Merge branch 'main' into mbg/csharp/more-cache-locations

src/actions-util.ts

@@ -80,7 +80,7 @@ export function isRunningLocalAction(): boolean {
  *
  * This can be used to get the Action's name or tell if we're running a local Action.
  */
-export function getRelativeScriptPath(): string {
+function getRelativeScriptPath(): string {
   const runnerTemp = getRequiredEnvParam("RUNNER_TEMP");
   const actionsDirectory = path.join(path.dirname(runnerTemp), "_actions");
   return path.relative(actionsDirectory, __filename);

src/analyses.ts

@@ -98,7 +98,7 @@ export async function getAnalysisKinds(
 export const codeQualityQueries: string[] = ["code-quality"];
 
 // Enumerates API endpoints that accept SARIF files.
-export enum SARIF_UPLOAD_ENDPOINT {
+enum SARIF_UPLOAD_ENDPOINT {
   CODE_SCANNING = "PUT /repos/:owner/:repo/code-scanning/analysis",
   CODE_QUALITY = "PUT /repos/:owner/:repo/code-quality/analysis",
 }

src/analyze-action.ts

@@ -25,7 +25,7 @@ import {
   isCodeQualityEnabled,
   isCodeScanningEnabled,
 } from "./config-utils";
-import { uploadDatabases } from "./database-upload";
+import { cleanupAndUploadDatabases } from "./database-upload";
 import {
   DependencyCacheUploadStatusReport,
   uploadDependencyCaches,
@@ -35,7 +35,7 @@ import { EnvVar } from "./environment";
 import { Feature, Features } from "./feature-flags";
 import { KnownLanguage } from "./languages";
 import { getActionsLogger, Logger } from "./logging";
-import { uploadOverlayBaseDatabaseToCache } from "./overlay-database-utils";
+import { cleanupAndUploadOverlayBaseDatabaseToCache } from "./overlay-database-utils";
 import { getRepositoryNwo } from "./repository";
 import * as statusReport from "./status-report";
 import {
@@ -418,12 +418,21 @@ async function run() {
     }
 
     // Possibly upload the overlay-base database to actions cache.
-    // If databases are to be uploaded, they will first be cleaned up at the overlay level.
-    await uploadOverlayBaseDatabaseToCache(codeql, config, logger);
+    // Note: Take care with the ordering of this call since databases may be cleaned up
+    // at the `overlay` level.
+    await cleanupAndUploadOverlayBaseDatabaseToCache(codeql, config, logger);
 
     // Possibly upload the database bundles for remote queries.
-    // If databases are to be uploaded, they will first be cleaned up at the clear level.
-    await uploadDatabases(repositoryNwo, codeql, config, apiDetails, logger);
+    // Note: Take care with the ordering of this call since databases may be cleaned up
+    // at the `overlay` or `clear` level.
+    await cleanupAndUploadDatabases(
+      repositoryNwo,
+      codeql,
+      config,
+      apiDetails,
+      features,
+      logger,
+    );
 
     // Possibly upload the TRAP caches for later re-use
     const trapCacheUploadStartTime = performance.now();

src/api-client.ts

@@ -18,11 +18,6 @@ import {
 
 const GITHUB_ENTERPRISE_VERSION_HEADER = "x-github-enterprise-version";
 
-export enum DisallowedAPIVersionReason {
-  ACTION_TOO_OLD,
-  ACTION_TOO_NEW,
-}
-
 export type GitHubApiCombinedDetails = GitHubApiDetails &
   GitHubApiExternalRepoDetails;
 

src/cli-errors.ts

@@ -159,10 +159,7 @@ type CliErrorConfiguration = {
  * All of our caught CLI error messages that we handle specially: ie. if we
  * would like to categorize an error as a configuration error or not.
  */
-export const cliErrorsConfig: Record<
-  CliConfigErrorCategory,
-  CliErrorConfiguration
-> = {
+const cliErrorsConfig: Record<CliConfigErrorCategory, CliErrorConfiguration> = {
   [CliConfigErrorCategory.AutobuildError]: {
     cliErrorMessageCandidates: [
       new RegExp("We were unable to automatically build your code"),

src/codeql.ts

@@ -35,7 +35,7 @@ import { ToolsDownloadStatusReport } from "./tools-download";
 import { ToolsFeature, isSupportedToolsFeature } from "./tools-features";
 import { shouldEnableIndirectTracing } from "./tracer-config";
 import * as util from "./util";
-import { BuildMode, getErrorMessage } from "./util";
+import { BuildMode, CleanupLevel, getErrorMessage } from "./util";
 
 type Options = Array<string | number | boolean>;
 
@@ -141,7 +141,10 @@ export interface CodeQL {
   /**
    * Clean up all the databases within a database cluster.
    */
-  databaseCleanupCluster(config: Config, cleanupLevel: string): Promise<void>;
+  databaseCleanupCluster(
+    config: Config,
+    cleanupLevel: CleanupLevel,
+  ): Promise<void>;
   /**
    * Run 'codeql database bundle'.
    */
@@ -513,7 +516,7 @@ export async function getCodeQLForTesting(
  *        version requirement. Must be set to true outside tests.
  * @returns A new CodeQL object
  */
-export async function getCodeQLForCmd(
+async function getCodeQLForCmd(
   cmd: string,
   checkVersion: boolean,
 ): Promise<CodeQL> {
@@ -878,7 +881,7 @@ export async function getCodeQLForCmd(
     },
     async databaseCleanupCluster(
       config: Config,
-      cleanupLevel: string,
+      cleanupLevel: CleanupLevel,
     ): Promise<void> {
       const cacheCleanupFlag = (await util.codeQlVersionAtLeast(
         this,
@@ -1222,7 +1225,7 @@ export async function getTrapCachingExtractorConfigArgsForLang(
  *
  * This will not exist if the configuration is being parsed in the Action.
  */
-export function getGeneratedCodeScanningConfigPath(config: Config): string {
+function getGeneratedCodeScanningConfigPath(config: Config): string {
   return path.resolve(config.tempDir, "user-config.yaml");
 }
 

src/config-utils.test.ts

@@ -37,7 +37,9 @@ import {
   ConfigurationError,
   withTmpDir,
   BuildMode,
+  DiskUsage,
 } from "./util";
+import * as util from "./util";
 
 setupTests(test);
 
@@ -200,12 +202,9 @@ test("load code quality config", async (t) => {
     );
 
     // And the config we expect it to result in
-    const expectedConfig: configUtils.Config = {
-      version: actionsUtil.getActionVersion(),
+    const expectedConfig = createTestConfig({
       analysisKinds: [AnalysisKind.CodeQuality],
       languages: [KnownLanguage.actions],
-      buildMode: undefined,
-      originalUserInput: {},
       // This gets set because we only have `AnalysisKind.CodeQuality`
       computedConfig: {
         "disable-default-queries": true,
@@ -219,14 +218,7 @@ test("load code quality config", async (t) => {
       debugMode: false,
       debugArtifactName: "",
       debugDatabaseName: "",
-      trapCaches: {},
-      trapCacheDownloadTime: 0,
-      dependencyCachingEnabled: CachingKind.None,
-      extraQueryExclusions: [],
-      overlayDatabaseMode: OverlayDatabaseMode.None,
-      useOverlayDatabaseCaching: false,
-      repositoryProperties: {},
-    };
+    });
 
     t.deepEqual(config, expectedConfig);
   });
@@ -507,9 +499,7 @@ test("load non-empty input", async (t) => {
     };
 
     // And the config we expect it to parse to
-    const expectedConfig: configUtils.Config = {
-      version: actionsUtil.getActionVersion(),
-      analysisKinds: [AnalysisKind.CodeScanning],
+    const expectedConfig = createTestConfig({
       languages: [KnownLanguage.javascript],
       buildMode: BuildMode.None,
       originalUserInput: userConfig,
@@ -521,14 +511,7 @@ test("load non-empty input", async (t) => {
       debugMode: false,
       debugArtifactName: "my-artifact",
       debugDatabaseName: "my-db",
-      trapCaches: {},
-      trapCacheDownloadTime: 0,
-      dependencyCachingEnabled: CachingKind.None,
-      extraQueryExclusions: [],
-      overlayDatabaseMode: OverlayDatabaseMode.None,
-      useOverlayDatabaseCaching: false,
-      repositoryProperties: {},
-    };
+    });
 
     const languagesInput = "javascript";
     const configFilePath = createConfigFile(inputFileContents, tempDir);
@@ -990,12 +973,12 @@ interface OverlayDatabaseModeTestSetup {
   features: Feature[];
   isPullRequest: boolean;
   isDefaultBranch: boolean;
-  repositoryOwner: string;
   buildMode: BuildMode | undefined;
   languages: Language[];
   codeqlVersion: string;
   gitRoot: string | undefined;
   codeScanningConfig: configUtils.UserConfig;
+  diskUsage: DiskUsage | undefined;
 }
 
 const defaultOverlayDatabaseModeTestSetup: OverlayDatabaseModeTestSetup = {
@@ -1003,12 +986,15 @@ const defaultOverlayDatabaseModeTestSetup: OverlayDatabaseModeTestSetup = {
   features: [],
   isPullRequest: false,
   isDefaultBranch: false,
-  repositoryOwner: "github",
   buildMode: BuildMode.None,
   languages: [KnownLanguage.javascript],
   codeqlVersion: CODEQL_OVERLAY_MINIMUM_VERSION,
   gitRoot: "/some/git/root",
   codeScanningConfig: {},
+  diskUsage: {
+    numAvailableBytes: 50_000_000_000,
+    numTotalBytes: 100_000_000_000,
+  },
 };
 
 const getOverlayDatabaseModeMacro = test.macro({
@@ -1041,6 +1027,8 @@ const getOverlayDatabaseModeMacro = test.macro({
             setup.overlayDatabaseEnvVar;
         }
 
+        sinon.stub(util, "checkDiskUsage").resolves(setup.diskUsage);
+
         // Mock feature flags
         const features = createFeatures(setup.features);
 
@@ -1049,12 +1037,6 @@ const getOverlayDatabaseModeMacro = test.macro({
           .stub(actionsUtil, "isAnalyzingPullRequest")
           .returns(setup.isPullRequest);
 
-        // Mock repository owner
-        const repository = {
-          owner: setup.repositoryOwner,
-          repo: "test-repo",
-        };
-
         // Set up CodeQL mock
         const codeql = mockCodeQLVersion(setup.codeqlVersion);
 
@@ -1077,7 +1059,6 @@ const getOverlayDatabaseModeMacro = test.macro({
 
         const result = await configUtils.getOverlayDatabaseMode(
           codeql,
-          repository,
           features,
           setup.languages,
           tempDir, // sourceRoot
@@ -1205,6 +1186,45 @@ test(
   },
 );
 
+test(
+  getOverlayDatabaseModeMacro,
+  "No overlay-base database on default branch if runner disk space is too low",
+  {
+    languages: [KnownLanguage.javascript],
+    features: [
+      Feature.OverlayAnalysis,
+      Feature.OverlayAnalysisCodeScanningJavascript,
+    ],
+    isDefaultBranch: true,
+    diskUsage: {
+      numAvailableBytes: 1_000_000_000,
+      numTotalBytes: 100_000_000_000,
+    },
+  },
+  {
+    overlayDatabaseMode: OverlayDatabaseMode.None,
+    useOverlayDatabaseCaching: false,
+  },
+);
+
+test(
+  getOverlayDatabaseModeMacro,
+  "No overlay-base database on default branch if we can't determine runner disk space",
+  {
+    languages: [KnownLanguage.javascript],
+    features: [
+      Feature.OverlayAnalysis,
+      Feature.OverlayAnalysisCodeScanningJavascript,
+    ],
+    isDefaultBranch: true,
+    diskUsage: undefined,
+  },
+  {
+    overlayDatabaseMode: OverlayDatabaseMode.None,
+    useOverlayDatabaseCaching: false,
+  },
+);
+
 test(
   getOverlayDatabaseModeMacro,
   "No overlay-base database on default branch when code-scanning feature enabled with disable-default-queries",
@@ -1375,6 +1395,45 @@ test(
   },
 );
 
+test(
+  getOverlayDatabaseModeMacro,
+  "No overlay analysis on PR if runner disk space is too low",
+  {
+    languages: [KnownLanguage.javascript],
+    features: [
+      Feature.OverlayAnalysis,
+      Feature.OverlayAnalysisCodeScanningJavascript,
+    ],
+    isPullRequest: true,
+    diskUsage: {
+      numAvailableBytes: 1_000_000_000,
+      numTotalBytes: 100_000_000_000,
+    },
+  },
+  {
+    overlayDatabaseMode: OverlayDatabaseMode.None,
+    useOverlayDatabaseCaching: false,
+  },
+);
+
+test(
+  getOverlayDatabaseModeMacro,
+  "No overlay analysis on PR if we can't determine runner disk space",
+  {
+    languages: [KnownLanguage.javascript],
+    features: [
+      Feature.OverlayAnalysis,
+      Feature.OverlayAnalysisCodeScanningJavascript,
+    ],
+    isPullRequest: true,
+    diskUsage: undefined,
+  },
+  {
+    overlayDatabaseMode: OverlayDatabaseMode.None,
+    useOverlayDatabaseCaching: false,
+  },
+);
+
 test(
   getOverlayDatabaseModeMacro,
   "No overlay analysis on PR when code-scanning feature enabled with disable-default-queries",
@@ -1499,10 +1558,9 @@ test(
 
 test(
   getOverlayDatabaseModeMacro,
-  "Overlay PR analysis by env for dsp-testing",
+  "Overlay PR analysis by env",
   {
     overlayDatabaseEnvVar: "overlay",
-    repositoryOwner: "dsp-testing",
   },
   {
     overlayDatabaseMode: OverlayDatabaseMode.Overlay,
@@ -1512,10 +1570,10 @@ test(
 
 test(
   getOverlayDatabaseModeMacro,
-  "Overlay PR analysis by env for other-org",
+  "Overlay PR analysis by env on a runner with low disk space",
   {
     overlayDatabaseEnvVar: "overlay",
-    repositoryOwner: "other-org",
+    diskUsage: { numAvailableBytes: 0, numTotalBytes: 100_000_000_000 },
   },
   {
     overlayDatabaseMode: OverlayDatabaseMode.Overlay,
@@ -1525,12 +1583,11 @@ test(
 
 test(
   getOverlayDatabaseModeMacro,
-  "Overlay PR analysis by feature flag for dsp-testing",
+  "Overlay PR analysis by feature flag",
   {
     languages: [KnownLanguage.javascript],
     features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
     isPullRequest: true,
-    repositoryOwner: "dsp-testing",
   },
   {
     overlayDatabaseMode: OverlayDatabaseMode.Overlay,
@@ -1538,21 +1595,6 @@ test(
   },
 );
 
-test(
-  getOverlayDatabaseModeMacro,
-  "No overlay PR analysis by feature flag for other-org",
-  {
-    languages: [KnownLanguage.javascript],
-    features: [Feature.OverlayAnalysis, Feature.OverlayAnalysisJavascript],
-    isPullRequest: true,
-    repositoryOwner: "other-org",
-  },
-  {
-    overlayDatabaseMode: OverlayDatabaseMode.None,
-    useOverlayDatabaseCaching: false,
-  },
-);
-
 test(
   getOverlayDatabaseModeMacro,
   "Fallback due to autobuild with traced language",

src/config-utils.ts

@@ -43,10 +43,22 @@ import {
   codeQlVersionAtLeast,
   cloneObject,
   isDefined,
+  checkDiskUsage,
 } from "./util";
 
 export * from "./config/db-config";
 
+/**
+ * The minimum available disk space (in MB) required to perform overlay analysis.
+ * If the available disk space on the runner is below the threshold when deciding
+ * whether to perform overlay analysis, then the action will not perform overlay
+ * analysis unless overlay analysis has been explicitly enabled via environment
+ * variable.
+ */
+const OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 20000;
+const OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES =
+  OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1_000_000;
+
 export type RegistryConfigWithCredentials = RegistryConfigNoCredentials & {
   // Token to use when downloading packs from this registry.
   token: string;
@@ -148,6 +160,9 @@ export interface Config {
   /** A value indicating how dependency caching should be used. */
   dependencyCachingEnabled: CachingKind;
 
+  /** The keys of caches that we restored, if any. */
+  dependencyCachingRestoredKeys: string[];
+
   /**
    * Extra query exclusions to append to the config.
    */
@@ -176,7 +191,7 @@ export interface Config {
   repositoryProperties: RepositoryProperties;
 }
 
-export async function getSupportedLanguageMap(
+async function getSupportedLanguageMap(
   codeql: CodeQL,
   logger: Logger,
 ): Promise<Record<string, string>> {
@@ -239,7 +254,7 @@ export function hasActionsWorkflows(sourceRoot: string): boolean {
 /**
  * Gets the set of languages in the current repository.
  */
-export async function getRawLanguagesInRepo(
+async function getRawLanguagesInRepo(
   repository: RepositoryNwo,
   sourceRoot: string,
   logger: Logger,
@@ -348,7 +363,7 @@ export function getRawLanguagesNoAutodetect(
  * @returns A tuple containing a list of languages in this repository that might be
  * analyzable and whether or not this list was determined automatically.
  */
-export async function getRawLanguages(
+async function getRawLanguages(
   languagesInput: string | undefined,
   repository: RepositoryNwo,
   sourceRoot: string,
@@ -496,6 +511,7 @@ export async function initActionState(
     trapCaches,
     trapCacheDownloadTime,
     dependencyCachingEnabled: getCachingKind(dependencyCachingEnabled),
+    dependencyCachingRestoredKeys: [],
     extraQueryExclusions: [],
     overlayDatabaseMode: OverlayDatabaseMode.None,
     useOverlayDatabaseCaching: false,
@@ -579,17 +595,11 @@ const OVERLAY_ANALYSIS_CODE_SCANNING_FEATURES: Record<Language, Feature> = {
 };
 
 async function isOverlayAnalysisFeatureEnabled(
-  repository: RepositoryNwo,
   features: FeatureEnablement,
   codeql: CodeQL,
   languages: Language[],
   codeScanningConfig: UserConfig,
 ): Promise<boolean> {
-  // TODO: Remove the repository owner check once support for overlay analysis
-  // stabilizes, and no more backward-incompatible changes are expected.
-  if (!["github", "dsp-testing"].includes(repository.owner)) {
-    return false;
-  }
   if (!(await features.getValue(Feature.OverlayAnalysis, codeql))) {
     return false;
   }
@@ -647,7 +657,6 @@ async function isOverlayAnalysisFeatureEnabled(
  */
 export async function getOverlayDatabaseMode(
   codeql: CodeQL,
-  repository: RepositoryNwo,
   features: FeatureEnablement,
   languages: Language[],
   sourceRoot: string,
@@ -676,27 +685,43 @@ export async function getOverlayDatabaseMode(
     );
   } else if (
     await isOverlayAnalysisFeatureEnabled(
-      repository,
       features,
       codeql,
       languages,
       codeScanningConfig,
     )
   ) {
-    if (isAnalyzingPullRequest()) {
-      overlayDatabaseMode = OverlayDatabaseMode.Overlay;
-      useOverlayDatabaseCaching = true;
+    const diskUsage = await checkDiskUsage(logger);
+    if (
+      diskUsage === undefined ||
+      diskUsage.numAvailableBytes < OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES
+    ) {
+      const diskSpaceMb =
+        diskUsage === undefined
+          ? 0
+          : Math.round(diskUsage.numAvailableBytes / 1_000_000);
+      overlayDatabaseMode = OverlayDatabaseMode.None;
+      useOverlayDatabaseCaching = false;
       logger.info(
         `Setting overlay database mode to ${overlayDatabaseMode} ` +
-          "with caching because we are analyzing a pull request.",
-      );
-    } else if (await isAnalyzingDefaultBranch()) {
-      overlayDatabaseMode = OverlayDatabaseMode.OverlayBase;
-      useOverlayDatabaseCaching = true;
-      logger.info(
-        `Setting overlay database mode to ${overlayDatabaseMode} ` +
-          "with caching because we are analyzing the default branch.",
+          `due to insufficient disk space (${diskSpaceMb} MB).`,
       );
+    } else {
+      if (isAnalyzingPullRequest()) {
+        overlayDatabaseMode = OverlayDatabaseMode.Overlay;
+        useOverlayDatabaseCaching = true;
+        logger.info(
+          `Setting overlay database mode to ${overlayDatabaseMode} ` +
+            "with caching because we are analyzing a pull request.",
+        );
+      } else if (await isAnalyzingDefaultBranch()) {
+        overlayDatabaseMode = OverlayDatabaseMode.OverlayBase;
+        useOverlayDatabaseCaching = true;
+        logger.info(
+          `Setting overlay database mode to ${overlayDatabaseMode} ` +
+            "with caching because we are analyzing the default branch.",
+        );
+      }
     }
   }
 
@@ -846,7 +871,6 @@ export async function initConfig(
   const { overlayDatabaseMode, useOverlayDatabaseCaching } =
     await getOverlayDatabaseMode(
       inputs.codeql,
-      inputs.repository,
       inputs.features,
       config.languages,
       inputs.sourceRoot,
@@ -1235,7 +1259,7 @@ export function isCodeQualityEnabled(config: Config): boolean {
  * @returns Returns `AnalysisKind.CodeScanning` if `AnalysisKind.CodeScanning` is enabled;
  * otherwise `AnalysisKind.CodeQuality`.
  */
-export function getPrimaryAnalysisKind(config: Config): AnalysisKind {
+function getPrimaryAnalysisKind(config: Config): AnalysisKind {
   return isCodeScanningEnabled(config)
     ? AnalysisKind.CodeScanning
     : AnalysisKind.CodeQuality;

src/database-upload.test.ts

@@ -10,11 +10,12 @@ import { GitHubApiDetails } from "./api-client";
 import * as apiClient from "./api-client";
 import { createStubCodeQL } from "./codeql";
 import { Config } from "./config-utils";
-import { uploadDatabases } from "./database-upload";
+import { cleanupAndUploadDatabases } from "./database-upload";
 import * as gitUtils from "./git-utils";
 import { KnownLanguage } from "./languages";
 import { RepositoryNwo } from "./repository";
 import {
+  createFeatures,
   createTestConfig,
   getRecordingLogger,
   LoggedMessage,
@@ -91,11 +92,12 @@ test("Abort database upload if 'upload-database' input set to false", async (t)
     sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);
 
     const loggedMessages = [];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
       testApiDetails,
+      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
     t.assert(
@@ -121,7 +123,7 @@ test("Abort database upload if 'analysis-kinds: code-scanning' is not enabled",
     await mockHttpRequests(201);
 
     const loggedMessages = [];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       {
@@ -129,6 +131,7 @@ test("Abort database upload if 'analysis-kinds: code-scanning' is not enabled",
         analysisKinds: [AnalysisKind.CodeQuality],
       },
       testApiDetails,
+      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
     t.assert(
@@ -155,11 +158,12 @@ test("Abort database upload if running against GHES", async (t) => {
     config.gitHubVersion = { type: GitHubVariant.GHES, version: "3.0" };
 
     const loggedMessages = [];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       config,
       testApiDetails,
+      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
     t.assert(
@@ -183,11 +187,12 @@ test("Abort database upload if not analyzing default branch", async (t) => {
     sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(false);
 
     const loggedMessages = [];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
       testApiDetails,
+      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
     t.assert(
@@ -212,11 +217,12 @@ test("Don't crash if uploading a database fails", async (t) => {
     await mockHttpRequests(500);
 
     const loggedMessages = [] as LoggedMessage[];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
       testApiDetails,
+      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
 
@@ -243,11 +249,12 @@ test("Successfully uploading a database to github.com", async (t) => {
     await mockHttpRequests(201);
 
     const loggedMessages = [] as LoggedMessage[];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
       testApiDetails,
+      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
     t.assert(
@@ -272,7 +279,7 @@ test("Successfully uploading a database to GHEC-DR", async (t) => {
     const databaseUploadSpy = await mockHttpRequests(201);
 
     const loggedMessages = [] as LoggedMessage[];
-    await uploadDatabases(
+    await cleanupAndUploadDatabases(
       testRepoName,
       getCodeQL(),
       getTestConfig(tmpDir),
@@ -281,6 +288,7 @@ test("Successfully uploading a database to GHEC-DR", async (t) => {
         url: "https://tenant.ghe.com",
         apiURL: undefined,
       },
+      createFeatures([]),
       getRecordingLogger(loggedMessages),
     );
     t.assert(

src/database-upload.ts

@@ -5,17 +5,20 @@ import { AnalysisKind } from "./analyses";
 import { getApiClient, GitHubApiDetails } from "./api-client";
 import { type CodeQL } from "./codeql";
 import { Config } from "./config-utils";
+import { Feature, FeatureEnablement } from "./feature-flags";
 import * as gitUtils from "./git-utils";
 import { Logger, withGroupAsync } from "./logging";
+import { OverlayDatabaseMode } from "./overlay-database-utils";
 import { RepositoryNwo } from "./repository";
 import * as util from "./util";
-import { bundleDb, parseGitHubUrl } from "./util";
+import { bundleDb, CleanupLevel, parseGitHubUrl } from "./util";
 
-export async function uploadDatabases(
+export async function cleanupAndUploadDatabases(
   repositoryNwo: RepositoryNwo,
   codeql: CodeQL,
   config: Config,
   apiDetails: GitHubApiDetails,
+  features: FeatureEnablement,
   logger: Logger,
 ): Promise<void> {
   if (actionsUtil.getRequiredInput("upload-database") !== "true") {
@@ -50,10 +53,16 @@ export async function uploadDatabases(
     return;
   }
 
+  const cleanupLevel =
+    config.overlayDatabaseMode === OverlayDatabaseMode.OverlayBase &&
+    (await features.getValue(Feature.UploadOverlayDbToApi))
+      ? CleanupLevel.Overlay
+      : CleanupLevel.Clear;
+
   // Clean up the database, since intermediate results may still be written to the
   // database if there is high RAM pressure.
   await withGroupAsync("Cleaning up databases", async () => {
-    await codeql.databaseCleanupCluster(config, "clear");
+    await codeql.databaseCleanupCluster(config, cleanupLevel);
   });
 
   const client = getApiClient();

src/defaults.json

@@ -1,6 +1,6 @@
 {
-  "bundleVersion": "codeql-bundle-v2.23.3",
-  "cliVersion": "2.23.3",
-  "priorBundleVersion": "codeql-bundle-v2.23.2",
-  "priorCliVersion": "2.23.2"
+  "bundleVersion": "codeql-bundle-v2.23.6",
+  "cliVersion": "2.23.6",
+  "priorBundleVersion": "codeql-bundle-v2.23.5",
+  "priorCliVersion": "2.23.5"
 }

src/dependency-caching.test.ts

@@ -7,6 +7,7 @@ import test from "ava";
 import * as sinon from "sinon";
 
 import { cacheKeyHashLength } from "./caching-utils";
+import * as cachingUtils from "./caching-utils";
 import { createStubCodeQL } from "./codeql";
 import {
   CacheConfig,
@@ -22,6 +23,8 @@ import {
   cacheKey,
   getCsharpDependencyDirs,
   getCsharpTempDependencyDir,
+  uploadDependencyCaches,
+  CacheStoreResult,
 } from "./dependency-caching";
 import { Feature } from "./feature-flags";
 import { KnownLanguage } from "./languages";
@@ -31,6 +34,7 @@ import {
   getRecordingLogger,
   checkExpectedLogMessages,
   LoggedMessage,
+  createTestConfig,
 } from "./testing-utils";
 import { withTmpDir } from "./util";
 
@@ -261,15 +265,17 @@ test("downloadDependencyCaches - does not restore caches with feature keys if no
     .resolves(CSHARP_BASE_PATTERNS);
   makePatternCheckStub.withArgs(CSHARP_EXTRA_PATTERNS).resolves(undefined);
 
-  const results = await downloadDependencyCaches(
+  const result = await downloadDependencyCaches(
     codeql,
     createFeatures([]),
     [KnownLanguage.csharp],
     logger,
   );
-  t.is(results.length, 1);
-  t.is(results[0].language, KnownLanguage.csharp);
-  t.is(results[0].hit_kind, CacheHitKind.Miss);
+  const statusReport = result.statusReport;
+  t.is(statusReport.length, 1);
+  t.is(statusReport[0].language, KnownLanguage.csharp);
+  t.is(statusReport[0].hit_kind, CacheHitKind.Miss);
+  t.deepEqual(result.restoredKeys, []);
   t.assert(restoreCacheStub.calledOnce);
 });
 
@@ -281,7 +287,8 @@ test("downloadDependencyCaches - restores caches with feature keys if features a
   const logger = getRecordingLogger(messages);
   const features = createFeatures([Feature.CsharpNewCacheKey]);
 
-  sinon.stub(glob, "hashFiles").resolves("abcdef");
+  const mockHash = "abcdef";
+  sinon.stub(glob, "hashFiles").resolves(mockHash);
 
   const keyWithFeature = await cacheKey(
     codeql,
@@ -301,15 +308,28 @@ test("downloadDependencyCaches - restores caches with feature keys if features a
     .resolves(CSHARP_BASE_PATTERNS);
   makePatternCheckStub.withArgs(CSHARP_EXTRA_PATTERNS).resolves(undefined);
 
-  const results = await downloadDependencyCaches(
+  const result = await downloadDependencyCaches(
     codeql,
     features,
     [KnownLanguage.csharp],
     logger,
   );
-  t.is(results.length, 1);
-  t.is(results[0].language, KnownLanguage.csharp);
-  t.is(results[0].hit_kind, CacheHitKind.Exact);
+
+  // Check that the status report for telemetry indicates that one cache was restored with an exact match.
+  const statusReport = result.statusReport;
+  t.is(statusReport.length, 1);
+  t.is(statusReport[0].language, KnownLanguage.csharp);
+  t.is(statusReport[0].hit_kind, CacheHitKind.Exact);
+
+  // Check that the restored key has been returned.
+  const restoredKeys = result.restoredKeys;
+  t.is(restoredKeys.length, 1);
+  t.assert(
+    restoredKeys[0].endsWith(mockHash),
+    "Expected restored key to end with hash returned by `hashFiles`",
+  );
+
+  // `restoreCache` should have been called exactly once.
   t.assert(restoreCacheStub.calledOnce);
 });
 
@@ -321,8 +341,14 @@ test("downloadDependencyCaches - restores caches with feature keys if features a
   const logger = getRecordingLogger(messages);
   const features = createFeatures([Feature.CsharpNewCacheKey]);
 
+  // We expect two calls to `hashFiles`: the first by the call to `cacheKey` below,
+  // and the second by `downloadDependencyCaches`. We use the result of the first
+  // call as part of the cache key that identifies a mock, existing cache. The result
+  // of the second call is for the primary restore key, which we don't want to match
+  // the first key so that we can test the restore keys logic.
+  const restoredHash = "abcdef";
   const hashFilesStub = sinon.stub(glob, "hashFiles");
-  hashFilesStub.onFirstCall().resolves("abcdef");
+  hashFilesStub.onFirstCall().resolves(restoredHash);
   hashFilesStub.onSecondCall().resolves("123456");
 
   const keyWithFeature = await cacheKey(
@@ -343,18 +369,230 @@ test("downloadDependencyCaches - restores caches with feature keys if features a
     .resolves(CSHARP_BASE_PATTERNS);
   makePatternCheckStub.withArgs(CSHARP_EXTRA_PATTERNS).resolves(undefined);
 
-  const results = await downloadDependencyCaches(
+  const result = await downloadDependencyCaches(
     codeql,
     features,
     [KnownLanguage.csharp],
     logger,
   );
-  t.is(results.length, 1);
-  t.is(results[0].language, KnownLanguage.csharp);
-  t.is(results[0].hit_kind, CacheHitKind.Partial);
+
+  // Check that the status report for telemetry indicates that one cache was restored with a partial match.
+  const statusReport = result.statusReport;
+  t.is(statusReport.length, 1);
+  t.is(statusReport[0].language, KnownLanguage.csharp);
+  t.is(statusReport[0].hit_kind, CacheHitKind.Partial);
+
+  // Check that the restored key has been returned.
+  const restoredKeys = result.restoredKeys;
+  t.is(restoredKeys.length, 1);
+  t.assert(
+    restoredKeys[0].endsWith(restoredHash),
+    "Expected restored key to end with hash returned by `hashFiles`",
+  );
+
   t.assert(restoreCacheStub.calledOnce);
 });
 
+test("uploadDependencyCaches - skips upload for a language with no cache config", async (t) => {
+  const codeql = createStubCodeQL({});
+  const messages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(messages);
+  const features = createFeatures([]);
+  const config = createTestConfig({
+    languages: [KnownLanguage.actions],
+  });
+
+  const result = await uploadDependencyCaches(codeql, features, config, logger);
+  t.is(result.length, 0);
+  checkExpectedLogMessages(t, messages, [
+    "Skipping upload of dependency cache for actions",
+  ]);
+});
+
+test("uploadDependencyCaches - skips upload if no files for the hash exist", async (t) => {
+  const codeql = createStubCodeQL({});
+  const messages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(messages);
+  const features = createFeatures([]);
+  const config = createTestConfig({
+    languages: [KnownLanguage.go],
+  });
+
+  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
+  makePatternCheckStub.resolves(undefined);
+
+  const result = await uploadDependencyCaches(codeql, features, config, logger);
+  t.is(result.length, 1);
+  t.is(result[0].language, KnownLanguage.go);
+  t.is(result[0].result, CacheStoreResult.NoHash);
+});
+
+test("uploadDependencyCaches - skips upload if we know the cache already exists", async (t) => {
+  process.env["RUNNER_OS"] = "Linux";
+
+  const codeql = createStubCodeQL({});
+  const messages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(messages);
+  const features = createFeatures([]);
+
+  const mockHash = "abcdef";
+  sinon.stub(glob, "hashFiles").resolves(mockHash);
+
+  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
+  makePatternCheckStub
+    .withArgs(CSHARP_BASE_PATTERNS)
+    .resolves(CSHARP_BASE_PATTERNS);
+
+  const primaryCacheKey = await cacheKey(
+    codeql,
+    features,
+    KnownLanguage.csharp,
+    CSHARP_BASE_PATTERNS,
+  );
+
+  const config = createTestConfig({
+    languages: [KnownLanguage.csharp],
+    dependencyCachingRestoredKeys: [primaryCacheKey],
+  });
+
+  const result = await uploadDependencyCaches(codeql, features, config, logger);
+  t.is(result.length, 1);
+  t.is(result[0].language, KnownLanguage.csharp);
+  t.is(result[0].result, CacheStoreResult.Duplicate);
+});
+
+test("uploadDependencyCaches - skips upload if cache size is 0", async (t) => {
+  process.env["RUNNER_OS"] = "Linux";
+
+  const codeql = createStubCodeQL({});
+  const messages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(messages);
+  const features = createFeatures([]);
+
+  const mockHash = "abcdef";
+  sinon.stub(glob, "hashFiles").resolves(mockHash);
+
+  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
+  makePatternCheckStub
+    .withArgs(CSHARP_BASE_PATTERNS)
+    .resolves(CSHARP_BASE_PATTERNS);
+
+  sinon.stub(cachingUtils, "getTotalCacheSize").resolves(0);
+
+  const config = createTestConfig({
+    languages: [KnownLanguage.csharp],
+  });
+
+  const result = await uploadDependencyCaches(codeql, features, config, logger);
+  t.is(result.length, 1);
+  t.is(result[0].language, KnownLanguage.csharp);
+  t.is(result[0].result, CacheStoreResult.Empty);
+
+  checkExpectedLogMessages(t, messages, [
+    "Skipping upload of dependency cache",
+  ]);
+});
+
+test("uploadDependencyCaches - uploads caches when all requirements are met", async (t) => {
+  process.env["RUNNER_OS"] = "Linux";
+
+  const codeql = createStubCodeQL({});
+  const messages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(messages);
+  const features = createFeatures([]);
+
+  const mockHash = "abcdef";
+  sinon.stub(glob, "hashFiles").resolves(mockHash);
+
+  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
+  makePatternCheckStub
+    .withArgs(CSHARP_BASE_PATTERNS)
+    .resolves(CSHARP_BASE_PATTERNS);
+
+  sinon.stub(cachingUtils, "getTotalCacheSize").resolves(1024);
+  sinon.stub(actionsCache, "saveCache").resolves();
+
+  const config = createTestConfig({
+    languages: [KnownLanguage.csharp],
+  });
+
+  const result = await uploadDependencyCaches(codeql, features, config, logger);
+  t.is(result.length, 1);
+  t.is(result[0].language, KnownLanguage.csharp);
+  t.is(result[0].result, CacheStoreResult.Stored);
+  t.is(result[0].upload_size_bytes, 1024);
+
+  checkExpectedLogMessages(t, messages, ["Uploading cache of size"]);
+});
+
+test("uploadDependencyCaches - catches `ReserveCacheError` exceptions", async (t) => {
+  process.env["RUNNER_OS"] = "Linux";
+
+  const codeql = createStubCodeQL({});
+  const messages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(messages);
+  const features = createFeatures([]);
+
+  const mockHash = "abcdef";
+  sinon.stub(glob, "hashFiles").resolves(mockHash);
+
+  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
+  makePatternCheckStub
+    .withArgs(CSHARP_BASE_PATTERNS)
+    .resolves(CSHARP_BASE_PATTERNS);
+
+  sinon.stub(cachingUtils, "getTotalCacheSize").resolves(1024);
+  sinon
+    .stub(actionsCache, "saveCache")
+    .throws(new actionsCache.ReserveCacheError("Already in use"));
+
+  const config = createTestConfig({
+    languages: [KnownLanguage.csharp],
+  });
+
+  await t.notThrowsAsync(async () => {
+    const result = await uploadDependencyCaches(
+      codeql,
+      features,
+      config,
+      logger,
+    );
+    t.is(result.length, 1);
+    t.is(result[0].language, KnownLanguage.csharp);
+    t.is(result[0].result, CacheStoreResult.Duplicate);
+
+    checkExpectedLogMessages(t, messages, ["Not uploading cache for"]);
+  });
+});
+
+test("uploadDependencyCaches - throws other exceptions", async (t) => {
+  process.env["RUNNER_OS"] = "Linux";
+
+  const codeql = createStubCodeQL({});
+  const messages: LoggedMessage[] = [];
+  const logger = getRecordingLogger(messages);
+  const features = createFeatures([]);
+
+  const mockHash = "abcdef";
+  sinon.stub(glob, "hashFiles").resolves(mockHash);
+
+  const makePatternCheckStub = sinon.stub(internal, "makePatternCheck");
+  makePatternCheckStub
+    .withArgs(CSHARP_BASE_PATTERNS)
+    .resolves(CSHARP_BASE_PATTERNS);
+
+  sinon.stub(cachingUtils, "getTotalCacheSize").resolves(1024);
+  sinon.stub(actionsCache, "saveCache").throws();
+
+  const config = createTestConfig({
+    languages: [KnownLanguage.csharp],
+  });
+
+  await t.throwsAsync(async () => {
+    await uploadDependencyCaches(codeql, features, config, logger);
+  });
+});
+
 test("getFeaturePrefix - returns empty string if no features are enabled", async (t) => {
   const codeql = createStubCodeQL({});
   const features = createFeatures([]);

src/dependency-caching.ts

@@ -228,6 +228,14 @@ export interface DependencyCacheRestoreStatus {
 /** An array of `DependencyCacheRestoreStatus` objects for each analysed language with a caching configuration. */
 export type DependencyCacheRestoreStatusReport = DependencyCacheRestoreStatus[];
 
+/** Represents the results of `downloadDependencyCaches`. */
+export interface DownloadDependencyCachesResult {
+  /** The status report for telemetry */
+  statusReport: DependencyCacheRestoreStatusReport;
+  /** An array of cache keys that we have restored and therefore know to exist. */
+  restoredKeys: string[];
+}
+
 /**
  * A wrapper around `cacheConfig.getHashPatterns` which logs when there are no files to calculate
  * a hash for the cache key from.
@@ -274,8 +282,9 @@ export async function downloadDependencyCaches(
   features: FeatureEnablement,
   languages: Language[],
   logger: Logger,
-): Promise<DependencyCacheRestoreStatusReport> {
+): Promise<DownloadDependencyCachesResult> {
   const status: DependencyCacheRestoreStatusReport = [];
+  const restoredKeys: string[] = [];
 
   for (const language of languages) {
     const cacheConfig = defaultCacheConfigs[language];
@@ -323,16 +332,27 @@ export async function downloadDependencyCaches(
 
     if (hitKey !== undefined) {
       logger.info(`Cache hit on key ${hitKey} for ${language}.`);
-      const hit_kind =
-        hitKey === primaryKey ? CacheHitKind.Exact : CacheHitKind.Partial;
-      status.push({ language, hit_kind, download_duration_ms });
+
+      // We have a partial cache hit, unless the key of the restored cache matches the
+      // primary restore key.
+      let hit_kind = CacheHitKind.Partial;
+      if (hitKey === primaryKey) {
+        hit_kind = CacheHitKind.Exact;
+      }
+
+      status.push({
+        language,
+        hit_kind,
+        download_duration_ms,
+      });
+      restoredKeys.push(hitKey);
     } else {
       status.push({ language, hit_kind: CacheHitKind.Miss });
       logger.info(`No suitable cache found for ${language}.`);
     }
   }
 
-  return status;
+  return { statusReport: status, restoredKeys };
 }
 
 /** Enumerates possible outcomes for storing caches. */
@@ -400,6 +420,18 @@ export async function uploadDependencyCaches(
       continue;
     }
 
+    // Now that we have verified that there are suitable files, compute the hash for the cache key.
+    const key = await cacheKey(codeql, features, language, patterns);
+
+    // Check that we haven't previously restored this exact key. If a cache with this key
+    // already exists in the Actions Cache, performing the next steps is pointless as the cache
+    // will not get overwritten. We can therefore skip the expensive work of measuring the size
+    // of the cache contents and attempting to upload it if we know that the cache already exists.
+    if (config.dependencyCachingRestoredKeys.includes(key)) {
+      status.push({ language, result: CacheStoreResult.Duplicate });
+      continue;
+    }
+
     // Calculate the size of the files that we would store in the cache. We use this to determine whether the
     // cache should be saved or not. For example, if there are no files to store, then we skip creating the
     // cache. In the future, we could also:
@@ -425,8 +457,6 @@ export async function uploadDependencyCaches(
       continue;
     }
 
-    const key = await cacheKey(codeql, features, language, patterns);
-
     logger.info(
       `Uploading cache of size ${size} for ${language} with key ${key}...`,
     );

src/environment.ts

@@ -20,12 +20,6 @@ export enum EnvVar {
   /** Whether the CodeQL Action has invoked the Go autobuilder. */
   DID_AUTOBUILD_GOLANG = "CODEQL_ACTION_DID_AUTOBUILD_GOLANG",
 
-  /**
-   * Whether to disable the SARIF post-processing in the Action that removes duplicate locations from
-   * notifications in the `run[].invocations[].toolExecutionNotifications` SARIF property.
-   */
-  DISABLE_DUPLICATE_LOCATION_FIX = "CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX",
-
   /**
    * Whether the CodeQL Action is using its own deprecated and non-standard way of scanning for
    * multiple languages.
@@ -56,20 +50,12 @@ export enum EnvVar {
   /** Whether the error for a deprecated version of the CodeQL Action was logged. */
   LOG_VERSION_DEPRECATION = "CODEQL_ACTION_DID_LOG_VERSION_DEPRECATION",
 
-  /**
-   * For macOS. Result of `csrutil status` to determine whether System Integrity
-   * Protection is enabled.
-   */
-  IS_SIP_ENABLED = "CODEQL_ACTION_IS_SIP_ENABLED",
-
   /** UUID representing the current job run. */
   JOB_RUN_UUID = "JOB_RUN_UUID",
 
   /** Status for the entire job, submitted to the status report in `init-post` */
   JOB_STATUS = "CODEQL_ACTION_JOB_STATUS",
 
-  ODASA_TRACER_CONFIGURATION = "ODASA_TRACER_CONFIGURATION",
-
   /** The value of the `output` input for the analyze action. */
   SARIF_RESULTS_OUTPUT_DIR = "CODEQL_ACTION_SARIF_RESULTS_OUTPUT_DIR",
 

src/feature-flags.ts

@@ -78,6 +78,7 @@ export enum Feature {
   OverlayAnalysisSwift = "overlay_analysis_swift",
   PythonDefaultIsToNotExtractStdlib = "python_default_is_to_not_extract_stdlib",
   QaTelemetryEnabled = "qa_telemetry_enabled",
+  UploadOverlayDbToApi = "upload_overlay_db_to_api",
   UseRepositoryProperties = "use_repository_properties",
   ValidateDbConfig = "validate_db_config",
 }
@@ -172,6 +173,11 @@ export const featureConfig: Record<
     legacyApi: true,
     minimumVersion: undefined,
   },
+  [Feature.JavaMinimizeDependencyJars]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_JAVA_MINIMIZE_DEPENDENCY_JARS",
+    minimumVersion: "2.23.0",
+  },
   [Feature.OverlayAnalysis]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_OVERLAY_ANALYSIS",
@@ -283,21 +289,21 @@ export const featureConfig: Record<
     minimumVersion: undefined,
     toolsFeature: ToolsFeature.PythonDefaultIsToNotExtractStdlib,
   },
-  [Feature.UseRepositoryProperties]: {
-    defaultValue: false,
-    envVar: "CODEQL_ACTION_USE_REPOSITORY_PROPERTIES",
-    minimumVersion: undefined,
-  },
   [Feature.QaTelemetryEnabled]: {
     defaultValue: false,
     envVar: "CODEQL_ACTION_QA_TELEMETRY",
     legacyApi: true,
     minimumVersion: undefined,
   },
-  [Feature.JavaMinimizeDependencyJars]: {
+  [Feature.UploadOverlayDbToApi]: {
     defaultValue: false,
-    envVar: "CODEQL_ACTION_JAVA_MINIMIZE_DEPENDENCY_JARS",
-    minimumVersion: "2.23.0",
+    envVar: "CODEQL_ACTION_UPLOAD_OVERLAY_DB_TO_API",
+    minimumVersion: undefined,
+  },
+  [Feature.UseRepositoryProperties]: {
+    defaultValue: false,
+    envVar: "CODEQL_ACTION_USE_REPOSITORY_PROPERTIES",
+    minimumVersion: undefined,
   },
   [Feature.ValidateDbConfig]: {
     defaultValue: false,

src/git-utils.ts

@@ -122,67 +122,6 @@ export const determineBaseBranchHeadCommitOid = async function (
   }
 };
 
-/**
- * Deepen the git history of HEAD by one level. Errors are logged.
- *
- * This function uses the `checkout_path` to determine the repository path and
- * works only when called from `analyze` or `upload-sarif`.
- */
-export const deepenGitHistory = async function () {
-  try {
-    await runGitCommand(
-      getOptionalInput("checkout_path"),
-      [
-        "fetch",
-        "origin",
-        "HEAD",
-        "--no-tags",
-        "--no-recurse-submodules",
-        "--deepen=1",
-      ],
-      "Cannot deepen the shallow repository.",
-    );
-  } catch {
-    // Errors are already logged by runGitCommand()
-  }
-};
-
-/**
- * Fetch the given remote branch. Errors are logged.
- *
- * This function uses the `checkout_path` to determine the repository path and
- * works only when called from `analyze` or `upload-sarif`.
- */
-export const gitFetch = async function (branch: string, extraFlags: string[]) {
-  try {
-    await runGitCommand(
-      getOptionalInput("checkout_path"),
-      ["fetch", "--no-tags", ...extraFlags, "origin", `${branch}:${branch}`],
-      `Cannot fetch ${branch}.`,
-    );
-  } catch {
-    // Errors are already logged by runGitCommand()
-  }
-};
-
-/**
- * Repack the git repository, using with the given flags. Errors are logged.
- *
- * This function uses the `checkout_path` to determine the repository path and
- * works only when called from `analyze` or `upload-sarif`.
- */
-export const gitRepack = async function (flags: string[]) {
-  try {
-    await runGitCommand(
-      getOptionalInput("checkout_path"),
-      ["repack", ...flags],
-      "Cannot repack the repository.",
-    );
-  } catch {
-    // Errors are already logged by runGitCommand()
-  }
-};
-
 /**
  * Decode, if necessary, a file path produced by Git. See
  * https://git-scm.com/docs/git-config#Documentation/git-config.txt-corequotePath

src/init-action.ts

@@ -371,7 +371,7 @@ async function run() {
   }
 
   let overlayBaseDatabaseStats: OverlayBaseDatabaseDownloadStats | undefined;
-  let dependencyCachingResults: DependencyCacheRestoreStatusReport | undefined;
+  let dependencyCachingStatus: DependencyCacheRestoreStatusReport | undefined;
   try {
     if (
       config.overlayDatabaseMode === OverlayDatabaseMode.Overlay &&
@@ -579,12 +579,15 @@ async function run() {
 
     // Restore dependency cache(s), if they exist.
     if (shouldRestoreCache(config.dependencyCachingEnabled)) {
-      dependencyCachingResults = await downloadDependencyCaches(
+      const dependencyCachingResult = await downloadDependencyCaches(
         codeql,
         features,
         config.languages,
         logger,
       );
+      dependencyCachingStatus = dependencyCachingResult.statusReport;
+      config.dependencyCachingRestoredKeys =
+        dependencyCachingResult.restoredKeys;
     }
 
     // Suppress warnings about disabled Python library extraction.
@@ -732,7 +735,7 @@ async function run() {
       toolsSource,
       toolsVersion,
       overlayBaseDatabaseStats,
-      dependencyCachingResults,
+      dependencyCachingStatus,
       logger,
       error,
     );
@@ -755,7 +758,7 @@ async function run() {
     toolsSource,
     toolsVersion,
     overlayBaseDatabaseStats,
-    dependencyCachingResults,
+    dependencyCachingStatus,
     logger,
   );
 }

src/overlay-database-utils.ts

@@ -16,6 +16,7 @@ import { type Config } from "./config-utils";
 import { getCommitOid, getFileOidsUnderPath } from "./git-utils";
 import { Logger, withGroupAsync } from "./logging";
 import {
+  CleanupLevel,
   getErrorMessage,
   isInTestMode,
   tryGetFolderBytes,
@@ -28,7 +29,7 @@ export enum OverlayDatabaseMode {
   None = "none",
 }
 
-export const CODEQL_OVERLAY_MINIMUM_VERSION = "2.22.4";
+export const CODEQL_OVERLAY_MINIMUM_VERSION = "2.23.5";
 
 /**
  * The maximum (uncompressed) size of the overlay base database that we will
@@ -175,7 +176,7 @@ const MAX_CACHE_OPERATION_MS = 600_000;
  * @param warningPrefix Prefix for the check failure warning message
  * @returns True if the verification succeeded, false otherwise
  */
-export function checkOverlayBaseDatabase(
+function checkOverlayBaseDatabase(
   config: Config,
   logger: Logger,
   warningPrefix: string,
@@ -204,7 +205,7 @@ export function checkOverlayBaseDatabase(
  * @returns A promise that resolves to true if the upload was performed and
  * successfully completed, or false otherwise
  */
-export async function uploadOverlayBaseDatabaseToCache(
+export async function cleanupAndUploadOverlayBaseDatabaseToCache(
   codeql: CodeQL,
   config: Config,
   logger: Logger,
@@ -242,7 +243,7 @@ export async function uploadOverlayBaseDatabaseToCache(
 
   // Clean up the database using the overlay cleanup level.
   await withGroupAsync("Cleaning up databases", async () => {
-    await codeql.databaseCleanupCluster(config, "overlay");
+    await codeql.databaseCleanupCluster(config, CleanupLevel.Overlay);
   });
 
   const dbLocation = config.dbLocation;

src/setup-codeql.ts

@@ -34,7 +34,7 @@ export enum ToolsSource {
   Download = "DOWNLOAD",
 }
 
-export const CODEQL_DEFAULT_ACTION_REPOSITORY = "github/codeql-action";
+const CODEQL_DEFAULT_ACTION_REPOSITORY = "github/codeql-action";
 const CODEQL_NIGHTLIES_REPOSITORY_OWNER = "dsp-testing";
 const CODEQL_NIGHTLIES_REPOSITORY_NAME = "codeql-cli-nightlies";
 
@@ -180,17 +180,6 @@ export function tryGetTagNameFromUrl(
   return match[1];
 }
 
-export function tryGetBundleVersionFromUrl(
-  url: string,
-  logger: Logger,
-): string | undefined {
-  const tagName = tryGetTagNameFromUrl(url, logger);
-  if (tagName === undefined) {
-    return undefined;
-  }
-  return tryGetBundleVersionFromTagName(tagName, logger);
-}
-
 export function convertToSemVer(version: string, logger: Logger): string {
   if (!semver.valid(version)) {
     logger.debug(
@@ -580,7 +569,7 @@ export async function getCodeQLSource(
  * Gets a fallback version number to use when looking for CodeQL in the toolcache if we didn't find
  * the `x.y.z` version. This is to support old versions of the toolcache.
  */
-export async function tryGetFallbackToolcacheVersion(
+async function tryGetFallbackToolcacheVersion(
   cliVersion: string | undefined,
   tagName: string,
   logger: Logger,
@@ -729,7 +718,7 @@ function getCanonicalToolcacheVersion(
   return cliVersion;
 }
 
-export interface SetupCodeQLResult {
+interface SetupCodeQLResult {
   codeqlFolder: string;
   toolsDownloadStatusReport?: ToolsDownloadStatusReport;
   toolsSource: ToolsSource;
@@ -750,7 +739,7 @@ export async function setupCodeQLBundle(
   defaultCliVersion: CodeQLDefaultVersionInfo,
   features: FeatureEnablement,
   logger: Logger,
-) {
+): Promise<SetupCodeQLResult> {
   if (!(await util.isBinaryAccessible("tar", logger))) {
     throw new util.ConfigurationError(
       "Could not find tar in PATH, so unable to extract CodeQL bundle.",

src/start-proxy.ts

@@ -8,7 +8,7 @@ import { ConfigurationError, getErrorMessage, isDefined } from "./util";
 
 export const UPDATEJOB_PROXY = "update-job-proxy";
 export const UPDATEJOB_PROXY_VERSION = "v2.0.20250624110901";
-export const UPDATEJOB_PROXY_URL_PREFIX =
+const UPDATEJOB_PROXY_URL_PREFIX =
   "https://github.com/github/codeql-action/releases/download/codeql-bundle-v2.22.0/";
 
 export type Credential = {
@@ -202,7 +202,7 @@ export function getFallbackUrl(proxyPackage: string): string {
  *
  * @returns The response from the GitHub API.
  */
-export async function getLinkedRelease() {
+async function getLinkedRelease() {
   return getApiClient().rest.repos.getReleaseByTag({
     owner: "github",
     repo: "codeql-action",

src/status-report.ts

@@ -54,7 +54,7 @@ export enum ActionName {
  * considered to be a third party analysis and is treated differently when calculating SLOs. To ensure
  * misconfigured workflows are not treated as third party, only the upload-sarif action can return false.
  */
-export function isFirstPartyAnalysis(actionName: ActionName): boolean {
+function isFirstPartyAnalysis(actionName: ActionName): boolean {
   if (actionName !== ActionName.UploadSarif) {
     return true;
   }

src/testing-utils.ts

@@ -392,6 +392,7 @@ export function createTestConfig(overrides: Partial<Config>): Config {
       trapCaches: {},
       trapCacheDownloadTime: 0,
       dependencyCachingEnabled: CachingKind.None,
+      dependencyCachingRestoredKeys: [],
       extraQueryExclusions: [],
       overlayDatabaseMode: OverlayDatabaseMode.None,
       useOverlayDatabaseCaching: false,

src/tools-download.ts

@@ -17,7 +17,7 @@ import { cleanUpPath, getErrorMessage, getRequiredEnvParam } from "./util";
 /**
  * High watermark to use when streaming the download and extraction of the CodeQL tools.
  */
-export const STREAMING_HIGH_WATERMARK_BYTES = 4 * 1024 * 1024; // 4 MiB
+const STREAMING_HIGH_WATERMARK_BYTES = 4 * 1024 * 1024; // 4 MiB
 
 /**
  * The name of the tool cache directory for the CodeQL tools.

src/tracer-config.ts

@@ -76,7 +76,7 @@ export async function endTracingForCluster(
   }
 }
 
-export async function getTracerConfigForCluster(
+async function getTracerConfigForCluster(
   config: Config,
 ): Promise<TracerConfig> {
   const tracingEnvVariables = JSON.parse(

src/upload-lib.ts

@@ -412,7 +412,7 @@ export function findSarifFilesInDir(
   return sarifFiles;
 }
 
-export function getSarifFilePaths(
+function getSarifFilePaths(
   sarifPath: string,
   isSarif: (name: string) => boolean,
 ) {

src/util.test.ts

@@ -476,7 +476,7 @@ for (const [
     githubVersion,
   )}`;
   test(`checkActionVersion ${reportErrorDescription} for ${versionsDescription}`, async (t) => {
-    const warningSpy = sinon.spy(core, "error");
+    const warningSpy = sinon.spy(core, "warning");
     const versionStub = sinon
       .stub(api, "getGitHubVersion")
       .resolves(githubVersion);

src/util.ts

@@ -4,7 +4,6 @@ import * as os from "os";
 import * as path from "path";
 
 import * as core from "@actions/core";
-import * as exec from "@actions/exec/lib/exec";
 import * as io from "@actions/io";
 import getFolderSize from "get-folder-size";
 import * as yaml from "js-yaml";
@@ -1026,34 +1025,6 @@ export function fixInvalidNotifications(
   return newSarif;
 }
 
-/**
- * Removes duplicates from the sarif file.
- *
- * When `CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX` is set to true, this will
- * simply rename the input file to the output file. Otherwise, it will parse the
- * input file as JSON, remove duplicate locations from the SARIF notification
- * objects, and write the result to the output file.
- *
- * For context, see documentation of:
- * `CODEQL_ACTION_DISABLE_DUPLICATE_LOCATION_FIX`. */
-export function fixInvalidNotificationsInFile(
-  inputPath: string,
-  outputPath: string,
-  logger: Logger,
-): void {
-  if (process.env[EnvVar.DISABLE_DUPLICATE_LOCATION_FIX] === "true") {
-    logger.info(
-      "SARIF notification object duplicate location fix disabled by the " +
-        `${EnvVar.DISABLE_DUPLICATE_LOCATION_FIX} environment variable.`,
-    );
-    fs.renameSync(inputPath, outputPath);
-  } else {
-    let sarif = JSON.parse(fs.readFileSync(inputPath, "utf8")) as SarifFile;
-    sarif = fixInvalidNotifications(sarif, logger);
-    fs.writeFileSync(outputPath, JSON.stringify(sarif));
-  }
-}
-
 export function wrapError(error: unknown): Error {
   return error instanceof Error ? error : new Error(String(error));
 }
@@ -1141,7 +1112,7 @@ export function checkActionVersion(
           ">=3.20",
         ))
     ) {
-      core.error(
+      core.warning(
         "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 " +
@@ -1197,49 +1168,6 @@ export function cloneObject<T>(obj: T): T {
   return JSON.parse(JSON.stringify(obj)) as T;
 }
 
-// The first time this function is called, it runs `csrutil status` to determine
-// whether System Integrity Protection is enabled; and saves the result in an
-// environment variable. Afterwards, simply return the value of the environment
-// variable.
-export async function checkSipEnablement(
-  logger: Logger,
-): Promise<boolean | undefined> {
-  if (
-    process.env[EnvVar.IS_SIP_ENABLED] !== undefined &&
-    ["true", "false"].includes(process.env[EnvVar.IS_SIP_ENABLED])
-  ) {
-    return process.env[EnvVar.IS_SIP_ENABLED] === "true";
-  }
-
-  try {
-    const sipStatusOutput = await exec.getExecOutput("csrutil status");
-    if (sipStatusOutput.exitCode === 0) {
-      if (
-        sipStatusOutput.stdout.includes(
-          "System Integrity Protection status: enabled.",
-        )
-      ) {
-        core.exportVariable(EnvVar.IS_SIP_ENABLED, "true");
-        return true;
-      }
-      if (
-        sipStatusOutput.stdout.includes(
-          "System Integrity Protection status: disabled.",
-        )
-      ) {
-        core.exportVariable(EnvVar.IS_SIP_ENABLED, "false");
-        return false;
-      }
-    }
-    return undefined;
-  } catch (e) {
-    logger.warning(
-      `Failed to determine if System Integrity Protection was enabled: ${e}`,
-    );
-    return undefined;
-  }
-}
-
 export async function cleanUpPath(file: string, name: string, logger: Logger) {
   logger.debug(`Cleaning up ${name}.`);
   try {
@@ -1291,17 +1219,6 @@ export function isDefined<T>(value: T | null | undefined): value is T {
   return value !== undefined && value !== null;
 }
 
-/** Like `Object.keys`, but typed so that the elements of the resulting array have the
- * same type as the keys of the input object. Note that this may not be sound if the input
- * object has been cast to `T` from a subtype of `T` and contains additional keys that
- * are not represented by `keyof T`.
- */
-export function unsafeKeysInvariant<T extends Record<string, any>>(
-  object: T,
-): Array<keyof T> {
-  return Object.keys(object) as Array<keyof T>;
-}
-
 /** Like `Object.entries`, but typed so that the key elements of the result have the
  * same type as the keys of the input object. Note that this may not be sound if the input
  * object has been cast to `T` from a subtype of `T` and contains additional keys that
@@ -1314,3 +1231,8 @@ export function unsafeEntriesInvariant<T extends Record<string, any>>(
     ([_, val]) => val !== undefined,
   ) as Array<[keyof T, Exclude<T[keyof T], undefined>]>;
 }
+
+export enum CleanupLevel {
+  Clear = "clear",
+  Overlay = "overlay",
+}