+      // ref lacks owner information and by itself does not uniquely identify
+      // the head branch (which may be in a forked repository).
+      head: pullRequest.head.label,
+    };
+  }
+
+  // PR analysis under Default Setup does not have the pull_request context,
+  // but it should set CODE_SCANNING_REF and CODE_SCANNING_BASE_BRANCH.
+  const codeScanningRef = process.env.CODE_SCANNING_REF;
+  const codeScanningBaseBranch = process.env.CODE_SCANNING_BASE_BRANCH;
+  if (codeScanningRef && codeScanningBaseBranch) {
+    return {
+      base: codeScanningBaseBranch,
+      // PR analysis under Default Setup analyzes the PR head commit instead of
+      // the merge commit, so we can use the provided ref directly.
+      head: codeScanningRef,
+    };
+  }
+  return undefined;
+}
+
 /**
 * Set up the diff-informed analysis feature.
 *
- * @param baseRef The base branch name, used for calculating the diff range.
- * @param headLabel The label that uniquely identifies the head branch across
- * repositories, used for calculating the diff range.
- * @param codeql
- * @param logger
- * @param features
 * @returns Absolute path to the directory containing the extension pack for
 * the diff range information, or `undefined` if the feature is disabled.
 */
 export async function setupDiffInformedQueryRun(
-  baseRef: string,
-  headLabel: string,
  codeql: CodeQL,
  logger: Logger,
  features: FeatureEnablement,
@@ -264,14 +300,23 @@ export async function setupDiffInformedQueryRun(
  if (!(await features.getValue(Feature.DiffInformedQueries, codeql))) {
    return undefined;
  }
+
+  const branches = getPullRequestBranches();
+  if (!branches) {
+    logger.info(
+      "Not performing diff-informed analysis " +
+        "because we are not analyzing a pull request.",
+    );
+    return undefined;
+  }
+
  return await withGroupAsync(
    "Generating diff range extension pack",
    async () => {
-      const diffRanges = await getPullRequestEditedDiffRanges(
-        baseRef,
-        headLabel,
-        logger,
+      logger.info(
+        `Calculating diff ranges for ${branches.base}...${branches.head}`,
      );
+      const diffRanges = await getPullRequestEditedDiffRanges(branches, logger);
      const packDir = writeDiffRangeDataExtensionPack(logger, diffRanges);
      if (packDir === undefined) {
        logger.warning(
@@ -291,9 +336,7 @@ export async function setupDiffInformedQueryRun(
 /**
 * Return the file line ranges that were added or modified in the pull request.
 *
- * @param baseRef The base branch name, used for calculating the diff range.
- * @param headLabel The label that uniquely identifies the head branch across
- * repositories, used for calculating the diff range.
+ * @param branches The base and head branches of the pull request.
 * @param logger
 * @returns An array of tuples, where each tuple contains the absolute path of a
 * file, the start line and the end line (both 1-based and inclusive) of an
@@ -301,11 +344,10 @@ export async function setupDiffInformedQueryRun(
 * not triggered by a pull request or if there was an error.
 */
 async function getPullRequestEditedDiffRanges(
-  baseRef: string,
-  headLabel: string,
+  branches: PullRequestBranches,
  logger: Logger,
 ): Promise<DiffThunkRange[] | undefined> {
-  const fileDiffs = await getFileDiffsWithBasehead(baseRef, headLabel, logger);
+  const fileDiffs = await getFileDiffsWithBasehead(branches, logger);
  if (fileDiffs === undefined) {
    return undefined;
  }
@@ -344,14 +386,13 @@ interface FileDiff {
 }

 async function getFileDiffsWithBasehead(
-  baseRef: string,
-  headLabel: string,
+  branches: PullRequestBranches,
  logger: Logger,
 ): Promise<FileDiff[] | undefined> {
  const ownerRepo = util.getRequiredEnvParam("GITHUB_REPOSITORY").split("/");
  const owner = ownerRepo[0];
  const repo = ownerRepo[1];
-  const basehead = `${baseRef}...${headLabel}`;
+  const basehead = `${branches.base}...${branches.head}`;
  try {
    const response = await getApiClient().rest.repos.compareCommitsWithBasehead(
      {
@@ -486,6 +527,15 @@ function writeDiffRangeDataExtensionPack(
    return undefined;
  }

+  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
+    // interprets an empty data extension differently, as an indication that
+    // all alerts should be included. So we need to specifically set the diff
+    // range to a non-empty list that cannot match any alert location.
+    ranges = [{ path: "", startLine: 0, endLine: 0 }];
+  }
+
  const diffRangeDir = path.join(
    actionsUtil.getTemporaryDirectory(),
    "pr-diff-range",
@@ -24,7 +24,11 @@ import {
 import { isAnalyzingDefaultBranch } from "./git-utils";
 import { Language } from "./languages";
 import { Logger } from "./logging";
-import { OverlayDatabaseMode } from "./overlay-database-utils";
+import {
+  OverlayDatabaseMode,
+  writeBaseDatabaseOidsFile,
+  writeOverlayChangesFile,
+} from "./overlay-database-utils";
 import * as setupCodeql from "./setup-codeql";
 import { ZstdAvailability } from "./tar";
 import { ToolsDownloadStatusReport } from "./tools-download";
@@ -610,7 +614,12 @@ export async function getCodeQLForCmd(
        : "--overwrite";

      if (overlayDatabaseMode === OverlayDatabaseMode.Overlay) {
-        extraArgs.push("--overlay");
+        const overlayChangesFile = await writeOverlayChangesFile(
+          config,
+          sourceRoot,
+          logger,
+        );
+        extraArgs.push(`--overlay-changes=${overlayChangesFile}`);
      } else if (overlayDatabaseMode === OverlayDatabaseMode.OverlayBase) {
        extraArgs.push("--overlay-base");
      }
@@ -636,6 +645,10 @@ export async function getCodeQLForCmd(
        ],
        { stdin: externalRepositoryToken },
      );
+
+      if (overlayDatabaseMode === OverlayDatabaseMode.OverlayBase) {
+        await writeBaseDatabaseOidsFile(config, sourceRoot);
+      }
    },
    async runAutobuild(config: Config, language: Language) {
      applyAutobuildAzurePipelinesTimeoutFix();
@@ -1,6 +1,6 @@
 {
-  "bundleVersion": "codeql-bundle-v2.20.6",
-  "cliVersion": "2.20.6",
-  "priorBundleVersion": "codeql-bundle-v2.20.5",
-  "priorCliVersion": "2.20.5"
+  "bundleVersion": "codeql-bundle-v2.20.7",
+  "cliVersion": "2.20.7",
+  "priorBundleVersion": "codeql-bundle-v2.20.6",
+  "priorCliVersion": "2.20.6"
 }
@@ -4,6 +4,7 @@ import { join } from "path";
 import * as actionsCache from "@actions/cache";
 import * as glob from "@actions/glob";

+import { getTemporaryDirectory } from "./actions-util";
 import { getTotalCacheSize } from "./caching-utils";
 import { Config } from "./config-utils";
 import { EnvVar } from "./environment";
@@ -28,6 +29,15 @@ interface CacheConfig {
 const CODEQL_DEPENDENCY_CACHE_PREFIX = "codeql-dependencies";
 const CODEQL_DEPENDENCY_CACHE_VERSION = 1;

+/**
+ * Returns a path to a directory intended to be used to store .jar files
+ * for the Java `build-mode: none` extractor.
+ * @returns The path to the directory that should be used by the `build-mode: none` extractor.
+ */
+export function getJavaTempDependencyDir(): string {
+  return join(getTemporaryDirectory(), "codeql_java", "repository");
+}
+
 /**
 * Default caching configurations per language.
 */
@@ -38,6 +48,8 @@ const CODEQL_DEFAULT_CACHE_CONFIG: { [language: string]: CacheConfig } = {
      join(os.homedir(), ".m2", "repository"),
      // Gradle
      join(os.homedir(), ".gradle", "caches"),
+      // CodeQL Java build-mode: none
+      getJavaTempDependencyDir(),
    ],
    hash: [
      // Maven
@@ -305,3 +305,90 @@ test("decodeGitFilePath quoted strings", async (t) => {
    "\x07\b\f\n\r\t\v",
  );
 });
+
+test("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",
+    );
+
+  try {
+    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(runGitCommandStub.firstCall.args, [
+      "/fake/path",
+      ["ls-files", "--recurse-submodules", "--format=%(objectname)_%(path)"],
+      "Cannot list Git OIDs of tracked files.",
+    ]);
+  } finally {
+    runGitCommandStub.restore();
+  }
+});
+
+test("getFileOidsUnderPath handles quoted paths", async (t) => {
+  const runGitCommandStub = 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"',
+    );
+
+  try {
+    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",
+    });
+  } finally {
+    runGitCommandStub.restore();
+  }
+});
+
+test("getFileOidsUnderPath handles empty output", async (t) => {
+  const runGitCommandStub = sinon
+    .stub(gitUtils as any, "runGitCommand")
+    .resolves("");
+
+  try {
+    const result = await gitUtils.getFileOidsUnderPath("/fake/path");
+    t.deepEqual(result, {});
+  } finally {
+    runGitCommandStub.restore();
+  }
+});
+
+test("getFileOidsUnderPath throws on unexpected output format", async (t) => {
+  const runGitCommandStub = sinon
+    .stub(gitUtils as any, "runGitCommand")
+    .resolves(
+      "30d998ded095371488be3a729eb61d86ed721a18_lib/git-utils.js\n" +
+        "invalid-line-format\n" +
+        "a47c11f5bfdca7661942d2c8f1b7209fb0dfdf96_src/git-utils.ts",
+    );
+
+  try {
+    await t.throwsAsync(
+      async () => {
+        await gitUtils.getFileOidsUnderPath("/fake/path");
+      },
+      {
+        instanceOf: Error,
+        message: 'Unexpected "git ls-files" output: invalid-line-format',
+      },
+    );
+  } finally {
+    runGitCommandStub.restore();
+  }
+});
@@ -9,8 +9,8 @@ import {
 } from "./actions-util";
 import { ConfigurationError, getRequiredEnvParam } from "./util";

-async function runGitCommand(
-  checkoutPath: string | undefined,
+export const runGitCommand = async function (
+  workingDirectory: string | undefined,
  args: string[],
  customErrorMessage: string,
 ): Promise<string> {
@@ -28,7 +28,7 @@ async function runGitCommand(
          stderr += data.toString();
        },
      },
-      cwd: checkoutPath,
+      cwd: workingDirectory,
    }).exec();
    return stdout;
  } catch (error) {
@@ -40,7 +40,7 @@ async function runGitCommand(
    core.info(`git call failed. ${customErrorMessage} Error: ${reason}`);
    throw error;
  }
-}
+};

 /**
 * Gets the SHA of the commit that is currently checked out.
@@ -253,6 +253,47 @@ export const getGitRoot = async function (
  }
 };

+/**
+ * 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
+ * submodules. Untracked files and files not under the given base path are
+ * ignored.
+ *
+ * @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.
+ */
+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.
+  const stdout = await runGitCommand(
+    basePath,
+    ["ls-files", "--recurse-submodules", "--format=%(objectname)_%(path)"],
+    "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})_(.+)$/;
+  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;
+      } else {
+        throw new Error(`Unexpected "git ls-files" output: ${line}`);
+      }
+    }
+  }
+  return fileOidMap;
+};
+
 function getRefFromEnv(): string {
  // To workaround a limitation of Actions dynamic workflows not setting
  // the GITHUB_REF in some cases, we accept also the ref within the
@@ -0,0 +1,77 @@
+import * as fs from "fs";
+import * as path from "path";
+
+import test from "ava";
+import * as sinon from "sinon";
+
+import * as actionsUtil from "./actions-util";
+import * as gitUtils from "./git-utils";
+import { getRunnerLogger } from "./logging";
+import {
+  writeBaseDatabaseOidsFile,
+  writeOverlayChangesFile,
+} from "./overlay-database-utils";
+import { createTestConfig, setupTests } from "./testing-utils";
+import { withTmpDir } from "./util";
+
+setupTests(test);
+
+test("writeOverlayChangesFile generates correct changes file", async (t) => {
+  await withTmpDir(async (tmpDir) => {
+    const dbLocation = path.join(tmpDir, "db");
+    await fs.promises.mkdir(dbLocation, { recursive: true });
+    const sourceRoot = path.join(tmpDir, "src");
+    await fs.promises.mkdir(sourceRoot, { recursive: true });
+    const tempDir = path.join(tmpDir, "temp");
+    await fs.promises.mkdir(tempDir, { recursive: true });
+
+    const logger = getRunnerLogger(true);
+    const config = createTestConfig({ dbLocation });
+
+    // Mock the getFileOidsUnderPath function to return base OIDs
+    const baseOids = {
+      "unchanged.js": "aaa111",
+      "modified.js": "bbb222",
+      "deleted.js": "ccc333",
+    };
+    const getFileOidsStubForBase = sinon
+      .stub(gitUtils, "getFileOidsUnderPath")
+      .resolves(baseOids);
+
+    // Write the base database OIDs file
+    await writeBaseDatabaseOidsFile(config, sourceRoot);
+    getFileOidsStubForBase.restore();
+
+    // Mock the getFileOidsUnderPath function to return overlay OIDs
+    const currentOids = {
+      "unchanged.js": "aaa111",
+      "modified.js": "ddd444", // Changed OID
+      "added.js": "eee555", // New file
+    };
+    const getFileOidsStubForOverlay = sinon
+      .stub(gitUtils, "getFileOidsUnderPath")
+      .resolves(currentOids);
+
+    // Write the overlay changes file, which uses the mocked overlay OIDs
+    // and the base database OIDs file
+    const getTempDirStub = sinon
+      .stub(actionsUtil, "getTemporaryDirectory")
+      .returns(tempDir);
+    const changesFilePath = await writeOverlayChangesFile(
+      config,
+      sourceRoot,
+      logger,
+    );
+    getFileOidsStubForOverlay.restore();
+    getTempDirStub.restore();
+
+    const fileContent = await fs.promises.readFile(changesFilePath, "utf-8");
+    const parsedContent = JSON.parse(fileContent) as { changes: string[] };
+
+    t.deepEqual(
+      parsedContent.changes.sort(),
+      ["added.js", "deleted.js", "modified.js"],
+      "Should identify added, deleted, and modified files",
+    );
+  });
+});
@@ -1,3 +1,11 @@
+import * as fs from "fs";
+import * as path from "path";
+
+import { getTemporaryDirectory } from "./actions-util";
+import { type Config } from "./config-utils";
+import { getFileOidsUnderPath } from "./git-utils";
+import { Logger } from "./logging";
+
 export enum OverlayDatabaseMode {
  Overlay = "overlay",
  OverlayBase = "overlay-base",
@@ -5,3 +13,112 @@ export enum OverlayDatabaseMode {
 }

 export const CODEQL_OVERLAY_MINIMUM_VERSION = "2.20.5";
+
+/**
+ * Writes a JSON file containing Git OIDs for all tracked files (represented
+ * by path relative to the source root) under the source root. The file is
+ * written into the database location specified in the config.
+ *
+ * @param config The configuration object containing the database location
+ * @param sourceRoot The root directory containing the source files to process
+ * @throws {Error} If the Git repository root cannot be determined
+ */
+export async function writeBaseDatabaseOidsFile(
+  config: Config,
+  sourceRoot: string,
+): Promise<void> {
+  const gitFileOids = await getFileOidsUnderPath(sourceRoot);
+  const gitFileOidsJson = JSON.stringify(gitFileOids);
+  const baseDatabaseOidsFilePath = getBaseDatabaseOidsFilePath(config);
+  await fs.promises.writeFile(baseDatabaseOidsFilePath, gitFileOidsJson);
+}
+
+/**
+ * Reads and parses the JSON file containing the base database Git OIDs.
+ * This file contains the mapping of file paths to their corresponding Git OIDs
+ * that was previously written by writeBaseDatabaseOidsFile().
+ *
+ * @param config The configuration object containing the database location
+ * @param logger The logger instance to use for error reporting
+ * @returns An object mapping file paths (relative to source root) to their Git OIDs
+ * @throws {Error} If the file cannot be read or parsed
+ */
+async function readBaseDatabaseOidsFile(
+  config: Config,
+  logger: Logger,
+): Promise<{ [key: string]: string }> {
+  const baseDatabaseOidsFilePath = getBaseDatabaseOidsFilePath(config);
+  try {
+    const contents = await fs.promises.readFile(
+      baseDatabaseOidsFilePath,
+      "utf-8",
+    );
+    return JSON.parse(contents) as { [key: string]: string };
+  } catch (e) {
+    logger.error(
+      "Failed to read overlay-base file OIDs from " +
+        `${baseDatabaseOidsFilePath}: ${(e as any).message || e}`,
+    );
+    throw e;
+  }
+}
+
+function getBaseDatabaseOidsFilePath(config: Config): string {
+  return path.join(config.dbLocation, "base-database-oids.json");
+}
+
+/**
+ * Writes a JSON file containing the source-root-relative paths of files under
+ * `sourceRoot` that have changed (added, removed, or modified) from the overlay
+ * base database.
+ *
+ * This function uses the Git index to determine which files have changed, so it
+ * requires the following preconditions, both when this function is called and
+ * when the overlay-base database was initialized:
+ *
+ * - It requires that `sourceRoot` is inside a Git repository.
+ * - It assumes that all changes in the working tree are staged in the index.
+ * - It assumes that all files of interest are tracked by Git, e.g. not covered
+ *   by `.gitignore`.
+ */
+export async function writeOverlayChangesFile(
+  config: Config,
+  sourceRoot: string,
+  logger: Logger,
+): Promise<string> {
+  const baseFileOids = await readBaseDatabaseOidsFile(config, logger);
+  const overlayFileOids = await getFileOidsUnderPath(sourceRoot);
+  const changedFiles = computeChangedFiles(baseFileOids, overlayFileOids);
+  logger.info(
+    `Found ${changedFiles.length} changed file(s) under ${sourceRoot}.`,
+  );
+
+  const changedFilesJson = JSON.stringify({ changes: changedFiles });
+  const overlayChangesFile = path.join(
+    getTemporaryDirectory(),
+    "overlay-changes.json",
+  );
+  logger.debug(
+    `Writing overlay changed files to ${overlayChangesFile}: ${changedFilesJson}`,
+  );
+  await fs.promises.writeFile(overlayChangesFile, changedFilesJson);
+  return overlayChangesFile;
+}
+
+function computeChangedFiles(
+  baseFileOids: { [key: string]: string },
+  overlayFileOids: { [key: string]: string },
+): string[] {
+  const changes: string[] = [];
+  for (const [file, oid] of Object.entries(overlayFileOids)) {
+    if (!(file in baseFileOids) || baseFileOids[file] !== oid) {
+      changes.push(file);
+    }
+  }
+  for (const file of Object.keys(baseFileOids)) {
+    if (!(file in overlayFileOids)) {
+      changes.push(file);
+    }
+  }
+  return changes;
+}
Author	SHA1	Message	Date
Chuan-kai Lin	1b549b9259	Merge pull request #2819 from github/update-v3.28.13-e0ea14102 Merge main into releases/v3	2025-03-24 06:42:41 -07:00
github-actions[bot]	82630c85f3	Update changelog for v3.28.13	2025-03-24 13:18:07 +00:00
Chuan-kai Lin	e0ea141027	Merge pull request #2818 from github/cklin/empty-pr-diff-range Diff-informed analysis: fix empty PR handling	2025-03-21 16:04:38 -07:00
Chuan-kai Lin	b361a91508	Diff-informed analysis: fix empty PR handling	2025-03-21 14:18:25 -07:00
Chuan-kai Lin	bd1d9ab4ed	Merge pull request #2816 from github/cklin/overlay-file-list Overlay databases: use --overlay-changes	2025-03-21 12:30:26 -07:00
Chuan-kai Lin	b98ae6ca52	Add overlay-database-utils tests	2025-03-21 11:31:28 -07:00
Chuan-kai Lin	9825184a0a	Add getFileOidsUnderPath() tests	2025-03-21 10:53:21 -07:00
Chuan-kai Lin	ac67cffe5c	Merge pull request #2817 from github/cklin/default-setup-diff-informed Support diff-informed queries under Default Setup	2025-03-21 09:47:20 -07:00
Chuan-kai Lin	9c674ba4f5	build: refresh js files	2025-03-21 09:25:30 -07:00
Chuan-kai Lin	d109dd5d33	Detect PR branches for Default Setup	2025-03-21 09:25:08 -07:00
Chuan-kai Lin	3e5446c3d2	Introduce PullRequestBranches	2025-03-21 09:24:16 -07:00
Chuan-kai Lin	6adda79888	Move PR branch detection into setupDiffInformedQueryRun()	2025-03-20 09:51:17 -07:00
Chuan-kai Lin	6be6984cc1	Overlay databases: use --overlay-changes This commit changes overlay database creation to use the --overlay-changes flag. It also implements Git-based file change detection to generate the list of files to extract for the overlay database.	2025-03-19 11:38:45 -07:00
Andrew Eisenberg	c50c157cc3	Merge pull request #2813 from github/NlightNFotis/enhance_justfile build: sync some utility just instructions I had locally	2025-03-19 10:57:36 -07:00
Fotis KoutoulakisandAndrew Eisenberg	c74c378e29	Update justfile Co-authored-by: Andrew Eisenberg <aeisenberg@github.com>	2025-03-19 17:11:02 +00:00
Fotis KoutoulakisandAndrew Eisenberg	d271bde0ec	Update justfile Co-authored-by: Andrew Eisenberg <aeisenberg@github.com>	2025-03-19 17:10:52 +00:00
Chris Smowton	df9f80e0f0	Merge pull request #2815 from github/mergeback/v3.28.12-to-main-5f8171a6 Mergeback v3.28.12 refs/heads/releases/v3 into main	2025-03-19 13:42:24 +00:00
github-actions[bot]	46371933a7	Update checked-in dependencies	2025-03-19 12:43:51 +00:00
github-actions[bot]	ee6a063cbd	Update changelog and version after v3.28.12	2025-03-19 12:41:18 +00:00
Chris Smowton	5f8171a638	Merge pull request #2814 from github/update-v3.28.12-6349095d1 Merge main into releases/v3	2025-03-19 12:40:51 +00:00
github-actions[bot]	bb59f7707d	Update changelog for v3.28.12	2025-03-19 12:17:24 +00:00
Fotis Koutoulakis (@NlightNFotis)	8b0dccd066	build: sync some utility just instructions I had locally	2025-03-19 11:56:11 +00:00
Chris Smowton	6349095d19	Merge pull request #2810 from github/update-bundle/codeql-bundle-v2.20.7 Update default bundle to 2.20.7	2025-03-18 12:35:37 +00:00
github-actions[bot]	d7d03fda12	Add changelog note	2025-03-18 12:21:54 +00:00
github-actions[bot]	4e3a5342c5	Update default bundle to codeql-bundle-v2.20.7	2025-03-18 12:21:54 +00:00
Michael B. Gale	55f023701c	Merge pull request #2802 from github/mbg/dependency-caching/java-buildless Set and cache dependency directory for Java `build-mode: none`	2025-03-18 10:28:36 +00:00
Angela P Wen	6a151cd774	Merge pull request #2811 from github/dependabot/github_actions/actions-c2c311daa1 build(deps): bump ruby/setup-ruby from 1.222.0 to 1.226.0 in the actions group	2025-03-17 12:15:27 -07:00
Angela P Wen	7866bcdb1b	Manually bump workflow to match autogenerated file	2025-03-17 12:00:05 -07:00
dependabot[bot]	611289e0b0	build(deps): bump ruby/setup-ruby in the actions group Bumps the actions group with 1 update: [ruby/setup-ruby](https://github.com/ruby/setup-ruby). Updates `ruby/setup-ruby` from 1.222.0 to 1.226.0 - [Release notes](https://github.com/ruby/setup-ruby/releases) - [Changelog](https://github.com/ruby/setup-ruby/blob/master/release.rb) - [Commits](https://github.com/ruby/setup-ruby/compare/277ba2a127aba66d45bad0fa2dc56f80dbfedffa...922ebc4c5262cd14e07bb0e1db020984b6c064fe) --- updated-dependencies: - dependency-name: ruby/setup-ruby dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions ... Signed-off-by: dependabot[bot] <support@github.com>	2025-03-17 18:11:32 +00:00
Michael B. Gale	4c409a5b66	Remove temporary dependency directory in `analyze` post action	2025-03-17 11:34:09 +00:00
Michael B. Gale	251c7fdf5d	Update changelog	2025-03-13 11:50:11 +00:00
Michael B. Gale	afa3ed33bb	Add more documentation	2025-03-13 11:45:27 +00:00
Michael B. Gale	f8367fb063	Set and cache dependency directory for Java `build-mode: none`	2025-03-13 11:39:39 +00:00
				`@@ -0,0 +1 @@`
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