Merge pull request #1527 from github/aeisenberg/qlconfig-in-cli

Ensure qlconfig file is created when config parsing in cli is on

.eslintrc.json

@@ -33,6 +33,12 @@
             "alphabetize": {"order": "asc"},
             "newlines-between": "always"
         }],
+        "max-len": ["error", {
+            "code": 120,
+            "ignoreUrls": true,
+            "ignoreStrings": true,
+            "ignoreTemplateLiterals": true
+        }],
         "no-async-foreach/no-async-foreach": "error",
         "no-console": "off",
         "no-sequences": "error",

.github/workflows/__init-with-registries.yml

@@ -25,6 +25,18 @@ jobs:
     strategy:
       matrix:
         include:
+        - os: ubuntu-latest
+          version: cached
+        - os: macos-latest
+          version: cached
+        - os: windows-latest
+          version: cached
+        - os: ubuntu-latest
+          version: latest
+        - os: macos-latest
+          version: latest
+        - os: windows-latest
+          version: latest
         - os: ubuntu-latest
           version: nightly-latest
         - os: macos-latest
@@ -75,5 +87,35 @@ jobs:
             echo "::error $CODEQL_PACK1 pack was not installed."
             exit 1
         fi
+
+    - name: Verify qlconfig.yml file was created
+      shell: bash
+      run: |
+        QLCONFIG_PATH=$RUNNER_TEMP/qlconfig.yml
+        echo "Expected qlconfig.yml file to be created at $QLCONFIG_PATH"
+        if [[ -f $QLCONFIG_PATH ]]
+        then
+            echo "qlconfig.yml file was created."
+        else
+            echo "::error qlconfig.yml file was not created."
+            exit 1
+        fi
+
+    - name: Verify contents of qlconfig.yml
+    # yq is not available on windows
+      if: runner.os != 'Windows'
+      shell: bash
+      run: |
+        QLCONFIG_PATH=$RUNNER_TEMP/qlconfig.yml
+        cat $QLCONFIG_PATH | yq -e '.registries[] | select(.url == "https://ghcr.io/v2/") | select(.packages == "*/*")'
+        if [[ $? -eq 0 ]]
+        then
+            echo "Registry was added to qlconfig.yml file."
+        else
+            echo "::error Registry was not added to qlconfig.yml file."
+            echo "Contents of qlconfig.yml file:"
+            cat $QLCONFIG_PATH
+            exit 1
+        fi
     env:
       CODEQL_ACTION_TEST_MODE: true

.github/workflows/script/check-node-modules.sh

@@ -7,13 +7,9 @@ if [ ! -z "$(git status --porcelain)" ]; then
     >&2 echo "Failed: Repo should be clean before testing!"
     exit 1
 fi
-# When updating this, make sure to update the npm version in
+
-# `.github/workflows/update-dependencies.yml` too.
+"$(dirname "$0")/update-node-modules.sh" check-only
-sudo npm install --force -g npm@9.2.0
+
-# Reinstall modules and then clean to remove absolute paths
-# Use 'npm ci' instead of 'npm install' as this is intended to be reproducible
-npm ci
-npm run removeNPMAbsolutePaths
 # Check that repo is still clean
 if [ ! -z "$(git status --porcelain)" ]; then
     # If we get a fail here then the PR needs attention

.github/workflows/script/update-node-modules.sh

@@ -0,0 +1,18 @@
+if [ "$1" != "update" && "$1" != "check-only" ]; then
+    >&2 echo "Failed: Invalid argument. Must be 'update' or 'check-only'"
+    exit 1
+fi
+
+sudo npm install --force -g npm@9.2.0
+
+# clean the npm cache to ensure we don't have any files owned by root
+sudo npm cache clean --force
+
+if [ "$1" = "update" ]; then
+    npm install
+fi
+
+# Reinstall modules and then clean to remove absolute paths
+# Use 'npm ci' instead of 'npm install' as this is intended to be reproducible
+npm ci
+npm run removeNPMAbsolutePaths

.github/workflows/update-dependencies.yml

@@ -27,12 +27,7 @@ jobs:
       run: |
         git fetch origin "$BRANCH" --depth=1
         git checkout "origin/$BRANCH"
-        # When updating this, make sure to update the npm version in
+        .github/workflows/script/update-node-modules.sh update
-        # `.github/workflows/script/check-node-modules.sh` too.
-        sudo npm install --force -g npm@9.2.0
-        npm install
-        npm ci
-        npm run removeNPMAbsolutePaths
         if [ ! -z "$(git status --porcelain)" ]; then
           git config --global user.email "github-actions@github.com"
           git config --global user.name "github-actions[bot]"

CHANGELOG.md

@@ -1,5 +1,21 @@
 # CodeQL Action Changelog
 
+## [UNRELEASED]
+
+No user facing changes.
+
+## 2.2.5 - 24 Feb 2023
+
+- Update default CodeQL bundle version to 2.12.3. [#1543](https://github.com/github/codeql-action/pull/1543)
+
+## 2.2.4 - 10 Feb 2023
+
+No user facing changes.
+
+## 2.2.3 - 08 Feb 2023
+
+- Update default CodeQL bundle version to 2.12.2. [#1518](https://github.com/github/codeql-action/pull/1518)
+
 ## 2.2.2 - 06 Feb 2023
 
 - Fix an issue where customers using the CodeQL Action with the [CodeQL Action sync tool](https://docs.github.com/en/enterprise-server@3.7/admin/code-security/managing-github-advanced-security-for-your-enterprise/configuring-code-scanning-for-your-appliance#configuring-codeql-analysis-on-a-server-without-internet-access) would not be able to obtain the CodeQL tools. [#1517](https://github.com/github/codeql-action/pull/1517)

CONTRIBUTING.md

@@ -67,12 +67,8 @@ Here are a few things you can do that will increase the likelihood of your pull
     This mergeback incorporates the changelog updates into `main`, tags the release using the merge commit of the "Merge main into releases/v2" pull request, and bumps the patch version of the CodeQL Action.
 
     Approve the mergeback PR and automerge it.
-1. When the "Merge main into releases/v2" pull request is merged into the `releases/v2` branch, the "Update release branch" workflow will create a "Merge releases/v2 into releases/v1" pull request to merge the changes since the last release into the `releases/v1` release branch.
-    This ensures we keep both the `releases/v1` and `releases/v2` release branches up to date and fully supported.
 
-    Review the checklist items in the pull request description.
+Once the mergeback has been merged to `main`, the release is complete.
-    Once you've checked off all the items, approve the PR and automerge it.
-1. Once the mergeback has been merged to `main` and the "Merge releases/v2 into releases/v1" PR has been merged to `releases/v1`, the release is complete.
 
 ## Keeping the PR checks up to date (admin access required)
 

lib/analyze.js

@@ -126,6 +126,7 @@ async function finalizeDatabaseCreation(config, threadsFlag, memoryFlag, logger)
 async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag, automationDetailsId, config, logger, featureEnablement) {
     const statusReport = {};
     const codeql = await (0, codeql_1.getCodeQL)(config.codeQLCmd);
+    const queryFlags = [memoryFlag, threadsFlag];
     await util.logCodeScanningConfigInCli(codeql, featureEnablement, logger);
     for (const language of config.languages) {
         const queries = config.queries[language];
@@ -140,7 +141,7 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
                 // another to interpret the results.
                 logger.startGroup(`Running queries for ${language}`);
                 const startTimeBuiltIn = new Date().getTime();
-                await runQueryGroup(language, "all", undefined, undefined);
+                await runQueryGroup(language, "all", undefined, undefined, true);
                 // TODO should not be using `builtin` here. We should be using `all` instead.
                 // The status report does not support `all` yet.
                 statusReport[`analyze_builtin_queries_${language}_duration_ms`] =
@@ -164,24 +165,29 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
                     !hasPackWithCustomQueries) {
                     throw new Error(`Unable to analyze ${language} as no queries were selected for this language`);
                 }
+                const customQueryIndices = [];
+                for (let i = 0; i < queries.custom.length; ++i) {
+                    if (queries.custom[i].queries.length > 0) {
+                        customQueryIndices.push(i);
+                    }
+                }
                 logger.startGroup(`Running queries for ${language}`);
                 const querySuitePaths = [];
-                if (queries["builtin"].length > 0) {
+                if (queries.builtin.length > 0) {
                     const startTimeBuiltIn = new Date().getTime();
-                    querySuitePaths.push((await runQueryGroup(language, "builtin", createQuerySuiteContents(queries["builtin"], queryFilters), undefined)));
+                    querySuitePaths.push((await runQueryGroup(language, "builtin", createQuerySuiteContents(queries.builtin, queryFilters), undefined, customQueryIndices.length === 0 && packsWithVersion.length === 0)));
                     statusReport[`analyze_builtin_queries_${language}_duration_ms`] =
                         new Date().getTime() - startTimeBuiltIn;
                 }
                 const startTimeCustom = new Date().getTime();
                 let ranCustom = false;
-                for (let i = 0; i < queries["custom"].length; ++i) {
+                for (const i of customQueryIndices) {
-                    if (queries["custom"][i].queries.length > 0) {
+                    querySuitePaths.push((await runQueryGroup(language, `custom-${i}`, createQuerySuiteContents(queries.custom[i].queries, queryFilters), queries.custom[i].searchPath, i === customQueryIndices[customQueryIndices.length - 1] &&
-                        querySuitePaths.push((await runQueryGroup(language, `custom-${i}`, createQuerySuiteContents(queries["custom"][i].queries, queryFilters), queries["custom"][i].searchPath)));
+                        packsWithVersion.length === 0)));
-                        ranCustom = true;
+                    ranCustom = true;
-                    }
                 }
                 if (packsWithVersion.length > 0) {
-                    querySuitePaths.push(await runQueryPacks(language, "packs", packsWithVersion, queryFilters));
+                    querySuitePaths.push(await runQueryPacks(language, "packs", packsWithVersion, queryFilters, true));
                     ranCustom = true;
                 }
                 if (ranCustom) {
@@ -218,7 +224,7 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
         const databasePath = util.getCodeQLDatabasePath(config, language);
         return await codeql.databasePrintBaseline(databasePath);
     }
-    async function runQueryGroup(language, type, querySuiteContents, searchPath) {
+    async function runQueryGroup(language, type, querySuiteContents, searchPath, optimizeForLastQueryRun) {
         const databasePath = util.getCodeQLDatabasePath(config, language);
         // Pass the queries to codeql using a file instead of using the command
         // line to avoid command line length restrictions, particularly on windows.
@@ -229,11 +235,11 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
             fs.writeFileSync(querySuitePath, querySuiteContents);
             logger.debug(`Query suite file for ${language}-${type}...\n${querySuiteContents}`);
         }
-        await codeql.databaseRunQueries(databasePath, searchPath, querySuitePath, memoryFlag, threadsFlag);
+        await codeql.databaseRunQueries(databasePath, searchPath, querySuitePath, queryFlags, optimizeForLastQueryRun);
         logger.debug(`BQRS results produced for ${language} (queries: ${type})"`);
         return querySuitePath;
     }
-    async function runQueryPacks(language, type, packs, queryFilters) {
+    async function runQueryPacks(language, type, packs, queryFilters, optimizeForLastQueryRun) {
         const databasePath = util.getCodeQLDatabasePath(config, language);
         for (const pack of packs) {
             logger.debug(`Running query pack for ${language}-${type}: ${pack}`);
@@ -243,7 +249,7 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
         const querySuitePath = `${databasePath}-queries-${type}.qls`;
         fs.writeFileSync(querySuitePath, yaml.dump(querySuite));
         logger.debug(`BQRS results produced for ${language} (queries: ${type})"`);
-        await codeql.databaseRunQueries(databasePath, undefined, querySuitePath, memoryFlag, threadsFlag);
+        await codeql.databaseRunQueries(databasePath, undefined, querySuitePath, queryFlags, optimizeForLastQueryRun);
         return querySuitePath;
     }
 }

lib/analyze.test.js

@@ -30,8 +30,10 @@ const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const ava_1 = __importDefault(require("ava"));
 const yaml = __importStar(require("js-yaml"));
+const sinon = __importStar(require("sinon"));
 const analyze_1 = require("./analyze");
 const codeql_1 = require("./codeql");
+const feature_flags_1 = require("./feature-flags");
 const languages_1 = require("./languages");
 const logging_1 = require("./logging");
 const testing_utils_1 = require("./testing-utils");
@@ -188,6 +190,126 @@ const util = __importStar(require("./util"));
         }
     }
 });
+function mockCodeQL() {
+    return {
+        getVersion: async () => "2.12.2",
+        databaseRunQueries: sinon.spy(),
+        databaseInterpretResults: async () => "",
+        databasePrintBaseline: async () => "",
+    };
+}
+function createBaseConfig(tmpDir) {
+    return {
+        languages: [],
+        queries: {},
+        pathsIgnore: [],
+        paths: [],
+        originalUserInput: {},
+        tempDir: "tempDir",
+        codeQLCmd: "",
+        gitHubVersion: {
+            type: util.GitHubVariant.DOTCOM,
+        },
+        dbLocation: path.resolve(tmpDir, "codeql_databases"),
+        packs: {},
+        debugMode: false,
+        debugArtifactName: util.DEFAULT_DEBUG_ARTIFACT_NAME,
+        debugDatabaseName: util.DEFAULT_DEBUG_DATABASE_NAME,
+        augmentationProperties: {
+            injectedMlQueries: false,
+            packsInputCombines: false,
+            queriesInputCombines: false,
+        },
+        trapCaches: {},
+        trapCacheDownloadTime: 0,
+    };
+}
+function createQueryConfig(builtin, custom) {
+    return {
+        builtin,
+        custom: custom.map((c) => ({ searchPath: "/search", queries: [c] })),
+    };
+}
+async function runQueriesWithConfig(config, features) {
+    for (const language of config.languages) {
+        fs.mkdirSync(util.getCodeQLDatabasePath(config, language), {
+            recursive: true,
+        });
+    }
+    return (0, analyze_1.runQueries)("sarif-folder", "--memFlag", "--addSnippetsFlag", "--threadsFlag", undefined, config, (0, logging_1.getRunnerLogger)(true), (0, testing_utils_1.createFeatures)(features));
+}
+function getDatabaseRunQueriesCalls(mock) {
+    return mock.databaseRunQueries.getCalls();
+}
+(0, ava_1.default)("optimizeForLastQueryRun for one language", async (t) => {
+    return await util.withTmpDir(async (tmpDir) => {
+        const codeql = mockCodeQL();
+        (0, codeql_1.setCodeQL)(codeql);
+        const config = createBaseConfig(tmpDir);
+        config.languages = [languages_1.Language.cpp];
+        config.queries.cpp = createQueryConfig(["foo.ql"], []);
+        await runQueriesWithConfig(config, []);
+        t.deepEqual(getDatabaseRunQueriesCalls(codeql).map((c) => c.args[4]), [true]);
+    });
+});
+(0, ava_1.default)("optimizeForLastQueryRun for two languages", async (t) => {
+    return await util.withTmpDir(async (tmpDir) => {
+        const codeql = mockCodeQL();
+        (0, codeql_1.setCodeQL)(codeql);
+        const config = createBaseConfig(tmpDir);
+        config.languages = [languages_1.Language.cpp, languages_1.Language.java];
+        config.queries.cpp = createQueryConfig(["foo.ql"], []);
+        config.queries.java = createQueryConfig(["bar.ql"], []);
+        await runQueriesWithConfig(config, []);
+        t.deepEqual(getDatabaseRunQueriesCalls(codeql).map((c) => c.args[4]), [true, true]);
+    });
+});
+(0, ava_1.default)("optimizeForLastQueryRun for two languages, with custom queries", async (t) => {
+    return await util.withTmpDir(async (tmpDir) => {
+        const codeql = mockCodeQL();
+        (0, codeql_1.setCodeQL)(codeql);
+        const config = createBaseConfig(tmpDir);
+        config.languages = [languages_1.Language.cpp, languages_1.Language.java];
+        config.queries.cpp = createQueryConfig(["foo.ql"], ["c1.ql", "c2.ql"]);
+        config.queries.java = createQueryConfig(["bar.ql"], ["c3.ql"]);
+        await runQueriesWithConfig(config, []);
+        t.deepEqual(getDatabaseRunQueriesCalls(codeql).map((c) => c.args[4]), [false, false, true, false, true]);
+    });
+});
+(0, ava_1.default)("optimizeForLastQueryRun for two languages, with custom queries and packs", async (t) => {
+    return await util.withTmpDir(async (tmpDir) => {
+        const codeql = mockCodeQL();
+        (0, codeql_1.setCodeQL)(codeql);
+        const config = createBaseConfig(tmpDir);
+        config.languages = [languages_1.Language.cpp, languages_1.Language.java];
+        config.queries.cpp = createQueryConfig(["foo.ql"], ["c1.ql", "c2.ql"]);
+        config.queries.java = createQueryConfig(["bar.ql"], ["c3.ql"]);
+        config.packs.cpp = ["a/cpp-pack1@0.1.0"];
+        config.packs.java = ["b/java-pack1@0.2.0", "b/java-pack2@0.3.3"];
+        await runQueriesWithConfig(config, []);
+        t.deepEqual(getDatabaseRunQueriesCalls(codeql).map((c) => c.args[4]), [false, false, false, true, false, false, true]);
+    });
+});
+(0, ava_1.default)("optimizeForLastQueryRun for one language, CliConfigFileEnabled", async (t) => {
+    return await util.withTmpDir(async (tmpDir) => {
+        const codeql = mockCodeQL();
+        (0, codeql_1.setCodeQL)(codeql);
+        const config = createBaseConfig(tmpDir);
+        config.languages = [languages_1.Language.cpp];
+        await runQueriesWithConfig(config, [feature_flags_1.Feature.CliConfigFileEnabled]);
+        t.deepEqual(getDatabaseRunQueriesCalls(codeql).map((c) => c.args[4]), [true]);
+    });
+});
+(0, ava_1.default)("optimizeForLastQueryRun for two languages, CliConfigFileEnabled", async (t) => {
+    return await util.withTmpDir(async (tmpDir) => {
+        const codeql = mockCodeQL();
+        (0, codeql_1.setCodeQL)(codeql);
+        const config = createBaseConfig(tmpDir);
+        config.languages = [languages_1.Language.cpp, languages_1.Language.java];
+        await runQueriesWithConfig(config, [feature_flags_1.Feature.CliConfigFileEnabled]);
+        t.deepEqual(getDatabaseRunQueriesCalls(codeql).map((c) => c.args[4]), [true, true]);
+    });
+});
 (0, ava_1.default)("validateQueryFilters", (t) => {
     t.notThrows(() => (0, analyze_1.validateQueryFilters)([]));
     t.notThrows(() => (0, analyze_1.validateQueryFilters)(undefined));

lib/codeql.js

@@ -23,7 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getExtraOptions = exports.getCodeQLForCmd = exports.getCodeQLForTesting = exports.getCachedCodeQL = exports.setCodeQL = exports.getCodeQL = exports.setupCodeQL = exports.CODEQL_VERSION_BETTER_RESOLVE_LANGUAGES = exports.CODEQL_VERSION_ML_POWERED_QUERIES_WINDOWS = exports.CODEQL_VERSION_TRACING_GLIBC_2_34 = exports.CODEQL_VERSION_NEW_TRACING = exports.CODEQL_VERSION_GHES_PACK_DOWNLOAD = exports.CommandInvocationError = void 0;
+exports.getExtraOptions = exports.getCodeQLForCmd = exports.getCodeQLForTesting = exports.getCachedCodeQL = exports.setCodeQL = exports.getCodeQL = exports.setupCodeQL = exports.CODEQL_VERSION_INIT_WITH_QLCONFIG = exports.CODEQL_VERSION_SECURITY_EXPERIMENTAL_SUITE = exports.CODEQL_VERSION_BETTER_RESOLVE_LANGUAGES = exports.CODEQL_VERSION_ML_POWERED_QUERIES_WINDOWS = exports.CODEQL_VERSION_TRACING_GLIBC_2_34 = exports.CODEQL_VERSION_NEW_TRACING = exports.CODEQL_VERSION_GHES_PACK_DOWNLOAD = exports.CommandInvocationError = void 0;
 const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const toolrunner = __importStar(require("@actions/exec/lib/toolrunner"));
@@ -94,6 +94,14 @@ exports.CODEQL_VERSION_ML_POWERED_QUERIES_WINDOWS = "2.9.0";
  * --extractor-options-verbosity that we need.
  */
 exports.CODEQL_VERSION_BETTER_RESOLVE_LANGUAGES = "2.10.3";
+/**
+ * Versions 2.11.1+ of the CodeQL Bundle include a `security-experimental` built-in query suite for each language.
+ */
+exports.CODEQL_VERSION_SECURITY_EXPERIMENTAL_SUITE = "2.12.1";
+/**
+ * Versions 2.12.4+ of the CodeQL CLI support the `--qlconfig` flag in calls to `database init`.
+ */
+exports.CODEQL_VERSION_INIT_WITH_QLCONFIG = "2.12.4";
 /**
  * Set up CodeQL CLI access.
  *
@@ -101,16 +109,15 @@ exports.CODEQL_VERSION_BETTER_RESOLVE_LANGUAGES = "2.10.3";
  * @param apiDetails
  * @param tempDir
  * @param variant
- * @param bypassToolcache
  * @param defaultCliVersion
  * @param logger
  * @param checkVersion Whether to check that CodeQL CLI meets the minimum
  *        version requirement. Must be set to true outside tests.
  * @returns a { CodeQL, toolsVersion } object.
  */
-async function setupCodeQL(toolsInput, apiDetails, tempDir, variant, bypassToolcache, defaultCliVersion, logger, checkVersion) {
+async function setupCodeQL(toolsInput, apiDetails, tempDir, variant, defaultCliVersion, logger, checkVersion) {
     try {
-        const { codeqlFolder, toolsDownloadDurationMs, toolsSource, toolsVersion } = await setupCodeql.setupCodeQLBundle(toolsInput, apiDetails, tempDir, variant, bypassToolcache, defaultCliVersion, logger);
+        const { codeqlFolder, toolsDownloadDurationMs, toolsSource, toolsVersion } = await setupCodeql.setupCodeQLBundle(toolsInput, apiDetails, tempDir, variant, defaultCliVersion, logger);
         let codeqlCmd = path.join(codeqlFolder, "codeql", "codeql");
         if (process.platform === "win32") {
             codeqlCmd += ".exe";
@@ -299,7 +306,7 @@ async function getCodeQLForCmd(cmd, checkVersion) {
                 ...getExtraOptionsFromEnv(["database", "init"]),
             ]);
         },
-        async databaseInitCluster(config, sourceRoot, processName, featureEnablement, logger) {
+        async databaseInitCluster(config, sourceRoot, processName, featureEnablement, qlconfigFile, logger) {
             const extraArgs = config.languages.map((language) => `--language=${language}`);
             if (config.languages.filter((l) => (0, languages_1.isTracedLanguage)(l)).length > 0) {
                 extraArgs.push("--begin-tracing");
@@ -317,17 +324,20 @@ async function getCodeQLForCmd(cmd, checkVersion) {
                     extraArgs.push("--no-internal-use-lua-tracing");
                 }
             }
-            // A config file is only generated if the CliConfigFileEnabled feature flag is enabled.
+            // A code scanning config file is only generated if the CliConfigFileEnabled feature flag is enabled.
-            const configLocation = await generateCodeScanningConfig(codeql, config, featureEnablement, logger);
+            const codeScanningConfigFile = await generateCodeScanningConfig(codeql, config, featureEnablement, logger);
             // Only pass external repository token if a config file is going to be parsed by the CLI.
             let externalRepositoryToken;
-            if (configLocation) {
+            if (codeScanningConfigFile) {
-                extraArgs.push(`--codescanning-config=${configLocation}`);
                 externalRepositoryToken = (0, actions_util_1.getOptionalInput)("external-repository-token");
+                extraArgs.push(`--codescanning-config=${codeScanningConfigFile}`);
                 if (externalRepositoryToken) {
                     extraArgs.push("--external-repository-token-stdin");
                 }
             }
+            if (await util.codeQlVersionAbove(this, exports.CODEQL_VERSION_INIT_WITH_QLCONFIG)) {
+                extraArgs.push(`--qlconfig=${qlconfigFile}`);
+            }
             await runTool(cmd, [
                 "database",
                 "init",
@@ -469,17 +479,20 @@ async function getCodeQLForCmd(cmd, checkVersion) {
                 throw new Error(`Unexpected output from codeql resolve queries: ${e}`);
             }
         },
-        async databaseRunQueries(databasePath, extraSearchPath, querySuitePath, memoryFlag, threadsFlag) {
+        async databaseRunQueries(databasePath, extraSearchPath, querySuitePath, flags, optimizeForLastQueryRun) {
             const codeqlArgs = [
                 "database",
                 "run-queries",
-                memoryFlag,
+                ...flags,
-                threadsFlag,
                 databasePath,
                 "--min-disk-free=1024",
                 "-v",
                 ...getExtraOptionsFromEnv(["database", "run-queries"]),
             ];
+            if (optimizeForLastQueryRun &&
+                (await util.supportExpectDiscardedCache(this))) {
+                codeqlArgs.push("--expect-discarded-cache");
+            }
             if (extraSearchPath !== undefined) {
                 codeqlArgs.push("--additional-packs", extraSearchPath);
             }
@@ -712,7 +725,7 @@ async function generateCodeScanningConfig(codeql, config, featureEnablement, log
     if (!(await util.useCodeScanningConfigInCli(codeql, featureEnablement))) {
         return;
     }
-    const configLocation = path.resolve(config.tempDir, "user-config.yaml");
+    const codeScanningConfigFile = path.resolve(config.tempDir, "user-config.yaml");
     // make a copy so we can modify it
     const augmentedConfig = cloneObject(config.originalUserInput);
     // Inject the queries from the input
@@ -766,12 +779,12 @@ async function generateCodeScanningConfig(codeql, config, featureEnablement, log
             augmentedConfig.packs["javascript"].push(packString);
         }
     }
-    logger.info(`Writing augmented user configuration file to ${configLocation}`);
+    logger.info(`Writing augmented user configuration file to ${codeScanningConfigFile}`);
     logger.startGroup("Augmented user configuration file contents");
     logger.info(yaml.dump(augmentedConfig));
     logger.endGroup();
-    fs.writeFileSync(configLocation, yaml.dump(augmentedConfig));
+    fs.writeFileSync(codeScanningConfigFile, yaml.dump(augmentedConfig));
-    return configLocation;
+    return codeScanningConfigFile;
 }
 function cloneObject(obj) {
     return JSON.parse(JSON.stringify(obj));

lib/codeql.test.js

@@ -114,7 +114,7 @@ function mockDownloadApi({ apiDetails = sampleApiDetails, isPinned, repo = "gith
 }
 async function installIntoToolcache({ apiDetails = sampleApiDetails, cliVersion, isPinned, tagName, tmpDir, }) {
     const url = mockDownloadApi({ apiDetails, isPinned, tagName });
-    await codeql.setupCodeQL(cliVersion !== undefined ? undefined : url, apiDetails, tmpDir, util.GitHubVariant.GHES, false, cliVersion !== undefined
+    await codeql.setupCodeQL(cliVersion !== undefined ? undefined : url, apiDetails, tmpDir, util.GitHubVariant.GHES, cliVersion !== undefined
         ? { cliVersion, tagName, variant: util.GitHubVariant.GHES }
         : SAMPLE_DEFAULT_CLI_VERSION, (0, logging_1.getRunnerLogger)(true), false);
 }
@@ -153,7 +153,7 @@ function mockApiDetails(apiDetails) {
                 tagName: `codeql-bundle-${version}`,
                 isPinned: false,
             });
-            const result = await codeql.setupCodeQL(url, sampleApiDetails, tmpDir, util.GitHubVariant.DOTCOM, false, SAMPLE_DEFAULT_CLI_VERSION, (0, logging_1.getRunnerLogger)(true), false);
+            const result = await codeql.setupCodeQL(url, sampleApiDetails, tmpDir, util.GitHubVariant.DOTCOM, SAMPLE_DEFAULT_CLI_VERSION, (0, logging_1.getRunnerLogger)(true), false);
             t.assert(toolcache.find("CodeQL", `0.0.0-${version}`));
             t.is(result.toolsVersion, `0.0.0-${version}`);
             t.is(result.toolsSource, init_1.ToolsSource.Download);
@@ -173,7 +173,7 @@ function mockApiDetails(apiDetails) {
         const url = mockDownloadApi({
             tagName: "codeql-bundle-20200610",
         });
-        const result = await codeql.setupCodeQL(url, sampleApiDetails, tmpDir, util.GitHubVariant.DOTCOM, false, SAMPLE_DEFAULT_CLI_VERSION, (0, logging_1.getRunnerLogger)(true), false);
+        const result = await codeql.setupCodeQL(url, sampleApiDetails, tmpDir, util.GitHubVariant.DOTCOM, SAMPLE_DEFAULT_CLI_VERSION, (0, logging_1.getRunnerLogger)(true), false);
         t.assert(toolcache.find("CodeQL", "0.0.0-20200610"));
         t.deepEqual(result.toolsVersion, "0.0.0-20200610");
         t.is(result.toolsSource, init_1.ToolsSource.Download);
@@ -207,7 +207,7 @@ for (const { cliVersion, expectedToolcacheVersion, } of EXPLICITLY_REQUESTED_BUN
             const url = mockDownloadApi({
                 tagName: "codeql-bundle-20200610",
             });
-            const result = await codeql.setupCodeQL(url, sampleApiDetails, tmpDir, util.GitHubVariant.DOTCOM, false, SAMPLE_DEFAULT_CLI_VERSION, (0, logging_1.getRunnerLogger)(true), false);
+            const result = await codeql.setupCodeQL(url, sampleApiDetails, tmpDir, util.GitHubVariant.DOTCOM, SAMPLE_DEFAULT_CLI_VERSION, (0, logging_1.getRunnerLogger)(true), false);
             t.assert(releaseApiMock.isDone(), "Releases API should have been called");
             t.assert(toolcache.find("CodeQL", expectedToolcacheVersion));
             t.deepEqual(result.toolsVersion, cliVersion);
@@ -256,7 +256,7 @@ for (const { githubReleases, toolcacheVersion } of [
                     }))),
                 }));
             }
-            const result = await codeql.setupCodeQL(undefined, sampleApiDetails, tmpDir, util.GitHubVariant.DOTCOM, false, SAMPLE_DEFAULT_CLI_VERSION, (0, logging_1.getRunnerLogger)(true), false);
+            const result = await codeql.setupCodeQL(undefined, sampleApiDetails, tmpDir, util.GitHubVariant.DOTCOM, SAMPLE_DEFAULT_CLI_VERSION, (0, logging_1.getRunnerLogger)(true), false);
             t.is(result.toolsVersion, SAMPLE_DEFAULT_CLI_VERSION.cliVersion);
             t.is(result.toolsSource, init_1.ToolsSource.Toolcache);
             t.is(result.toolsDownloadDurationMs, undefined);
@@ -272,7 +272,7 @@ for (const variant of [util.GitHubVariant.GHAE, util.GitHubVariant.GHES]) {
                 isPinned: true,
                 tmpDir,
             });
-            const result = await codeql.setupCodeQL(undefined, sampleApiDetails, tmpDir, variant, false, {
+            const result = await codeql.setupCodeQL(undefined, sampleApiDetails, tmpDir, variant, {
                 cliVersion: defaults.cliVersion,
                 tagName: defaults.bundleVersion,
                 variant,
@@ -295,7 +295,7 @@ for (const variant of [util.GitHubVariant.GHAE, util.GitHubVariant.GHES]) {
             mockDownloadApi({
                 tagName: defaults.bundleVersion,
             });
-            const result = await codeql.setupCodeQL(undefined, sampleApiDetails, tmpDir, variant, false, {
+            const result = await codeql.setupCodeQL(undefined, sampleApiDetails, tmpDir, variant, {
                 cliVersion: defaults.cliVersion,
                 tagName: defaults.bundleVersion,
                 variant,
@@ -319,7 +319,7 @@ for (const variant of [util.GitHubVariant.GHAE, util.GitHubVariant.GHES]) {
         mockDownloadApi({
             tagName: defaults.bundleVersion,
         });
-        const result = await codeql.setupCodeQL("latest", sampleApiDetails, tmpDir, util.GitHubVariant.DOTCOM, false, SAMPLE_DEFAULT_CLI_VERSION, (0, logging_1.getRunnerLogger)(true), false);
+        const result = await codeql.setupCodeQL("latest", sampleApiDetails, tmpDir, util.GitHubVariant.DOTCOM, SAMPLE_DEFAULT_CLI_VERSION, (0, logging_1.getRunnerLogger)(true), false);
         t.deepEqual(result.toolsVersion, defaults.cliVersion);
         t.is(result.toolsSource, init_1.ToolsSource.Download);
         t.assert(Number.isInteger(result.toolsDownloadDurationMs));
@@ -360,7 +360,7 @@ for (const isBundleVersionInUrl of [true, false]) {
             mockApiDetails(sampleGHAEApiDetails);
             sinon.stub(actionsUtil, "isRunningLocalAction").returns(false);
             process.env["GITHUB_ACTION_REPOSITORY"] = "github/codeql-action";
-            const result = await codeql.setupCodeQL(undefined, sampleGHAEApiDetails, tmpDir, util.GitHubVariant.GHAE, false, {
+            const result = await codeql.setupCodeQL(undefined, sampleGHAEApiDetails, tmpDir, util.GitHubVariant.GHAE, {
                 cliVersion: defaults.cliVersion,
                 tagName: defaults.bundleVersion,
                 variant: util.GitHubVariant.GHAE,
@@ -386,7 +386,7 @@ for (const isBundleVersionInUrl of [true, false]) {
             platformSpecific: false,
             tagName: "codeql-bundle-20230203",
         });
-        const result = await codeql.setupCodeQL("https://github.com/dsp-testing/codeql-cli-nightlies/releases/download/codeql-bundle-20230203/codeql-bundle.tar.gz", sampleApiDetails, tmpDir, util.GitHubVariant.DOTCOM, false, SAMPLE_DEFAULT_CLI_VERSION, (0, logging_1.getRunnerLogger)(true), false);
+        const result = await codeql.setupCodeQL("https://github.com/dsp-testing/codeql-cli-nightlies/releases/download/codeql-bundle-20230203/codeql-bundle.tar.gz", sampleApiDetails, tmpDir, util.GitHubVariant.DOTCOM, SAMPLE_DEFAULT_CLI_VERSION, (0, logging_1.getRunnerLogger)(true), false);
         t.is(result.toolsVersion, "0.0.0-20230203");
         t.is(result.toolsSource, init_1.ToolsSource.Download);
         t.true(Number.isInteger(result.toolsDownloadDurationMs));
@@ -452,11 +452,11 @@ for (const isBundleVersionInUrl of [true, false]) {
                 packsInputCombines: false,
             },
         };
-        await codeqlObject.databaseInitCluster(thisStubConfig, "", undefined, (0, testing_utils_1.createFeatures)([]), (0, logging_1.getRunnerLogger)(true));
+        await codeqlObject.databaseInitCluster(thisStubConfig, "", undefined, (0, testing_utils_1.createFeatures)([]), "/path/to/qlconfig.yml", (0, logging_1.getRunnerLogger)(true));
         const args = runnerConstructorStub.firstCall.args[1];
         // should NOT have used an config file
         const configArg = args.find((arg) => arg.startsWith("--codescanning-config="));
-        t.falsy(configArg, "Should have injected a codescanning config");
+        t.falsy(configArg, "Should NOT have injected a codescanning config");
     });
 });
 // Test macro for ensuring different variants of injected augmented configurations
@@ -474,7 +474,7 @@ const injectedConfigMacro = ava_1.default.macro({
                 tempDir,
                 augmentationProperties,
             };
-            await codeqlObject.databaseInitCluster(thisStubConfig, "", undefined, (0, testing_utils_1.createFeatures)([feature_flags_1.Feature.CliConfigFileEnabled]), (0, logging_1.getRunnerLogger)(true));
+            await codeqlObject.databaseInitCluster(thisStubConfig, "", undefined, (0, testing_utils_1.createFeatures)([feature_flags_1.Feature.CliConfigFileEnabled]), undefined, (0, logging_1.getRunnerLogger)(true));
             const args = runnerConstructorStub.firstCall.args[1];
             // should have used an config file
             const configArg = args.find((arg) => arg.startsWith("--codescanning-config="));
@@ -665,24 +665,47 @@ const injectedConfigMacro = ava_1.default.macro({
         queries: [],
     },
 }, {});
-(0, ava_1.default)("does not use injected config", async (t) => {
+(0, ava_1.default)("does not pass a code scanning config or qlconfig file to the CLI when CLI config passing is disabled", async (t) => {
-    const origCODEQL_PASS_CONFIG_TO_CLI = process.env.CODEQL_PASS_CONFIG_TO_CLI;
+    const runnerConstructorStub = stubToolRunnerConstructor();
-    process.env["CODEQL_PASS_CONFIG_TO_CLI"] = "false";
+    const codeqlObject = await codeql.getCodeQLForTesting();
-    try {
+    // stubbed version doesn't matter. It just needs to be valid semver.
-        const runnerConstructorStub = stubToolRunnerConstructor();
+    sinon.stub(codeqlObject, "getVersion").resolves("0.0.0");
-        const codeqlObject = await codeql.getCodeQLForTesting();
+    await codeqlObject.databaseInitCluster(stubConfig, "", undefined, (0, testing_utils_1.createFeatures)([]), "/path/to/qlconfig.yml", (0, logging_1.getRunnerLogger)(true));
-        sinon
+    const args = runnerConstructorStub.firstCall.args[1];
-            .stub(codeqlObject, "getVersion")
+    // should not have used a config file
-            .resolves(feature_flags_1.featureConfig[feature_flags_1.Feature.CliConfigFileEnabled].minimumVersion);
+    const hasConfigArg = args.some((arg) => arg.startsWith("--codescanning-config="));
-        await codeqlObject.databaseInitCluster(stubConfig, "", undefined, (0, testing_utils_1.createFeatures)([]), (0, logging_1.getRunnerLogger)(true));
+    t.false(hasConfigArg, "Should NOT have injected a codescanning config");
-        const args = runnerConstructorStub.firstCall.args[1];
+    // should not have passed a qlconfig file
-        // should have used an config file
+    const hasQlconfigArg = args.some((arg) => arg.startsWith("--qlconfig="));
-        const configArg = args.find((arg) => arg.startsWith("--codescanning-config="));
+    t.false(hasQlconfigArg, "Should NOT have passed a qlconfig file");
-        t.falsy(configArg, "Should NOT have injected a codescanning config");
+});
-    }
+(0, ava_1.default)("passes a code scanning config AND qlconfig to the CLI when CLI config passing is enabled", async (t) => {
-    finally {
+    const runnerConstructorStub = stubToolRunnerConstructor();
-        process.env["CODEQL_PASS_CONFIG_TO_CLI"] = origCODEQL_PASS_CONFIG_TO_CLI;
+    const codeqlObject = await codeql.getCodeQLForTesting();
-    }
+    sinon
+        .stub(codeqlObject, "getVersion")
+        .resolves(codeql.CODEQL_VERSION_INIT_WITH_QLCONFIG);
+    await codeqlObject.databaseInitCluster(stubConfig, "", undefined, (0, testing_utils_1.createFeatures)([feature_flags_1.Feature.CliConfigFileEnabled]), "/path/to/qlconfig.yml", (0, logging_1.getRunnerLogger)(true));
+    const args = runnerConstructorStub.firstCall.args[1];
+    // should have used a config file
+    const hasCodeScanningConfigArg = args.some((arg) => arg.startsWith("--codescanning-config="));
+    t.true(hasCodeScanningConfigArg, "Should have injected a qlconfig");
+    // should have passed a qlconfig file
+    const hasQlconfigArg = args.some((arg) => arg.startsWith("--qlconfig="));
+    t.truthy(hasQlconfigArg, "Should have injected a codescanning config");
+});
+(0, ava_1.default)("passes a code scanning config BUT NOT a qlconfig to the CLI when CLI config passing is enabled", async (t) => {
+    const runnerConstructorStub = stubToolRunnerConstructor();
+    const codeqlObject = await codeql.getCodeQLForTesting();
+    sinon.stub(codeqlObject, "getVersion").resolves("2.12.2");
+    await codeqlObject.databaseInitCluster(stubConfig, "", undefined, (0, testing_utils_1.createFeatures)([feature_flags_1.Feature.CliConfigFileEnabled]), "/path/to/qlconfig.yml", (0, logging_1.getRunnerLogger)(true));
+    const args = runnerConstructorStub.firstCall.args[1];
+    // should have used a config file
+    const hasCodeScanningConfigArg = args.some((arg) => arg.startsWith("--codescanning-config="));
+    t.true(hasCodeScanningConfigArg, "Should NOT have injected a qlconfig");
+    // should have passed a qlconfig file
+    const hasQlconfigArg = args.some((arg) => arg.startsWith("--qlconfig="));
+    t.false(hasQlconfigArg, "Should have injected a codescanning config");
 });
 (0, ava_1.default)("databaseInterpretResults() sets --sarif-add-baseline-file-info for 2.11.3", async (t) => {
     const runnerConstructorStub = stubToolRunnerConstructor();

lib/config-utils.js

@@ -23,7 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.downloadPacks = exports.getConfig = exports.getPathToParsedConfigFile = exports.initConfig = exports.parsePacks = exports.validatePackSpecification = exports.prettyPrintPack = exports.parsePacksSpecification = exports.parsePacksFromConfig = exports.calculateAugmentation = exports.getDefaultConfig = exports.getRawLanguages = exports.getLanguages = exports.getLanguagesInRepo = exports.getUnknownLanguagesError = exports.getNoLanguagesError = exports.getConfigFileDirectoryGivenMessage = exports.getConfigFileFormatInvalidMessage = exports.getConfigFileRepoFormatInvalidMessage = exports.getConfigFileDoesNotExistErrorMessage = exports.getConfigFileOutsideWorkspaceErrorMessage = exports.getLocalPathDoesNotExist = exports.getLocalPathOutsideOfRepository = exports.getPacksStrInvalid = exports.getPacksInvalid = exports.getPacksInvalidSplit = exports.getPathsInvalid = exports.getPathsIgnoreInvalid = exports.getQueryUsesInvalid = exports.getQueriesMissingUses = exports.getQueriesInvalid = exports.getDisableDefaultQueriesInvalid = exports.getNameInvalid = exports.validateAndSanitisePath = exports.defaultAugmentationProperties = void 0;
+exports.wrapEnvironment = exports.generateRegistries = exports.downloadPacks = exports.getConfig = exports.getPathToParsedConfigFile = exports.initConfig = exports.parsePacks = exports.validatePackSpecification = exports.prettyPrintPack = exports.parsePacksSpecification = exports.parsePacksFromConfig = exports.calculateAugmentation = exports.getDefaultConfig = exports.getRawLanguages = exports.getLanguages = exports.getLanguagesInRepo = exports.getUnknownLanguagesError = exports.getNoLanguagesError = exports.getConfigFileDirectoryGivenMessage = exports.getConfigFileFormatInvalidMessage = exports.getConfigFileRepoFormatInvalidMessage = exports.getConfigFileDoesNotExistErrorMessage = exports.getConfigFileOutsideWorkspaceErrorMessage = exports.getLocalPathDoesNotExist = exports.getLocalPathOutsideOfRepository = exports.getPacksStrInvalid = exports.getPacksInvalid = exports.getPacksInvalidSplit = exports.getPathsInvalid = exports.getPathsIgnoreInvalid = exports.getQueryUsesInvalid = exports.getQueriesMissingUses = exports.getQueriesInvalid = exports.getDisableDefaultQueriesInvalid = exports.getNameInvalid = exports.validateAndSanitisePath = exports.defaultAugmentationProperties = void 0;
 const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const perf_hooks_1 = require("perf_hooks");
@@ -131,7 +131,11 @@ async function addDefaultQueries(codeQL, languages, resultMap) {
     await runResolveQueries(codeQL, resultMap, suites, undefined);
 }
 // The set of acceptable values for built-in suites from the codeql bundle
-const builtinSuites = ["security-extended", "security-and-quality"];
+const builtinSuites = [
+    "security-experimental",
+    "security-extended",
+    "security-and-quality",
+];
 /**
  * Determine the set of queries associated with suiteName's suites and add them to resultMap.
  * Throws an error if suiteName is not a valid builtin suite.
@@ -143,6 +147,12 @@ async function addBuiltinSuiteQueries(languages, codeQL, resultMap, packs, suite
     if (!found) {
         throw new Error(getQueryUsesInvalid(configFile, suiteName));
     }
+    if (suiteName === "security-experimental" &&
+        !(await (0, util_1.codeQlVersionAbove)(codeQL, codeql_1.CODEQL_VERSION_SECURITY_EXPERIMENTAL_SUITE))) {
+        throw new Error(`The 'security-experimental' suite is not supported on CodeQL CLI versions earlier than
+      ${codeql_1.CODEQL_VERSION_SECURITY_EXPERIMENTAL_SUITE}. Please upgrade to CodeQL CLI version
+      ${codeql_1.CODEQL_VERSION_SECURITY_EXPERIMENTAL_SUITE} or later.`);
+    }
     // If we're running the JavaScript security-extended analysis (or a superset of it), the repo is
     // opted into the ML-powered queries beta, and a user hasn't already added the ML-powered query
     // pack, then add the ML-powered query pack so that we run ML-powered queries.
@@ -151,7 +161,9 @@ async function addBuiltinSuiteQueries(languages, codeQL, resultMap, packs, suite
     (process.platform !== "win32" ||
         (await (0, util_1.codeQlVersionAbove)(codeQL, codeql_1.CODEQL_VERSION_ML_POWERED_QUERIES_WINDOWS))) &&
         languages.includes("javascript") &&
-        (found === "security-extended" || found === "security-and-quality") &&
+        (found === "security-experimental" ||
+            found === "security-extended" ||
+            found === "security-and-quality") &&
         !packs.javascript?.some(isMlPoweredJsQueriesPack) &&
         (await featureEnablement.getValue(feature_flags_1.Feature.MlPoweredQueriesEnabled, codeQL))) {
         if (!packs.javascript) {
@@ -713,7 +725,7 @@ function parseQueriesFromInput(rawQueriesInput, queriesInputCombines) {
     }
     const trimmedInput = queriesInputCombines
         ? rawQueriesInput.trim().slice(1).trim()
-        : rawQueriesInput?.trim();
+        : rawQueriesInput?.trim() ?? "";
     if (queriesInputCombines && trimmedInput.length === 0) {
         throw new Error(getConfigFilePropertyError(undefined, "queries", "A '+' was used in the 'queries' input to specify that you wished to add some packs to your CodeQL analysis. However, no packs were specified. Please either remove the '+' or specify some packs."));
     }
@@ -893,7 +905,8 @@ exports.parsePacks = parsePacks;
  * Without a '+', an input value will override the corresponding value in the config file.
  *
  * @param inputValue The input value to process.
- * @returns true if the input value should replace the corresponding value in the config file, false if it should be appended.
+ * @returns true if the input value should replace the corresponding value in the config file,
+ *          false if it should be appended.
  */
 function shouldCombine(inputValue) {
     return !!inputValue?.trim().startsWith("+");
@@ -946,8 +959,7 @@ async function initConfig(languagesInput, queriesInput, packsInput, registriesIn
                     "Please make sure that the default queries are enabled, or you are specifying queries to run.");
             }
         }
-        const registries = parseRegistries(registriesInput);
+        await downloadPacks(codeQL, config.languages, config.packs, apiDetails, registriesInput, config.tempDir, logger);
-        await downloadPacks(codeQL, config.languages, config.packs, registries, apiDetails, config.tempDir, logger);
     }
     // Save the config so we can easily access it again in the future
     await saveConfig(config, logger);
@@ -1043,21 +1055,9 @@ async function getConfig(tempDir, logger) {
     return JSON.parse(configString);
 }
 exports.getConfig = getConfig;
-async function downloadPacks(codeQL, languages, packs, registries, apiDetails, tmpDir, logger) {
+async function downloadPacks(codeQL, languages, packs, apiDetails, registriesInput, tempDir, logger) {
-    let qlconfigFile;
+    // This code path is only used when config parsing occurs in the Action.
-    let registriesAuthTokens;
+    const { registriesAuthTokens, qlconfigFile } = await generateRegistries(registriesInput, codeQL, tempDir, logger);
-    if (registries) {
-        if (!(await (0, util_1.codeQlVersionAbove)(codeQL, codeql_1.CODEQL_VERSION_GHES_PACK_DOWNLOAD))) {
-            throw new Error(`'registries' input is not supported on CodeQL versions less than ${codeql_1.CODEQL_VERSION_GHES_PACK_DOWNLOAD}.`);
-        }
-        // generate a qlconfig.yml file to hold the registry configs.
-        const qlconfig = createRegistriesBlock(registries);
-        qlconfigFile = path.join(tmpDir, "qlconfig.yml");
-        fs.writeFileSync(qlconfigFile, yaml.dump(qlconfig), "utf8");
-        registriesAuthTokens = registries
-            .map((registry) => `${registry.url}=${registry.token}`)
-            .join(",");
-    }
     await wrapEnvironment({
         GITHUB_TOKEN: apiDetails.auth,
         CODEQL_REGISTRIES_AUTH: registriesAuthTokens,
@@ -1085,6 +1085,48 @@ async function downloadPacks(codeQL, languages, packs, registries, apiDetails, t
     });
 }
 exports.downloadPacks = downloadPacks;
+/**
+ * Generate a `qlconfig.yml` file from the `registries` input.
+ * This file is used by the CodeQL CLI to list the registries to use for each
+ * pack.
+ *
+ * @param registriesInput The value of the `registries` input.
+ * @param codeQL a codeQL object, used only for checking the version of CodeQL.
+ * @param tempDir a temporary directory to store the generated qlconfig.yml file.
+ * @param logger a logger object.
+ * @returns The path to the generated `qlconfig.yml` file and the auth tokens to
+ *        use for each registry.
+ */
+async function generateRegistries(registriesInput, codeQL, tempDir, logger) {
+    const registries = parseRegistries(registriesInput);
+    let registriesAuthTokens;
+    let qlconfigFile;
+    if (registries) {
+        if (!(await (0, util_1.codeQlVersionAbove)(codeQL, codeql_1.CODEQL_VERSION_GHES_PACK_DOWNLOAD))) {
+            throw new Error(`The 'registries' input is not supported on CodeQL CLI versions earlier than ${codeql_1.CODEQL_VERSION_GHES_PACK_DOWNLOAD}. Please upgrade to CodeQL CLI version ${codeql_1.CODEQL_VERSION_GHES_PACK_DOWNLOAD} or later.`);
+        }
+        // generate a qlconfig.yml file to hold the registry configs.
+        const qlconfig = createRegistriesBlock(registries);
+        qlconfigFile = path.join(tempDir, "qlconfig.yml");
+        const qlconfigContents = yaml.dump(qlconfig);
+        fs.writeFileSync(qlconfigFile, qlconfigContents, "utf8");
+        logger.debug("Generated qlconfig.yml:");
+        logger.debug(qlconfigContents);
+        registriesAuthTokens = registries
+            .map((registry) => `${registry.url}=${registry.token}`)
+            .join(",");
+    }
+    if (typeof process.env.CODEQL_REGISTRIES_AUTH === "string") {
+        logger.debug("Using CODEQL_REGISTRIES_AUTH environment variable to authenticate with registries.");
+    }
+    return {
+        registriesAuthTokens: 
+        // if the user has explicitly set the CODEQL_REGISTRIES_AUTH env var then use that
+        process.env.CODEQL_REGISTRIES_AUTH ?? registriesAuthTokens,
+        qlconfigFile,
+    };
+}
+exports.generateRegistries = generateRegistries;
 function createRegistriesBlock(registries) {
     if (!Array.isArray(registries) ||
         registries.some((r) => !r.url || !r.packages)) {
@@ -1134,4 +1176,5 @@ async function wrapEnvironment(env, operation) {
         }
     }
 }
+exports.wrapEnvironment = wrapEnvironment;
 //# sourceMappingURL=config-utils.js.map

lib/config-utils.test.js

@@ -1014,7 +1014,7 @@ const mlPoweredQueriesMacro = ava_1.default.macro({
 // Test that the ~0.1.0 version of ML-powered queries is run on v2.8.3 of the CLI.
 (0, ava_1.default)(mlPoweredQueriesMacro, "2.8.3", true, undefined, "security-extended", process.platform === "win32" ? undefined : "~0.1.0");
 // Test that ML-powered queries aren't run when the user hasn't specified that we should run the
-// `security-extended` or `security-and-quality` query suite.
+//  `security-extended`, `security-and-quality`, or `security-experimental` query suite.
 (0, ava_1.default)(mlPoweredQueriesMacro, "2.7.5", true, undefined, undefined, undefined);
 // Test that ML-powered queries are run on non-Windows platforms running `security-extended` on
 // versions of the CodeQL CLI prior to 2.9.0.
@@ -1042,6 +1042,9 @@ const mlPoweredQueriesMacro = ava_1.default.macro({
 // Test that ML-powered queries are run on all platforms running `security-and-quality` on CodeQL
 // CLI 2.11.3+.
 (0, ava_1.default)(mlPoweredQueriesMacro, "2.11.3", true, undefined, "security-and-quality", "~0.4.0");
+// Test that ML-powered queries are run on all platforms running `security-experimental` on CodeQL
+// CLI 2.12.1+.
+(0, ava_1.default)(mlPoweredQueriesMacro, "2.12.1", true, undefined, "security-experimental", "~0.4.0");
 const calculateAugmentationMacro = ava_1.default.macro({
     exec: async (t, _title, rawPacksInput, rawQueriesInput, languages, expectedAugmentationProperties) => {
         const actualAugmentationProperties = configUtils.calculateAugmentation(rawPacksInput, rawQueriesInput, languages);
@@ -1111,8 +1114,8 @@ const calculateAugmentationErrorMacro = ava_1.default.macro({
             java: ["a", "b"],
             go: ["c", "d"],
             python: ["e", "f"],
-        }, undefined, // registries
+        }, sampleApiDetails, undefined, // registriesAuthTokens
-        sampleApiDetails, tmpDir, logger);
+        tmpDir, logger);
         // Expecting packs to be downloaded once for java and once for python
         t.deepEqual(packDownloadStub.callCount, 2);
         // no config file was created, so pass `undefined` as the config file path
@@ -1125,9 +1128,9 @@ const calculateAugmentationErrorMacro = ava_1.default.macro({
     // associated env vars
     return await util.withTmpDir(async (tmpDir) => {
         process.env.GITHUB_TOKEN = "not-a-token";
-        process.env.CODEQL_REGISTRIES_AUTH = "not-a-registries-auth";
+        process.env.CODEQL_REGISTRIES_AUTH = undefined;
         const logger = (0, logging_1.getRunnerLogger)(true);
-        const registries = [
+        const registriesInput = yaml.dump([
             {
                 // no slash
                 url: "http://ghcr.io",
@@ -1140,8 +1143,9 @@ const calculateAugmentationErrorMacro = ava_1.default.macro({
                 packages: "semmle/*",
                 token: "still-not-a-token",
             },
-        ];
+        ]);
         // append a slash to the first url
+        const registries = yaml.load(registriesInput);
         const expectedRegistries = registries.map((r, i) => ({
             packages: r.packages,
             url: i === 0 ? `${r.url}/` : r.url,
@@ -1170,7 +1174,7 @@ const calculateAugmentationErrorMacro = ava_1.default.macro({
             java: ["a", "b"],
             go: ["c", "d"],
             python: ["e", "f"],
-        }, registries, sampleApiDetails, tmpDir, logger);
+        }, sampleApiDetails, registriesInput, tmpDir, logger);
         // Same packs are downloaded as in previous test
         t.deepEqual(packDownloadStub.callCount, 2);
         t.deepEqual(packDownloadStub.firstCall.args, [
@@ -1183,7 +1187,7 @@ const calculateAugmentationErrorMacro = ava_1.default.macro({
         ]);
         // Verify that the env vars were unset.
         t.deepEqual(process.env.GITHUB_TOKEN, "not-a-token");
-        t.deepEqual(process.env.CODEQL_REGISTRIES_AUTH, "not-a-registries-auth");
+        t.deepEqual(process.env.CODEQL_REGISTRIES_AUTH, undefined);
     });
 });
 (0, ava_1.default)("downloadPacks-with-registries fails on 2.10.3", async (t) => {
@@ -1193,7 +1197,7 @@ const calculateAugmentationErrorMacro = ava_1.default.macro({
         process.env.GITHUB_TOKEN = "not-a-token";
         process.env.CODEQL_REGISTRIES_AUTH = "not-a-registries-auth";
         const logger = (0, logging_1.getRunnerLogger)(true);
-        const registries = [
+        const registriesInput = yaml.dump([
             {
                 url: "http://ghcr.io",
                 packages: ["codeql/*", "dsp-testing/*"],
@@ -1204,12 +1208,12 @@ const calculateAugmentationErrorMacro = ava_1.default.macro({
                 packages: "semmle/*",
                 token: "still-not-a-token",
             },
-        ];
+        ]);
         const codeQL = (0, codeql_1.setCodeQL)({
             getVersion: () => Promise.resolve("2.10.3"),
         });
         await t.throwsAsync(async () => {
-            return await configUtils.downloadPacks(codeQL, [languages_1.Language.javascript, languages_1.Language.java, languages_1.Language.python], {}, registries, sampleApiDetails, tmpDir, logger);
+            return await configUtils.downloadPacks(codeQL, [languages_1.Language.javascript, languages_1.Language.java, languages_1.Language.python], {}, sampleApiDetails, registriesInput, tmpDir, logger);
         }, { instanceOf: Error }, "'registries' input is not supported on CodeQL versions less than 2.10.4.");
     });
 });
@@ -1220,7 +1224,7 @@ const calculateAugmentationErrorMacro = ava_1.default.macro({
         process.env.GITHUB_TOKEN = "not-a-token";
         process.env.CODEQL_REGISTRIES_AUTH = "not-a-registries-auth";
         const logger = (0, logging_1.getRunnerLogger)(true);
-        const registries = [
+        const registriesInput = yaml.dump([
             {
                 // missing url property
                 packages: ["codeql/*", "dsp-testing/*"],
@@ -1231,15 +1235,68 @@ const calculateAugmentationErrorMacro = ava_1.default.macro({
                 packages: "semmle/*",
                 token: "still-not-a-token",
             },
-        ];
+        ]);
         const codeQL = (0, codeql_1.setCodeQL)({
             getVersion: () => Promise.resolve("2.10.4"),
         });
         await t.throwsAsync(async () => {
-            return await configUtils.downloadPacks(codeQL, [languages_1.Language.javascript, languages_1.Language.java, languages_1.Language.python], {}, registries, sampleApiDetails, tmpDir, logger);
+            return await configUtils.downloadPacks(codeQL, [languages_1.Language.javascript, languages_1.Language.java, languages_1.Language.python], {}, sampleApiDetails, registriesInput, tmpDir, logger);
         }, { instanceOf: Error }, "Invalid 'registries' input. Must be an array of objects with 'url' and 'packages' properties.");
     });
 });
+// the happy path for generateRegistries is already tested in downloadPacks.
+// these following tests are for the error cases and when nothing is generated.
+(0, ava_1.default)("no generateRegistries when CLI is too old", async (t) => {
+    return await util.withTmpDir(async (tmpDir) => {
+        const registriesInput = yaml.dump([
+            {
+                // no slash
+                url: "http://ghcr.io",
+                packages: ["codeql/*", "dsp-testing/*"],
+                token: "not-a-token",
+            },
+        ]);
+        const codeQL = (0, codeql_1.setCodeQL)({
+            // Accepted CLI versions are 2.10.4 or higher
+            getVersion: () => Promise.resolve("2.10.3"),
+        });
+        const logger = (0, logging_1.getRunnerLogger)(true);
+        await t.throwsAsync(async () => await configUtils.generateRegistries(registriesInput, codeQL, tmpDir, logger), undefined, "'registries' input is not supported on CodeQL versions less than 2.10.4.");
+    });
+});
+(0, ava_1.default)("no generateRegistries when registries is undefined", async (t) => {
+    return await util.withTmpDir(async (tmpDir) => {
+        const registriesInput = undefined;
+        const codeQL = (0, codeql_1.setCodeQL)({
+            // Accepted CLI versions are 2.10.4 or higher
+            getVersion: () => Promise.resolve(codeql_1.CODEQL_VERSION_GHES_PACK_DOWNLOAD),
+        });
+        const logger = (0, logging_1.getRunnerLogger)(true);
+        const { registriesAuthTokens, qlconfigFile } = await configUtils.generateRegistries(registriesInput, codeQL, tmpDir, logger);
+        t.is(registriesAuthTokens, undefined);
+        t.is(qlconfigFile, undefined);
+    });
+});
+(0, ava_1.default)("generateRegistries prefers original CODEQL_REGISTRIES_AUTH", async (t) => {
+    return await util.withTmpDir(async (tmpDir) => {
+        process.env.CODEQL_REGISTRIES_AUTH = "original";
+        const registriesInput = yaml.dump([
+            {
+                url: "http://ghcr.io",
+                packages: ["codeql/*", "dsp-testing/*"],
+                token: "not-a-token",
+            },
+        ]);
+        const codeQL = (0, codeql_1.setCodeQL)({
+            // Accepted CLI versions are 2.10.4 or higher
+            getVersion: () => Promise.resolve(codeql_1.CODEQL_VERSION_GHES_PACK_DOWNLOAD),
+        });
+        const logger = (0, logging_1.getRunnerLogger)(true);
+        const { registriesAuthTokens, qlconfigFile } = await configUtils.generateRegistries(registriesInput, codeQL, tmpDir, logger);
+        t.is(registriesAuthTokens, "original");
+        t.is(qlconfigFile, path.join(tmpDir, "qlconfig.yml"));
+    });
+});
 // getLanguages
 const mockRepositoryNwo = (0, repository_1.parseRepositoryNwo)("owner/repo");
 // eslint-disable-next-line github/array-foreach

lib/defaults.json

@@ -1,6 +1,6 @@
 {
-    "bundleVersion": "codeql-bundle-20230120",
+    "bundleVersion": "codeql-bundle-20230217",
-    "cliVersion": "2.12.1",
+    "cliVersion": "2.12.3",
-    "priorBundleVersion": "codeql-bundle-20230105",
+    "priorBundleVersion": "codeql-bundle-20230207",
-    "priorCliVersion": "2.12.0"
+    "priorCliVersion": "2.12.2"
 }

lib/feature-flags.js

@@ -34,27 +34,12 @@ const DEFAULT_VERSION_FEATURE_FLAG_PREFIX = "default_codeql_version_";
 const DEFAULT_VERSION_FEATURE_FLAG_SUFFIX = "_enabled";
 var Feature;
 (function (Feature) {
-    Feature["BypassToolcacheEnabled"] = "bypass_toolcache_enabled";
-    Feature["BypassToolcacheKotlinSwiftEnabled"] = "bypass_toolcache_kotlin_swift_enabled";
     Feature["CliConfigFileEnabled"] = "cli_config_file_enabled";
     Feature["DisableKotlinAnalysisEnabled"] = "disable_kotlin_analysis_enabled";
     Feature["MlPoweredQueriesEnabled"] = "ml_powered_queries_enabled";
-    Feature["TrapCachingEnabled"] = "trap_caching_enabled";
     Feature["UploadFailedSarifEnabled"] = "upload_failed_sarif_enabled";
 })(Feature = exports.Feature || (exports.Feature = {}));
 exports.featureConfig = {
-    [Feature.BypassToolcacheEnabled]: {
-        envVar: "CODEQL_BYPASS_TOOLCACHE",
-        // Cannot specify a minimum version because this flag is checked before we have
-        // access to the CodeQL instance.
-        minimumVersion: undefined,
-    },
-    [Feature.BypassToolcacheKotlinSwiftEnabled]: {
-        envVar: "CODEQL_BYPASS_TOOLCACHE_KOTLIN_SWIFT",
-        // Cannot specify a minimum version because this flag is checked before we have
-        // access to the CodeQL instance.
-        minimumVersion: undefined,
-    },
     [Feature.DisableKotlinAnalysisEnabled]: {
         envVar: "CODEQL_DISABLE_KOTLIN_ANALYSIS",
         minimumVersion: undefined,
@@ -67,10 +52,6 @@ exports.featureConfig = {
         envVar: "CODEQL_ML_POWERED_QUERIES",
         minimumVersion: "2.7.5",
     },
-    [Feature.TrapCachingEnabled]: {
-        envVar: "CODEQL_TRAP_CACHING",
-        minimumVersion: undefined,
-    },
     [Feature.UploadFailedSarifEnabled]: {
         envVar: "CODEQL_ACTION_UPLOAD_FAILED_SARIF",
         minimumVersion: "2.11.3",
@@ -105,10 +86,6 @@ class Features {
         if (!codeql && exports.featureConfig[feature].minimumVersion) {
             throw new Error(`Internal error: A minimum version is specified for feature ${feature}, but no instance of CodeQL was provided.`);
         }
-        // Bypassing the toolcache is disabled in test mode.
-        if (feature === Feature.BypassToolcacheEnabled && util.isInTestMode()) {
-            return false;
-        }
         const envVar = (process.env[exports.featureConfig[feature].envVar] || "").toLocaleLowerCase();
         // Do not use this feature if user explicitly disables it via an environment variable.
         if (envVar === "false") {
@@ -136,7 +113,7 @@ class GitHubFeatureFlags {
         this.repositoryNwo = repositoryNwo;
         this.featureFlagsFile = featureFlagsFile;
         this.logger = logger;
-        /**/
+        this.hasAccessedRemoteFeatureFlags = false; // Not accessed by default.
     }
     getCliVersionFromFeatureFlag(f) {
         if (!f.startsWith(DEFAULT_VERSION_FEATURE_FLAG_PREFIX) ||
@@ -157,7 +134,9 @@ class GitHubFeatureFlags {
             const defaultDotComCliVersion = await this.getDefaultDotcomCliVersion();
             return {
                 cliVersion: defaultDotComCliVersion.version,
-                toolsFeatureFlagsValid: defaultDotComCliVersion.toolsFeatureFlagsValid,
+                toolsFeatureFlagsValid: this.hasAccessedRemoteFeatureFlags
+                    ? defaultDotComCliVersion.toolsFeatureFlagsValid
+                    : undefined,
                 variant,
             };
         }
@@ -188,7 +167,9 @@ class GitHubFeatureFlags {
                 `shipped with the Action. This is ${defaults.cliVersion}.`);
             return {
                 version: defaults.cliVersion,
-                toolsFeatureFlagsValid: false,
+                toolsFeatureFlagsValid: this.hasAccessedRemoteFeatureFlags
+                    ? false
+                    : undefined,
             };
         }
         const maxCliVersion = enabledFeatureFlagCliVersions.reduce((maxVersion, currentVersion) => currentVersion > maxVersion ? currentVersion : maxVersion, enabledFeatureFlagCliVersions[0]);
@@ -255,6 +236,7 @@ class GitHubFeatureFlags {
         // Do nothing when not running against github.com
         if (this.gitHubVersion.type !== util.GitHubVariant.DOTCOM) {
             this.logger.debug("Not running against github.com. Disabling all toggleable features.");
+            this.hasAccessedRemoteFeatureFlags = false;
             return {};
         }
         try {
@@ -265,6 +247,7 @@ class GitHubFeatureFlags {
             const remoteFlags = response.data;
             this.logger.debug("Loaded the following default values for the feature flags from the Code Scanning API: " +
                 `${JSON.stringify(remoteFlags)}`);
+            this.hasAccessedRemoteFeatureFlags = true;
             return remoteFlags;
         }
         catch (e) {
@@ -273,6 +256,7 @@ class GitHubFeatureFlags {
                     "As a result, it will not be opted into any experimental features. " +
                     "This could be because the Action is running on a pull request from a fork. If not, " +
                     `please ensure the Action has the 'security-events: write' permission. Details: ${e}`);
+                this.hasAccessedRemoteFeatureFlags = false;
                 return {};
             }
             else {
@@ -283,7 +267,6 @@ class GitHubFeatureFlags {
                 throw new Error(`Encountered an error while trying to determine feature enablement: ${e}`);
             }
         }
-        return {};
     }
 }
 //# sourceMappingURL=feature-flags.js.map

lib/init-action.js

@@ -46,12 +46,13 @@ async function sendInitStatusReport(actionStatus, startedAt, config, toolsDownlo
         tools_source: toolsSource || init_1.ToolsSource.Unknown,
         workflow_languages: workflowLanguages || "",
     };
-    let initToolsDownloadFields = {};
+    const initToolsDownloadFields = {};
-    if (toolsSource === init_1.ToolsSource.Download) {
+    if (toolsDownloadDurationMs !== undefined) {
-        initToolsDownloadFields = {
+        initToolsDownloadFields.tools_download_duration_ms =
-            tools_download_duration_ms: toolsDownloadDurationMs,
+            toolsDownloadDurationMs;
-            tools_feature_flags_valid: toolsFeatureFlagsValid,
+    }
-        };
+    if (toolsFeatureFlagsValid !== undefined) {
+        initToolsDownloadFields.tools_feature_flags_valid = toolsFeatureFlagsValid;
     }
     if (config !== undefined) {
         const languages = config.languages.join(",");
@@ -112,6 +113,7 @@ async function run() {
     const gitHubVersion = await (0, api_client_1.getGitHubVersion)();
     (0, util_1.checkGitHubVersionInRange)(gitHubVersion, logger);
     const repositoryNwo = (0, repository_1.parseRepositoryNwo)((0, util_1.getRequiredEnvParam)("GITHUB_REPOSITORY"));
+    const registriesInput = (0, actions_util_1.getOptionalInput)("registries");
     const features = new feature_flags_1.Features(gitHubVersion, repositoryNwo, (0, actions_util_1.getTemporaryDirectory)(), logger);
     try {
         const workflowErrors = await (0, workflow_1.validateWorkflow)();
@@ -122,13 +124,13 @@ async function run() {
         if (codeQLDefaultVersionInfo.variant === util_1.GitHubVariant.DOTCOM) {
             toolsFeatureFlagsValid = codeQLDefaultVersionInfo.toolsFeatureFlagsValid;
         }
-        const initCodeQLResult = await (0, init_1.initCodeQL)((0, actions_util_1.getOptionalInput)("tools"), apiDetails, (0, actions_util_1.getTemporaryDirectory)(), gitHubVersion.type, await (0, util_1.shouldBypassToolcache)(features, (0, actions_util_1.getOptionalInput)("tools"), (0, actions_util_1.getOptionalInput)("languages"), repositoryNwo, logger), codeQLDefaultVersionInfo, logger);
+        const initCodeQLResult = await (0, init_1.initCodeQL)((0, actions_util_1.getOptionalInput)("tools"), apiDetails, (0, actions_util_1.getTemporaryDirectory)(), gitHubVersion.type, codeQLDefaultVersionInfo, logger);
         codeql = initCodeQLResult.codeql;
         toolsDownloadDurationMs = initCodeQLResult.toolsDownloadDurationMs;
         toolsVersion = initCodeQLResult.toolsVersion;
         toolsSource = initCodeQLResult.toolsSource;
         await (0, util_1.enrichEnvironment)(codeql);
-        config = await (0, init_1.initConfig)((0, actions_util_1.getOptionalInput)("languages"), (0, actions_util_1.getOptionalInput)("queries"), (0, actions_util_1.getOptionalInput)("packs"), (0, actions_util_1.getOptionalInput)("registries"), (0, actions_util_1.getOptionalInput)("config-file"), (0, actions_util_1.getOptionalInput)("db-location"), await getTrapCachingEnabled(features), 
+        config = await (0, init_1.initConfig)((0, actions_util_1.getOptionalInput)("languages"), (0, actions_util_1.getOptionalInput)("queries"), (0, actions_util_1.getOptionalInput)("packs"), registriesInput, (0, actions_util_1.getOptionalInput)("config-file"), (0, actions_util_1.getOptionalInput)("db-location"), getTrapCachingEnabled(), 
         // Debug mode is enabled if:
         // - The `init` Action is passed `debug: true`.
         // - Actions step debugging is enabled (e.g. by [enabling debug logging for a rerun](https://docs.github.com/en/actions/managing-workflow-runs/re-running-workflows-and-jobs#re-running-all-the-jobs-in-a-workflow),
@@ -172,7 +174,7 @@ async function run() {
             core.exportVariable("CODEQL_EXTRACTOR_JAVA_AGENT_DISABLE_KOTLIN", "true");
         }
         const sourceRoot = path.resolve((0, util_1.getRequiredEnvParam)("GITHUB_WORKSPACE"), (0, actions_util_1.getOptionalInput)("source-root") || "");
-        const tracerConfig = await (0, init_1.runInit)(codeql, config, sourceRoot, "Runner.Worker.exe", features, logger);
+        const tracerConfig = await (0, init_1.runInit)(codeql, config, sourceRoot, "Runner.Worker.exe", registriesInput, features, apiDetails, logger);
         if (tracerConfig !== undefined) {
             for (const [key, value] of Object.entries(tracerConfig.env)) {
                 core.exportVariable(key, value);
@@ -192,7 +194,7 @@ async function run() {
     }
     await sendInitStatusReport("success", startedAt, config, toolsDownloadDurationMs, toolsFeatureFlagsValid, toolsSource, toolsVersion, logger);
 }
-async function getTrapCachingEnabled(featureEnablement) {
+function getTrapCachingEnabled() {
     // If the workflow specified something always respect that
     const trapCaching = (0, actions_util_1.getOptionalInput)("trap-caching");
     if (trapCaching !== undefined)
@@ -200,8 +202,8 @@ async function getTrapCachingEnabled(featureEnablement) {
     // On self-hosted runners which may have slow network access, disable TRAP caching by default
     if (!(0, util_1.isHostedRunner)())
         return false;
-    // On hosted runners, respect the feature flag
+    // On hosted runners, enable TRAP caching by default
-    return await featureEnablement.getValue(feature_flags_1.Feature.TrapCachingEnabled);
+    return true;
 }
 async function runWrapper() {
     try {

lib/init.js

@@ -41,9 +41,9 @@ var ToolsSource;
     ToolsSource["Toolcache"] = "TOOLCACHE";
     ToolsSource["Download"] = "DOWNLOAD";
 })(ToolsSource = exports.ToolsSource || (exports.ToolsSource = {}));
-async function initCodeQL(toolsInput, apiDetails, tempDir, variant, bypassToolcache, defaultCliVersion, logger) {
+async function initCodeQL(toolsInput, apiDetails, tempDir, variant, defaultCliVersion, logger) {
     logger.startGroup("Setup CodeQL tools");
-    const { codeql, toolsDownloadDurationMs, toolsSource, toolsVersion } = await (0, codeql_1.setupCodeQL)(toolsInput, apiDetails, tempDir, variant, bypassToolcache, defaultCliVersion, logger, true);
+    const { codeql, toolsDownloadDurationMs, toolsSource, toolsVersion } = await (0, codeql_1.setupCodeQL)(toolsInput, apiDetails, tempDir, variant, defaultCliVersion, logger, true);
     await codeql.printVersion();
     logger.endGroup();
     return { codeql, toolsDownloadDurationMs, toolsSource, toolsVersion };
@@ -57,12 +57,26 @@ async function initConfig(languagesInput, queriesInput, packsInput, registriesIn
     return config;
 }
 exports.initConfig = initConfig;
-async function runInit(codeql, config, sourceRoot, processName, featureEnablement, logger) {
+async function runInit(codeql, config, sourceRoot, processName, registriesInput, featureEnablement, apiDetails, logger) {
     fs.mkdirSync(config.dbLocation, { recursive: true });
     try {
         if (await (0, util_1.codeQlVersionAbove)(codeql, codeql_1.CODEQL_VERSION_NEW_TRACING)) {
+            // When parsing the codeql config in the CLI, we have not yet created the qlconfig file.
+            // So, create it now.
+            // If we are parsing the config file in the Action, then the qlconfig file was already created
+            // before the `pack download` command was invoked. It is not required for the init command.
+            let registriesAuthTokens;
+            let qlconfigFile;
+            if (await util.useCodeScanningConfigInCli(codeql, featureEnablement)) {
+                ({ registriesAuthTokens, qlconfigFile } =
+                    await configUtils.generateRegistries(registriesInput, codeql, config.tempDir, logger));
+            }
+            await configUtils.wrapEnvironment({
+                GITHUB_TOKEN: apiDetails.auth,
+                CODEQL_REGISTRIES_AUTH: registriesAuthTokens,
+            }, 
             // Init a database cluster
-            await codeql.databaseInitCluster(config, sourceRoot, processName, featureEnablement, logger);
+            async () => await codeql.databaseInitCluster(config, sourceRoot, processName, featureEnablement, qlconfigFile, logger));
         }
         else {
             for (const language of config.languages) {

lib/languages.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isScannedLanguage = exports.isTracedLanguage = exports.parseLanguage = exports.resolveAlias = exports.KOTLIN_SWIFT_BYPASS = exports.LANGUAGE_ALIASES = exports.Language = void 0;
+exports.isScannedLanguage = exports.isTracedLanguage = exports.parseLanguage = exports.resolveAlias = exports.LANGUAGE_ALIASES = exports.Language = void 0;
 // All the languages supported by CodeQL
 var Language;
 (function (Language) {
@@ -21,7 +21,6 @@ exports.LANGUAGE_ALIASES = {
     kotlin: Language.java,
     typescript: Language.javascript,
 };
-exports.KOTLIN_SWIFT_BYPASS = ["kotlin", "swift"];
 function resolveAlias(lang) {
     return exports.LANGUAGE_ALIASES[lang] || lang;
 }

lib/languages.js.map

@@ -1 +1 @@
-{"version":3,"file":"languages.js","sourceRoot":"","sources":["../src/languages.ts"],"names":[],"mappings":";;;AAAA,wCAAwC;AACxC,IAAY,QASX;AATD,WAAY,QAAQ;IAClB,6BAAiB,CAAA;IACjB,uBAAW,CAAA;IACX,qBAAS,CAAA;IACT,yBAAa,CAAA;IACb,qCAAyB,CAAA;IACzB,6BAAiB,CAAA;IACjB,yBAAa,CAAA;IACb,2BAAe,CAAA;AACjB,CAAC,EATW,QAAQ,GAAR,gBAAQ,KAAR,gBAAQ,QASnB;AAED,iCAAiC;AACpB,QAAA,gBAAgB,GAAiC;IAC5D,CAAC,EAAE,QAAQ,CAAC,GAAG;IACf,KAAK,EAAE,QAAQ,CAAC,GAAG;IACnB,IAAI,EAAE,QAAQ,CAAC,MAAM;IACrB,MAAM,EAAE,QAAQ,CAAC,IAAI;IACrB,UAAU,EAAE,QAAQ,CAAC,UAAU;CAChC,CAAC;AAIW,QAAA,mBAAmB,GAAG,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;AAEvD,SAAgB,YAAY,CAAC,IAAqB;IAChD,OAAO,wBAAgB,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC;AACxC,CAAC;AAFD,oCAEC;AAED;;;;;;;;;GASG;AACH,SAAgB,aAAa,CAAC,QAAgB;IAC5C,0BAA0B;IAC1B,QAAQ,GAAG,QAAQ,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IAEzC,6BAA6B;IAC7B,IAAI,QAAQ,IAAI,QAAQ,EAAE;QACxB,OAAO,QAAoB,CAAC;KAC7B;IAED,iEAAiE;IACjE,oCAAoC;IACpC,IAAI,QAAQ,IAAI,wBAAgB,EAAE;QAChC,OAAO,QAAQ,CAAC;KACjB;IAED,OAAO,SAAS,CAAC;AACnB,CAAC;AAhBD,sCAgBC;AAED,SAAgB,gBAAgB,CAAC,QAAkB;IACjD,OAAO;QACL,QAAQ,CAAC,GAAG;QACZ,QAAQ,CAAC,MAAM;QACf,QAAQ,CAAC,EAAE;QACX,QAAQ,CAAC,IAAI;QACb,QAAQ,CAAC,KAAK;KACf,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;AACvB,CAAC;AARD,4CAQC;AAED,SAAgB,iBAAiB,CAAC,QAAkB;IAClD,OAAO,CAAC,gBAAgB,CAAC,QAAQ,CAAC,CAAC;AACrC,CAAC;AAFD,8CAEC"}
+{"version":3,"file":"languages.js","sourceRoot":"","sources":["../src/languages.ts"],"names":[],"mappings":";;;AAAA,wCAAwC;AACxC,IAAY,QASX;AATD,WAAY,QAAQ;IAClB,6BAAiB,CAAA;IACjB,uBAAW,CAAA;IACX,qBAAS,CAAA;IACT,yBAAa,CAAA;IACb,qCAAyB,CAAA;IACzB,6BAAiB,CAAA;IACjB,yBAAa,CAAA;IACb,2BAAe,CAAA;AACjB,CAAC,EATW,QAAQ,GAAR,gBAAQ,KAAR,gBAAQ,QASnB;AAED,iCAAiC;AACpB,QAAA,gBAAgB,GAAiC;IAC5D,CAAC,EAAE,QAAQ,CAAC,GAAG;IACf,KAAK,EAAE,QAAQ,CAAC,GAAG;IACnB,IAAI,EAAE,QAAQ,CAAC,MAAM;IACrB,MAAM,EAAE,QAAQ,CAAC,IAAI;IACrB,UAAU,EAAE,QAAQ,CAAC,UAAU;CAChC,CAAC;AAIF,SAAgB,YAAY,CAAC,IAAqB;IAChD,OAAO,wBAAgB,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC;AACxC,CAAC;AAFD,oCAEC;AAED;;;;;;;;;GASG;AACH,SAAgB,aAAa,CAAC,QAAgB;IAC5C,0BAA0B;IAC1B,QAAQ,GAAG,QAAQ,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IAEzC,6BAA6B;IAC7B,IAAI,QAAQ,IAAI,QAAQ,EAAE;QACxB,OAAO,QAAoB,CAAC;KAC7B;IAED,iEAAiE;IACjE,oCAAoC;IACpC,IAAI,QAAQ,IAAI,wBAAgB,EAAE;QAChC,OAAO,QAAQ,CAAC;KACjB;IAED,OAAO,SAAS,CAAC;AACnB,CAAC;AAhBD,sCAgBC;AAED,SAAgB,gBAAgB,CAAC,QAAkB;IACjD,OAAO;QACL,QAAQ,CAAC,GAAG;QACZ,QAAQ,CAAC,MAAM;QACf,QAAQ,CAAC,EAAE;QACX,QAAQ,CAAC,IAAI;QACb,QAAQ,CAAC,KAAK;KACf,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;AACvB,CAAC;AARD,4CAQC;AAED,SAAgB,iBAAiB,CAAC,QAAkB;IAClD,OAAO,CAAC,gBAAgB,CAAC,QAAQ,CAAC,CAAC;AACrC,CAAC;AAFD,8CAEC"}

lib/setup-codeql.js

@@ -277,7 +277,7 @@ async function findOverridingToolsInCache(humanReadableVersion, logger) {
     }
     return undefined;
 }
-async function getCodeQLSource(toolsInput, bypassToolcache, defaultCliVersion, apiDetails, variant, logger) {
+async function getCodeQLSource(toolsInput, defaultCliVersion, apiDetails, variant, logger) {
     if (toolsInput && toolsInput !== "latest" && !toolsInput.startsWith("http")) {
         return {
             codeqlTarPath: toolsInput,
@@ -285,24 +285,17 @@ async function getCodeQLSource(toolsInput, bypassToolcache, defaultCliVersion, a
             toolsVersion: "local",
         };
     }
-    /** The reason why the tools shipped with the Action have been forced. */
+    /**
-    const forceShippedToolsReason = 
+     * Whether the tools shipped with the Action, i.e. those in `defaults.json`, have been forced.
-    // We use the special value of 'latest' to prioritize the version in the
+     *
-    // defaults over any pinned cached version.
+     * We use the special value of 'latest' to prioritize the version in `defaults.json` over the
-    toolsInput === "latest"
+     * version specified by the feature flags on Dotcom and over any pinned cached version on
-        ? '"tools: latest" was requested'
+     * Enterprise Server.
-        : // If the user hasn't requested a particular CodeQL version, then bypass
+     */
-            // the toolcache when the appropriate feature is enabled. This
+    const forceShippedTools = toolsInput === "latest";
-            // allows us to quickly rollback a broken bundle that has made its way
-            // into the toolcache.
-            toolsInput === undefined && bypassToolcache
-                ? "a specific version of the CodeQL tools was not requested and the bypass toolcache feature is enabled"
-                : undefined;
-    /** Whether the tools shipped with the Action, i.e. those in `defaults.json`, have been forced. */
-    const forceShippedTools = forceShippedToolsReason !== undefined;
     if (forceShippedTools) {
         logger.info("Overriding the version of the CodeQL tools by the version shipped with the Action since " +
-            `${forceShippedToolsReason}.`);
+            `"tools: latest" was requested.`);
     }
     /** CLI version number, for example 2.12.1. */
     let cliVersion;
@@ -530,15 +523,14 @@ exports.getCodeQLURLVersion = getCodeQLURLVersion;
  * @param apiDetails
  * @param tempDir
  * @param variant
- * @param bypassToolcache
  * @param defaultCliVersion
  * @param logger
  * @param checkVersion Whether to check that CodeQL CLI meets the minimum
  *        version requirement. Must be set to true outside tests.
  * @returns the path to the extracted bundle, and the version of the tools
  */
-async function setupCodeQLBundle(toolsInput, apiDetails, tempDir, variant, bypassToolcache, defaultCliVersion, logger) {
+async function setupCodeQLBundle(toolsInput, apiDetails, tempDir, variant, defaultCliVersion, logger) {
-    const source = await getCodeQLSource(toolsInput, bypassToolcache, defaultCliVersion, apiDetails, variant, logger);
+    const source = await getCodeQLSource(toolsInput, defaultCliVersion, apiDetails, variant, logger);
     let codeqlFolder;
     let toolsVersion = source.toolsVersion;
     let toolsDownloadDurationMs;

lib/upload-lib.js

@@ -293,7 +293,8 @@ async function waitForProcessing(repositoryNwo, sarifID, logger, options = {
             if (Date.now() >
                 statusCheckingStarted + STATUS_CHECK_TIMEOUT_MILLISECONDS) {
                 // If the analysis hasn't finished processing in the allotted time, we continue anyway rather than failing.
-                // It's possible the analysis will eventually finish processing, but it's not worth spending more Actions time waiting.
+                // It's possible the analysis will eventually finish processing, but it's not worth spending more
+                // Actions time waiting.
                 logger.warning("Timed out waiting for analysis to finish processing. Continuing.");
                 break;
             }
@@ -329,7 +330,9 @@ async function waitForProcessing(repositoryNwo, sarifID, logger, options = {
             else {
                 util.assertNever(status);
             }
-            await util.delay(STATUS_CHECK_FREQUENCY_MILLISECONDS);
+            await util.delay(STATUS_CHECK_FREQUENCY_MILLISECONDS, {
+                allowProcessExit: false,
+            });
         }
     }
     finally {

lib/util.js

@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseMatrixInput = exports.shouldBypassToolcache = exports.isHostedRunner = exports.checkForTimeout = exports.withTimeout = exports.tryGetFolderBytes = exports.listFolder = exports.doesDirectoryExist = exports.logCodeScanningConfigInCli = exports.useCodeScanningConfigInCli = exports.isInTestMode = exports.getMlPoweredJsQueriesStatus = exports.getMlPoweredJsQueriesPack = exports.ML_POWERED_JS_QUERIES_PACK_NAME = exports.isGoodVersion = exports.delay = exports.bundleDb = exports.codeQlVersionAbove = exports.getCachedCodeQlVersion = exports.cacheCodeQlVersion = exports.isHTTPError = exports.UserError = exports.HTTPError = exports.getRequiredEnvParam = exports.enrichEnvironment = exports.initializeEnvironment = exports.EnvVar = exports.assertNever = exports.apiVersionInRange = exports.DisallowedAPIVersionReason = exports.checkGitHubVersionInRange = exports.getGitHubVersion = exports.GitHubVariant = exports.parseGitHubUrl = exports.getCodeQLDatabasePath = exports.getThreadsFlag = exports.getThreadsFlagValue = exports.getAddSnippetsFlag = exports.getMemoryFlag = exports.getMemoryFlagValue = exports.withTmpDir = exports.getToolNames = exports.getExtraOptionsEnvParam = exports.DID_AUTOBUILD_GO_ENV_VAR_NAME = exports.DEFAULT_DEBUG_DATABASE_NAME = exports.DEFAULT_DEBUG_ARTIFACT_NAME = exports.GITHUB_DOTCOM_URL = void 0;
+exports.parseMatrixInput = exports.isHostedRunner = exports.checkForTimeout = exports.withTimeout = exports.tryGetFolderBytes = exports.listFolder = exports.doesDirectoryExist = exports.logCodeScanningConfigInCli = exports.useCodeScanningConfigInCli = exports.isInTestMode = exports.getMlPoweredJsQueriesStatus = exports.getMlPoweredJsQueriesPack = exports.ML_POWERED_JS_QUERIES_PACK_NAME = exports.supportExpectDiscardedCache = exports.isGoodVersion = exports.delay = exports.bundleDb = exports.codeQlVersionAbove = exports.getCachedCodeQlVersion = exports.cacheCodeQlVersion = exports.isHTTPError = exports.UserError = exports.HTTPError = exports.getRequiredEnvParam = exports.enrichEnvironment = exports.initializeEnvironment = exports.EnvVar = exports.assertNever = exports.apiVersionInRange = exports.DisallowedAPIVersionReason = exports.checkGitHubVersionInRange = exports.getGitHubVersion = exports.GitHubVariant = exports.parseGitHubUrl = exports.getCodeQLDatabasePath = exports.getThreadsFlag = exports.getThreadsFlagValue = exports.getAddSnippetsFlag = exports.getMemoryFlag = exports.getMemoryFlagValue = exports.withTmpDir = exports.getToolNames = exports.getExtraOptionsEnvParam = exports.DID_AUTOBUILD_GO_ENV_VAR_NAME = exports.DEFAULT_DEBUG_DATABASE_NAME = exports.DEFAULT_DEBUG_ARTIFACT_NAME = exports.GITHUB_DOTCOM_URL = void 0;
 const fs = __importStar(require("fs"));
 const os = __importStar(require("os"));
 const path = __importStar(require("path"));
@@ -40,7 +40,6 @@ const apiCompatibility = __importStar(require("./api-compatibility.json"));
 const codeql_1 = require("./codeql");
 const config_utils_1 = require("./config-utils");
 const feature_flags_1 = require("./feature-flags");
-const languages_1 = require("./languages");
 const shared_environment_1 = require("./shared-environment");
 /**
  * Specifies bundle versions that are known to be broken
@@ -456,16 +455,33 @@ async function bundleDb(config, language, codeql, dbName) {
     return databaseBundlePath;
 }
 exports.bundleDb = bundleDb;
-async function delay(milliseconds) {
+/**
-    // Immediately `unref` the timer such that it only prevents the process from exiting if the
+ * @param milliseconds time to delay
-    // surrounding promise is being awaited.
+ * @param opts options
-    return new Promise((resolve) => setTimeout(resolve, milliseconds).unref());
+ * @param opts.allowProcessExit if true, the timer will not prevent the process from exiting
+ */
+async function delay(milliseconds, { allowProcessExit }) {
+    return new Promise((resolve) => {
+        const timer = setTimeout(resolve, milliseconds);
+        if (allowProcessExit) {
+            // Immediately `unref` the timer such that it only prevents the process from exiting if the
+            // surrounding promise is being awaited.
+            timer.unref();
+        }
+    });
 }
 exports.delay = delay;
 function isGoodVersion(versionSpec) {
     return !BROKEN_VERSIONS.includes(versionSpec);
 }
 exports.isGoodVersion = isGoodVersion;
+/**
+ * Checks whether the CodeQL CLI supports the `--expect-discarded-cache` command-line flag.
+ */
+async function supportExpectDiscardedCache(codeQL) {
+    return codeQlVersionAbove(codeQL, "2.12.1");
+}
+exports.supportExpectDiscardedCache = supportExpectDiscardedCache;
 exports.ML_POWERED_JS_QUERIES_PACK_NAME = "codeql/javascript-experimental-atm-queries";
 /**
  * Gets the ML-powered JS query pack to add to the analysis if a repo is opted into the ML-powered
@@ -637,7 +653,7 @@ async function withTimeout(timeoutMs, promise, onTimeout) {
         return result;
     };
     const timeoutTask = async () => {
-        await delay(timeoutMs);
+        await delay(timeoutMs, { allowProcessExit: true });
         if (!finished) {
             // Workaround: While the promise racing below will allow the main code
             // to continue, the process won't normally exit until the asynchronous
@@ -660,7 +676,7 @@ exports.withTimeout = withTimeout;
 async function checkForTimeout() {
     if (hadTimeout === true) {
         core.info("A timeout occurred, force exiting the process after 30 seconds to prevent hanging.");
-        await delay(30000);
+        await delay(30000, { allowProcessExit: true });
         process.exit();
     }
 }
@@ -685,45 +701,6 @@ function isHostedRunner() {
         process.env["RUNNER_TOOL_CACHE"]?.includes("hostedtoolcache"));
 }
 exports.isHostedRunner = isHostedRunner;
-/**
- *
- * @param featuresEnablement The features enabled for the current run
- * @param languagesInput Languages input from the workflow
- * @param repository The owner/name of the repository
- * @param logger A logger
- * @returns A boolean indicating whether or not the toolcache should be bypassed and the latest codeql should be downloaded.
- */
-async function shouldBypassToolcache(featuresEnablement, codeqlUrl, languagesInput, repository, logger) {
-    // An explicit codeql url is specified, that means the toolcache will not be used.
-    if (codeqlUrl) {
-        return true;
-    }
-    // Check if the toolcache is disabled for all languages
-    if (await featuresEnablement.getValue(feature_flags_1.Feature.BypassToolcacheEnabled)) {
-        return true;
-    }
-    // Check if the toolcache is disabled for kotlin and swift.
-    if (!(await featuresEnablement.getValue(feature_flags_1.Feature.BypassToolcacheKotlinSwiftEnabled))) {
-        return false;
-    }
-    // Now check to see if kotlin or swift is one of the languages being analyzed.
-    const { rawLanguages, autodetected } = await (0, config_utils_1.getRawLanguages)(languagesInput, repository, logger);
-    let bypass = rawLanguages.some((lang) => languages_1.KOTLIN_SWIFT_BYPASS.includes(lang));
-    if (bypass) {
-        logger.info(`Bypassing toolcache for kotlin or swift. Languages: ${rawLanguages}`);
-    }
-    else if (!autodetected && rawLanguages.includes(languages_1.Language.java)) {
-        // special case: java was explicitly specified, but there might be
-        // some kotlin in the repository, so we need to make a request for that.
-        const langsInRepo = await (0, config_utils_1.getLanguagesInRepo)(repository, logger);
-        if (langsInRepo.includes("kotlin")) {
-            logger.info(`Bypassing toolcache for kotlin.`);
-            bypass = true;
-        }
-    }
-    return bypass;
-}
-exports.shouldBypassToolcache = shouldBypassToolcache;
 function parseMatrixInput(matrixInput) {
     if (matrixInput === undefined || matrixInput === "null") {
         return undefined;

lib/util.test.js

@@ -33,9 +33,7 @@ const github = __importStar(require("@actions/github"));
 const ava_1 = __importDefault(require("ava"));
 const sinon = __importStar(require("sinon"));
 const api = __importStar(require("./api-client"));
-const feature_flags_1 = require("./feature-flags");
 const logging_1 = require("./logging");
-const repository_1 = require("./repository");
 const testing_utils_1 = require("./testing-utils");
 const util = __importStar(require("./util"));
 (0, testing_utils_1.setupTests)(ava_1.default);
@@ -325,117 +323,4 @@ const shortTime = 10;
     t.deepEqual(shortTaskTimedOut, false);
     t.deepEqual(result, 99);
 });
-const mockRepositoryNwo = (0, repository_1.parseRepositoryNwo)("owner/repo");
-// eslint-disable-next-line github/array-foreach
-[
-    {
-        name: "disabled",
-        features: [],
-        hasCustomCodeQL: false,
-        languagesInput: undefined,
-        languagesInRepository: [],
-        expected: false,
-        expectedApiCall: false,
-    },
-    {
-        name: "disabled even though swift kotlin bypassed",
-        features: [feature_flags_1.Feature.BypassToolcacheKotlinSwiftEnabled],
-        hasCustomCodeQL: false,
-        languagesInput: undefined,
-        languagesInRepository: [],
-        expected: false,
-        expectedApiCall: true,
-    },
-    {
-        name: "disabled even though swift kotlin analyzed",
-        features: [],
-        hasCustomCodeQL: false,
-        languagesInput: " sWiFt , KoTlIn ",
-        languagesInRepository: [],
-        expected: false,
-        expectedApiCall: false,
-    },
-    {
-        name: "toolcache bypass all",
-        features: [feature_flags_1.Feature.BypassToolcacheEnabled],
-        hasCustomCodeQL: false,
-        languagesInput: undefined,
-        languagesInRepository: [],
-        expected: true,
-        expectedApiCall: false,
-    },
-    {
-        name: "custom CodeQL",
-        features: [],
-        hasCustomCodeQL: true,
-        languagesInput: undefined,
-        languagesInRepository: [],
-        expected: true,
-        expectedApiCall: false,
-    },
-    {
-        name: "bypass swift",
-        features: [feature_flags_1.Feature.BypassToolcacheKotlinSwiftEnabled],
-        hasCustomCodeQL: false,
-        languagesInput: " sWiFt ,other",
-        languagesInRepository: [],
-        expected: true,
-        expectedApiCall: false,
-    },
-    {
-        name: "bypass kotlin",
-        features: [feature_flags_1.Feature.BypassToolcacheKotlinSwiftEnabled],
-        hasCustomCodeQL: false,
-        languagesInput: "other, KoTlIn ",
-        languagesInRepository: [],
-        expected: true,
-        expectedApiCall: false,
-    },
-    {
-        name: "bypass kotlin language from repository",
-        features: [feature_flags_1.Feature.BypassToolcacheKotlinSwiftEnabled],
-        hasCustomCodeQL: false,
-        languagesInput: "",
-        languagesInRepository: ["KoTlIn", "other"],
-        expected: true,
-        expectedApiCall: true,
-    },
-    {
-        name: "bypass swift language from repository",
-        features: [feature_flags_1.Feature.BypassToolcacheKotlinSwiftEnabled],
-        hasCustomCodeQL: false,
-        languagesInput: "",
-        languagesInRepository: ["SwiFt", "other"],
-        expected: true,
-        expectedApiCall: true,
-    },
-    {
-        name: "bypass java from input if there is kotlin in repository",
-        features: [feature_flags_1.Feature.BypassToolcacheKotlinSwiftEnabled],
-        hasCustomCodeQL: false,
-        languagesInput: "java",
-        languagesInRepository: ["kotlin", "other"],
-        expected: true,
-        expectedApiCall: true,
-    },
-    {
-        name: "don't bypass java from input if there is no kotlin in repository",
-        features: [feature_flags_1.Feature.BypassToolcacheKotlinSwiftEnabled],
-        hasCustomCodeQL: false,
-        languagesInput: "java",
-        languagesInRepository: ["java", "other"],
-        expected: false,
-        expectedApiCall: true,
-    },
-].forEach((args) => {
-    (0, ava_1.default)(`shouldBypassToolcache: ${args.name}`, async (t) => {
-        const mockRequest = (0, testing_utils_1.mockLanguagesInRepo)(args.languagesInRepository);
-        const mockLogger = (0, logging_1.getRunnerLogger)(true);
-        const featureEnablement = (0, testing_utils_1.createFeatures)(args.features);
-        const codeqlUrl = args.hasCustomCodeQL ? "custom-codeql-url" : undefined;
-        const actual = await util.shouldBypassToolcache(featureEnablement, codeqlUrl, args.languagesInput, mockRepositoryNwo, mockLogger);
-        t.deepEqual(actual, args.expected);
-        t.deepEqual(mockRequest.called, args.expectedApiCall);
-    });
-});
 //# sourceMappingURL=util.test.js.map

node_modules/.package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "codeql",
-  "version": "2.2.2",
+  "version": "2.2.6",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {

package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "codeql",
-  "version": "2.2.2",
+  "version": "2.2.6",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "codeql",
-      "version": "2.2.2",
+      "version": "2.2.6",
       "license": "MIT",
       "dependencies": {
         "@actions/artifact": "^1.1.0",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "codeql",
-  "version": "2.2.2",
+  "version": "2.2.6",
   "private": true,
   "description": "CodeQL action",
   "scripts": {

pr-checks/checks/init-with-registries.yml

@@ -4,7 +4,12 @@
 # basic mechanics of multi-registry auth is working.
 name: "Packaging: Download using registries"
 description: "Checks that specifying a registries block and associated auth works as expected"
-versions: ["nightly-latest"] # This feature is not compatible with old CLIs
+versions: [
+    # This feature is not compatible with older CLIs
+    "cached",
+    "latest",
+    "nightly-latest",
+]
 
 steps:
   - name: Init with registries
@@ -40,3 +45,33 @@ steps:
           echo "::error $CODEQL_PACK1 pack was not installed."
           exit 1
       fi
+
+  - name: Verify qlconfig.yml file was created
+    shell: bash
+    run: |
+      QLCONFIG_PATH=$RUNNER_TEMP/qlconfig.yml
+      echo "Expected qlconfig.yml file to be created at $QLCONFIG_PATH"
+      if [[ -f $QLCONFIG_PATH ]]
+      then
+          echo "qlconfig.yml file was created."
+      else
+          echo "::error qlconfig.yml file was not created."
+          exit 1
+      fi
+
+  - name: Verify contents of qlconfig.yml
+    # yq is not available on windows
+    if: runner.os != 'Windows'
+    shell: bash
+    run: |
+      QLCONFIG_PATH=$RUNNER_TEMP/qlconfig.yml
+      cat $QLCONFIG_PATH | yq -e '.registries[] | select(.url == "https://ghcr.io/v2/") | select(.packages == "*/*")'
+      if [[ $? -eq 0 ]]
+      then
+          echo "Registry was added to qlconfig.yml file."
+      else
+          echo "::error Registry was not added to qlconfig.yml file."
+          echo "Contents of qlconfig.yml file:"
+          cat $QLCONFIG_PATH
+          exit 1
+      fi

src/analyze.test.ts

@@ -3,15 +3,18 @@ import * as path from "path";
 
 import test, { ExecutionContext } from "ava";
 import * as yaml from "js-yaml";
+import * as sinon from "sinon";
 
 import {
   convertPackToQuerySuiteEntry,
   createQuerySuiteContents,
   runQueries,
   validateQueryFilters,
+  QueriesStatusReport,
 } from "./analyze";
-import { setCodeQL } from "./codeql";
+import { CodeQL, setCodeQL } from "./codeql";
-import { Config } from "./config-utils";
+import { Config, QueriesWithSearchPath } from "./config-utils";
+import { Feature } from "./feature-flags";
 import { Language } from "./languages";
 import { getRunnerLogger } from "./logging";
 import { setupTests, setupActionsVars, createFeatures } from "./testing-utils";
@@ -229,6 +232,175 @@ test("status report fields and search path setting", async (t) => {
   }
 });
 
+function mockCodeQL(): Partial<CodeQL> {
+  return {
+    getVersion: async () => "2.12.2",
+    databaseRunQueries: sinon.spy(),
+    databaseInterpretResults: async () => "",
+    databasePrintBaseline: async () => "",
+  };
+}
+
+function createBaseConfig(tmpDir: string): Config {
+  return {
+    languages: [],
+    queries: {},
+    pathsIgnore: [],
+    paths: [],
+    originalUserInput: {},
+    tempDir: "tempDir",
+    codeQLCmd: "",
+    gitHubVersion: {
+      type: util.GitHubVariant.DOTCOM,
+    } as util.GitHubVersion,
+    dbLocation: path.resolve(tmpDir, "codeql_databases"),
+    packs: {},
+    debugMode: false,
+    debugArtifactName: util.DEFAULT_DEBUG_ARTIFACT_NAME,
+    debugDatabaseName: util.DEFAULT_DEBUG_DATABASE_NAME,
+    augmentationProperties: {
+      injectedMlQueries: false,
+      packsInputCombines: false,
+      queriesInputCombines: false,
+    },
+    trapCaches: {},
+    trapCacheDownloadTime: 0,
+  };
+}
+
+function createQueryConfig(
+  builtin: string[],
+  custom: string[]
+): { builtin: string[]; custom: QueriesWithSearchPath[] } {
+  return {
+    builtin,
+    custom: custom.map((c) => ({ searchPath: "/search", queries: [c] })),
+  };
+}
+
+async function runQueriesWithConfig(
+  config: Config,
+  features: Feature[]
+): Promise<QueriesStatusReport> {
+  for (const language of config.languages) {
+    fs.mkdirSync(util.getCodeQLDatabasePath(config, language), {
+      recursive: true,
+    });
+  }
+  return runQueries(
+    "sarif-folder",
+    "--memFlag",
+    "--addSnippetsFlag",
+    "--threadsFlag",
+    undefined,
+    config,
+    getRunnerLogger(true),
+    createFeatures(features)
+  );
+}
+
+function getDatabaseRunQueriesCalls(mock: Partial<CodeQL>) {
+  return (mock.databaseRunQueries as sinon.SinonSpy).getCalls();
+}
+
+test("optimizeForLastQueryRun for one language", async (t) => {
+  return await util.withTmpDir(async (tmpDir) => {
+    const codeql = mockCodeQL();
+    setCodeQL(codeql);
+    const config: Config = createBaseConfig(tmpDir);
+    config.languages = [Language.cpp];
+    config.queries.cpp = createQueryConfig(["foo.ql"], []);
+
+    await runQueriesWithConfig(config, []);
+    t.deepEqual(
+      getDatabaseRunQueriesCalls(codeql).map((c) => c.args[4]),
+      [true]
+    );
+  });
+});
+
+test("optimizeForLastQueryRun for two languages", async (t) => {
+  return await util.withTmpDir(async (tmpDir) => {
+    const codeql = mockCodeQL();
+    setCodeQL(codeql);
+    const config: Config = createBaseConfig(tmpDir);
+    config.languages = [Language.cpp, Language.java];
+    config.queries.cpp = createQueryConfig(["foo.ql"], []);
+    config.queries.java = createQueryConfig(["bar.ql"], []);
+
+    await runQueriesWithConfig(config, []);
+    t.deepEqual(
+      getDatabaseRunQueriesCalls(codeql).map((c) => c.args[4]),
+      [true, true]
+    );
+  });
+});
+
+test("optimizeForLastQueryRun for two languages, with custom queries", async (t) => {
+  return await util.withTmpDir(async (tmpDir) => {
+    const codeql = mockCodeQL();
+    setCodeQL(codeql);
+    const config: Config = createBaseConfig(tmpDir);
+    config.languages = [Language.cpp, Language.java];
+    config.queries.cpp = createQueryConfig(["foo.ql"], ["c1.ql", "c2.ql"]);
+    config.queries.java = createQueryConfig(["bar.ql"], ["c3.ql"]);
+
+    await runQueriesWithConfig(config, []);
+    t.deepEqual(
+      getDatabaseRunQueriesCalls(codeql).map((c) => c.args[4]),
+      [false, false, true, false, true]
+    );
+  });
+});
+
+test("optimizeForLastQueryRun for two languages, with custom queries and packs", async (t) => {
+  return await util.withTmpDir(async (tmpDir) => {
+    const codeql = mockCodeQL();
+    setCodeQL(codeql);
+    const config: Config = createBaseConfig(tmpDir);
+    config.languages = [Language.cpp, Language.java];
+    config.queries.cpp = createQueryConfig(["foo.ql"], ["c1.ql", "c2.ql"]);
+    config.queries.java = createQueryConfig(["bar.ql"], ["c3.ql"]);
+    config.packs.cpp = ["a/cpp-pack1@0.1.0"];
+    config.packs.java = ["b/java-pack1@0.2.0", "b/java-pack2@0.3.3"];
+    await runQueriesWithConfig(config, []);
+    t.deepEqual(
+      getDatabaseRunQueriesCalls(codeql).map((c) => c.args[4]),
+      [false, false, false, true, false, false, true]
+    );
+  });
+});
+
+test("optimizeForLastQueryRun for one language, CliConfigFileEnabled", async (t) => {
+  return await util.withTmpDir(async (tmpDir) => {
+    const codeql = mockCodeQL();
+    setCodeQL(codeql);
+    const config: Config = createBaseConfig(tmpDir);
+    config.languages = [Language.cpp];
+
+    await runQueriesWithConfig(config, [Feature.CliConfigFileEnabled]);
+    t.deepEqual(
+      getDatabaseRunQueriesCalls(codeql).map((c) => c.args[4]),
+      [true]
+    );
+  });
+});
+
+test("optimizeForLastQueryRun for two languages, CliConfigFileEnabled", async (t) => {
+  return await util.withTmpDir(async (tmpDir) => {
+    const codeql = mockCodeQL();
+    setCodeQL(codeql);
+    const config: Config = createBaseConfig(tmpDir);
+    config.languages = [Language.cpp, Language.java];
+
+    await runQueriesWithConfig(config, [Feature.CliConfigFileEnabled]);
+    t.deepEqual(
+      getDatabaseRunQueriesCalls(codeql).map((c) => c.args[4]),
+      [true, true]
+    );
+  });
+});
+
 test("validateQueryFilters", (t) => {
   t.notThrows(() => validateQueryFilters([]));
   t.notThrows(() => validateQueryFilters(undefined));

src/analyze.ts

@@ -212,6 +212,7 @@ export async function runQueries(
   const statusReport: QueriesStatusReport = {};
 
   const codeql = await getCodeQL(config.codeQLCmd);
+  const queryFlags = [memoryFlag, threadsFlag];
 
   await util.logCodeScanningConfigInCli(codeql, featureEnablement, logger);
 
@@ -231,7 +232,7 @@ export async function runQueries(
         // another to interpret the results.
         logger.startGroup(`Running queries for ${language}`);
         const startTimeBuiltIn = new Date().getTime();
-        await runQueryGroup(language, "all", undefined, undefined);
+        await runQueryGroup(language, "all", undefined, undefined, true);
         // TODO should not be using `builtin` here. We should be using `all` instead.
         // The status report does not support `all` yet.
         statusReport[`analyze_builtin_queries_${language}_duration_ms`] =
@@ -267,16 +268,24 @@ export async function runQueries(
           );
         }
 
+        const customQueryIndices: number[] = [];
+        for (let i = 0; i < queries.custom.length; ++i) {
+          if (queries.custom[i].queries.length > 0) {
+            customQueryIndices.push(i);
+          }
+        }
+
         logger.startGroup(`Running queries for ${language}`);
         const querySuitePaths: string[] = [];
-        if (queries["builtin"].length > 0) {
+        if (queries.builtin.length > 0) {
           const startTimeBuiltIn = new Date().getTime();
           querySuitePaths.push(
             (await runQueryGroup(
               language,
               "builtin",
-              createQuerySuiteContents(queries["builtin"], queryFilters),
+              createQuerySuiteContents(queries.builtin, queryFilters),
-              undefined
+              undefined,
+              customQueryIndices.length === 0 && packsWithVersion.length === 0
             )) as string
           );
           statusReport[`analyze_builtin_queries_${language}_duration_ms`] =
@@ -284,21 +293,18 @@ export async function runQueries(
         }
         const startTimeCustom = new Date().getTime();
         let ranCustom = false;
-        for (let i = 0; i < queries["custom"].length; ++i) {
+        for (const i of customQueryIndices) {
-          if (queries["custom"][i].queries.length > 0) {
+          querySuitePaths.push(
-            querySuitePaths.push(
+            (await runQueryGroup(
-              (await runQueryGroup(
+              language,
-                language,
+              `custom-${i}`,
-                `custom-${i}`,
+              createQuerySuiteContents(queries.custom[i].queries, queryFilters),
-                createQuerySuiteContents(
+              queries.custom[i].searchPath,
-                  queries["custom"][i].queries,
+              i === customQueryIndices[customQueryIndices.length - 1] &&
-                  queryFilters
+                packsWithVersion.length === 0
-                ),
+            )) as string
-                queries["custom"][i].searchPath
+          );
-              )) as string
+          ranCustom = true;
-            );
-            ranCustom = true;
-          }
         }
         if (packsWithVersion.length > 0) {
           querySuitePaths.push(
@@ -306,7 +312,8 @@ export async function runQueries(
               language,
               "packs",
               packsWithVersion,
-              queryFilters
+              queryFilters,
+              true
             )
           );
           ranCustom = true;
@@ -373,7 +380,8 @@ export async function runQueries(
     language: Language,
     type: string,
     querySuiteContents: string | undefined,
-    searchPath: string | undefined
+    searchPath: string | undefined,
+    optimizeForLastQueryRun: boolean
   ): Promise<string | undefined> {
     const databasePath = util.getCodeQLDatabasePath(config, language);
     // Pass the queries to codeql using a file instead of using the command
@@ -391,8 +399,8 @@ export async function runQueries(
       databasePath,
       searchPath,
       querySuitePath,
-      memoryFlag,
+      queryFlags,
-      threadsFlag
+      optimizeForLastQueryRun
     );
 
     logger.debug(`BQRS results produced for ${language} (queries: ${type})"`);
@@ -402,7 +410,8 @@ export async function runQueries(
     language: Language,
     type: string,
     packs: string[],
-    queryFilters: configUtils.QueryFilter[]
+    queryFilters: configUtils.QueryFilter[],
+    optimizeForLastQueryRun: boolean
   ): Promise<string> {
     const databasePath = util.getCodeQLDatabasePath(config, language);
 
@@ -424,8 +433,8 @@ export async function runQueries(
       databasePath,
       undefined,
       querySuitePath,
-      memoryFlag,
+      queryFlags,
-      threadsFlag
+      optimizeForLastQueryRun
     );
 
     return querySuitePath;

src/codeql.test.ts

@@ -143,7 +143,6 @@ async function installIntoToolcache({
     apiDetails,
     tmpDir,
     util.GitHubVariant.GHES,
-    false,
     cliVersion !== undefined
       ? { cliVersion, tagName, variant: util.GitHubVariant.GHES }
       : SAMPLE_DEFAULT_CLI_VERSION,
@@ -205,7 +204,6 @@ test("downloads and caches explicitly requested bundles that aren't in the toolc
         sampleApiDetails,
         tmpDir,
         util.GitHubVariant.DOTCOM,
-        false,
         SAMPLE_DEFAULT_CLI_VERSION,
         getRunnerLogger(true),
         false
@@ -239,7 +237,6 @@ test("downloads an explicitly requested bundle even if a different version is ca
       sampleApiDetails,
       tmpDir,
       util.GitHubVariant.DOTCOM,
-      false,
       SAMPLE_DEFAULT_CLI_VERSION,
       getRunnerLogger(true),
       false
@@ -290,7 +287,6 @@ for (const {
         sampleApiDetails,
         tmpDir,
         util.GitHubVariant.DOTCOM,
-        false,
         SAMPLE_DEFAULT_CLI_VERSION,
         getRunnerLogger(true),
         false
@@ -358,7 +354,6 @@ for (const { githubReleases, toolcacheVersion } of [
           sampleApiDetails,
           tmpDir,
           util.GitHubVariant.DOTCOM,
-          false,
           SAMPLE_DEFAULT_CLI_VERSION,
           getRunnerLogger(true),
           false
@@ -387,7 +382,6 @@ for (const variant of [util.GitHubVariant.GHAE, util.GitHubVariant.GHES]) {
         sampleApiDetails,
         tmpDir,
         variant,
-        false,
         {
           cliVersion: defaults.cliVersion,
           tagName: defaults.bundleVersion,
@@ -423,7 +417,6 @@ for (const variant of [util.GitHubVariant.GHAE, util.GitHubVariant.GHES]) {
         sampleApiDetails,
         tmpDir,
         variant,
-        false,
         {
           cliVersion: defaults.cliVersion,
           tagName: defaults.bundleVersion,
@@ -460,7 +453,6 @@ test('downloads bundle if "latest" tools specified but not cached', async (t) =>
       sampleApiDetails,
       tmpDir,
       util.GitHubVariant.DOTCOM,
-      false,
       SAMPLE_DEFAULT_CLI_VERSION,
       getRunnerLogger(true),
       false
@@ -533,7 +525,6 @@ for (const isBundleVersionInUrl of [true, false]) {
         sampleGHAEApiDetails,
         tmpDir,
         util.GitHubVariant.GHAE,
-        false,
         {
           cliVersion: defaults.cliVersion,
           tagName: defaults.bundleVersion,
@@ -573,7 +564,6 @@ test("bundle URL from another repo is cached as 0.0.0-bundleVersion", async (t)
       sampleApiDetails,
       tmpDir,
       util.GitHubVariant.DOTCOM,
-      false,
       SAMPLE_DEFAULT_CLI_VERSION,
       getRunnerLogger(true),
       false
@@ -681,6 +671,7 @@ test("databaseInitCluster() without injected codescanning config", async (t) =>
       "",
       undefined,
       createFeatures([]),
+      "/path/to/qlconfig.yml",
       getRunnerLogger(true)
     );
 
@@ -689,7 +680,7 @@ test("databaseInitCluster() without injected codescanning config", async (t) =>
     const configArg = args.find((arg: string) =>
       arg.startsWith("--codescanning-config=")
     );
-    t.falsy(configArg, "Should have injected a codescanning config");
+    t.falsy(configArg, "Should NOT have injected a codescanning config");
   });
 });
 
@@ -720,6 +711,7 @@ const injectedConfigMacro = test.macro({
         "",
         undefined,
         createFeatures([Feature.CliConfigFileEnabled]),
+        undefined,
         getRunnerLogger(true)
       );
 
@@ -1010,34 +1002,90 @@ test(
   {}
 );
 
-test("does not use injected config", async (t: ExecutionContext<unknown>) => {
+test("does not pass a code scanning config or qlconfig file to the CLI when CLI config passing is disabled", async (t: ExecutionContext<unknown>) => {
-  const origCODEQL_PASS_CONFIG_TO_CLI = process.env.CODEQL_PASS_CONFIG_TO_CLI;
+  const runnerConstructorStub = stubToolRunnerConstructor();
-  process.env["CODEQL_PASS_CONFIG_TO_CLI"] = "false";
+  const codeqlObject = await codeql.getCodeQLForTesting();
+  // stubbed version doesn't matter. It just needs to be valid semver.
+  sinon.stub(codeqlObject, "getVersion").resolves("0.0.0");
 
-  try {
+  await codeqlObject.databaseInitCluster(
-    const runnerConstructorStub = stubToolRunnerConstructor();
+    stubConfig,
-    const codeqlObject = await codeql.getCodeQLForTesting();
+    "",
-    sinon
+    undefined,
-      .stub(codeqlObject, "getVersion")
+    createFeatures([]),
-      .resolves(featureConfig[Feature.CliConfigFileEnabled].minimumVersion);
+    "/path/to/qlconfig.yml",
+    getRunnerLogger(true)
+  );
 
-    await codeqlObject.databaseInitCluster(
+  const args = runnerConstructorStub.firstCall.args[1];
-      stubConfig,
+  // should not have used a config file
-      "",
+  const hasConfigArg = args.some((arg: string) =>
-      undefined,
+    arg.startsWith("--codescanning-config=")
-      createFeatures([]),
+  );
-      getRunnerLogger(true)
+  t.false(hasConfigArg, "Should NOT have injected a codescanning config");
-    );
 
-    const args = runnerConstructorStub.firstCall.args[1];
+  // should not have passed a qlconfig file
-    // should have used an config file
+  const hasQlconfigArg = args.some((arg: string) =>
-    const configArg = args.find((arg: string) =>
+    arg.startsWith("--qlconfig=")
-      arg.startsWith("--codescanning-config=")
+  );
-    );
+  t.false(hasQlconfigArg, "Should NOT have passed a qlconfig file");
-    t.falsy(configArg, "Should NOT have injected a codescanning config");
+});
-  } finally {
+
-    process.env["CODEQL_PASS_CONFIG_TO_CLI"] = origCODEQL_PASS_CONFIG_TO_CLI;
+test("passes a code scanning config AND qlconfig to the CLI when CLI config passing is enabled", async (t: ExecutionContext<unknown>) => {
-  }
+  const runnerConstructorStub = stubToolRunnerConstructor();
+  const codeqlObject = await codeql.getCodeQLForTesting();
+  sinon
+    .stub(codeqlObject, "getVersion")
+    .resolves(codeql.CODEQL_VERSION_INIT_WITH_QLCONFIG);
+
+  await codeqlObject.databaseInitCluster(
+    stubConfig,
+    "",
+    undefined,
+    createFeatures([Feature.CliConfigFileEnabled]),
+    "/path/to/qlconfig.yml",
+    getRunnerLogger(true)
+  );
+
+  const args = runnerConstructorStub.firstCall.args[1];
+  // should have used a config file
+  const hasCodeScanningConfigArg = args.some((arg: string) =>
+    arg.startsWith("--codescanning-config=")
+  );
+  t.true(hasCodeScanningConfigArg, "Should have injected a qlconfig");
+
+  // should have passed a qlconfig file
+  const hasQlconfigArg = args.some((arg: string) =>
+    arg.startsWith("--qlconfig=")
+  );
+  t.truthy(hasQlconfigArg, "Should have injected a codescanning config");
+});
+test("passes a code scanning config BUT NOT a qlconfig to the CLI when CLI config passing is enabled", async (t: ExecutionContext<unknown>) => {
+  const runnerConstructorStub = stubToolRunnerConstructor();
+  const codeqlObject = await codeql.getCodeQLForTesting();
+  sinon.stub(codeqlObject, "getVersion").resolves("2.12.2");
+
+  await codeqlObject.databaseInitCluster(
+    stubConfig,
+    "",
+    undefined,
+    createFeatures([Feature.CliConfigFileEnabled]),
+    "/path/to/qlconfig.yml",
+    getRunnerLogger(true)
+  );
+
+  const args = runnerConstructorStub.firstCall.args[1] as any[];
+  // should have used a config file
+  const hasCodeScanningConfigArg = args.some((arg: string) =>
+    arg.startsWith("--codescanning-config=")
+  );
+  t.true(hasCodeScanningConfigArg, "Should NOT have injected a qlconfig");
+
+  // should have passed a qlconfig file
+  const hasQlconfigArg = args.some((arg: string) =>
+    arg.startsWith("--qlconfig=")
+  );
+  t.false(hasQlconfigArg, "Should have injected a codescanning config");
 });
 
 test("databaseInterpretResults() sets --sarif-add-baseline-file-info for 2.11.3", async (t) => {

src/codeql.ts

@@ -91,6 +91,7 @@ export interface CodeQL {
     sourceRoot: string,
     processName: string | undefined,
     featureEnablement: FeatureEnablement,
+    qlconfigFile: string | undefined,
     logger: Logger
   ): Promise<void>;
   /**
@@ -148,13 +149,19 @@ export interface CodeQL {
   ): Promise<void>;
   /**
    * Run 'codeql database run-queries'.
+   *
+   * @param optimizeForLastQueryRun Whether to apply additional optimization for
+   *                                the last database query run in the action.
+   *                                It is always safe to set it to false.
+   *                                It should be set to true only for the very
+   *                                last databaseRunQueries() call.
    */
   databaseRunQueries(
     databasePath: string,
     extraSearchPath: string | undefined,
     querySuitePath: string | undefined,
-    memoryFlag: string,
+    flags: string[],
-    threadsFlag: string
+    optimizeForLastQueryRun: boolean
   ): Promise<void>;
   /**
    * Run 'codeql database interpret-results'.
@@ -278,6 +285,16 @@ export const CODEQL_VERSION_ML_POWERED_QUERIES_WINDOWS = "2.9.0";
  */
 export const CODEQL_VERSION_BETTER_RESOLVE_LANGUAGES = "2.10.3";
 
+/**
+ * Versions 2.11.1+ of the CodeQL Bundle include a `security-experimental` built-in query suite for each language.
+ */
+export const CODEQL_VERSION_SECURITY_EXPERIMENTAL_SUITE = "2.12.1";
+
+/**
+ * Versions 2.12.4+ of the CodeQL CLI support the `--qlconfig` flag in calls to `database init`.
+ */
+export const CODEQL_VERSION_INIT_WITH_QLCONFIG = "2.12.4";
+
 /**
  * Set up CodeQL CLI access.
  *
@@ -285,7 +302,6 @@ export const CODEQL_VERSION_BETTER_RESOLVE_LANGUAGES = "2.10.3";
  * @param apiDetails
  * @param tempDir
  * @param variant
- * @param bypassToolcache
  * @param defaultCliVersion
  * @param logger
  * @param checkVersion Whether to check that CodeQL CLI meets the minimum
@@ -297,7 +313,6 @@ export async function setupCodeQL(
   apiDetails: api.GitHubApiDetails,
   tempDir: string,
   variant: util.GitHubVariant,
-  bypassToolcache: boolean,
   defaultCliVersion: CodeQLDefaultVersionInfo,
   logger: Logger,
   checkVersion: boolean
@@ -314,7 +329,6 @@ export async function setupCodeQL(
         apiDetails,
         tempDir,
         variant,
-        bypassToolcache,
         defaultCliVersion,
         logger
       );
@@ -557,6 +571,7 @@ export async function getCodeQLForCmd(
       sourceRoot: string,
       processName: string | undefined,
       featureEnablement: FeatureEnablement,
+      qlconfigFile: string | undefined,
       logger: Logger
     ) {
       const extraArgs = config.languages.map(
@@ -586,8 +601,8 @@ export async function getCodeQLForCmd(
         }
       }
 
-      // A config file is only generated if the CliConfigFileEnabled feature flag is enabled.
+      // A code scanning config file is only generated if the CliConfigFileEnabled feature flag is enabled.
-      const configLocation = await generateCodeScanningConfig(
+      const codeScanningConfigFile = await generateCodeScanningConfig(
         codeql,
         config,
         featureEnablement,
@@ -595,14 +610,19 @@ export async function getCodeQLForCmd(
       );
       // Only pass external repository token if a config file is going to be parsed by the CLI.
       let externalRepositoryToken: string | undefined;
-      if (configLocation) {
+      if (codeScanningConfigFile) {
-        extraArgs.push(`--codescanning-config=${configLocation}`);
         externalRepositoryToken = getOptionalInput("external-repository-token");
+        extraArgs.push(`--codescanning-config=${codeScanningConfigFile}`);
         if (externalRepositoryToken) {
           extraArgs.push("--external-repository-token-stdin");
         }
       }
 
+      if (
+        await util.codeQlVersionAbove(this, CODEQL_VERSION_INIT_WITH_QLCONFIG)
+      ) {
+        extraArgs.push(`--qlconfig=${qlconfigFile}`);
+      }
       await runTool(
         cmd,
         [
@@ -787,19 +807,24 @@ export async function getCodeQLForCmd(
       databasePath: string,
       extraSearchPath: string | undefined,
       querySuitePath: string | undefined,
-      memoryFlag: string,
+      flags: string[],
-      threadsFlag: string
+      optimizeForLastQueryRun: boolean
     ): Promise<void> {
       const codeqlArgs = [
         "database",
         "run-queries",
-        memoryFlag,
+        ...flags,
-        threadsFlag,
         databasePath,
         "--min-disk-free=1024", // Try to leave at least 1GB free
         "-v",
         ...getExtraOptionsFromEnv(["database", "run-queries"]),
       ];
+      if (
+        optimizeForLastQueryRun &&
+        (await util.supportExpectDiscardedCache(this))
+      ) {
+        codeqlArgs.push("--expect-discarded-cache");
+      }
       if (extraSearchPath !== undefined) {
         codeqlArgs.push("--additional-packs", extraSearchPath);
       }
@@ -1098,7 +1123,10 @@ async function generateCodeScanningConfig(
   if (!(await util.useCodeScanningConfigInCli(codeql, featureEnablement))) {
     return;
   }
-  const configLocation = path.resolve(config.tempDir, "user-config.yaml");
+  const codeScanningConfigFile = path.resolve(
+    config.tempDir,
+    "user-config.yaml"
+  );
   // make a copy so we can modify it
   const augmentedConfig = cloneObject(config.originalUserInput);
 
@@ -1155,13 +1183,15 @@ async function generateCodeScanningConfig(
       augmentedConfig.packs["javascript"].push(packString);
     }
   }
-  logger.info(`Writing augmented user configuration file to ${configLocation}`);
+  logger.info(
+    `Writing augmented user configuration file to ${codeScanningConfigFile}`
+  );
   logger.startGroup("Augmented user configuration file contents");
   logger.info(yaml.dump(augmentedConfig));
   logger.endGroup();
 
-  fs.writeFileSync(configLocation, yaml.dump(augmentedConfig));
+  fs.writeFileSync(codeScanningConfigFile, yaml.dump(augmentedConfig));
-  return configLocation;
+  return codeScanningConfigFile;
 }
 
 function cloneObject<T>(obj: T): T {

src/config-utils.test.ts

@@ -7,9 +7,13 @@ import * as yaml from "js-yaml";
 import * as sinon from "sinon";
 
 import * as api from "./api-client";
-import { getCachedCodeQL, PackDownloadOutput, setCodeQL } from "./codeql";
+import {
+  CODEQL_VERSION_GHES_PACK_DOWNLOAD,
+  getCachedCodeQL,
+  PackDownloadOutput,
+  setCodeQL,
+} from "./codeql";
 import * as configUtils from "./config-utils";
-import { RegistryConfigWithCredentials } from "./config-utils";
 import { Feature } from "./feature-flags";
 import { Language } from "./languages";
 import { getRunnerLogger, Logger } from "./logging";
@@ -1993,7 +1997,7 @@ test(
   process.platform === "win32" ? undefined : "~0.1.0"
 );
 // Test that ML-powered queries aren't run when the user hasn't specified that we should run the
-// `security-extended` or `security-and-quality` query suite.
+//  `security-extended`, `security-and-quality`, or `security-experimental` query suite.
 test(mlPoweredQueriesMacro, "2.7.5", true, undefined, undefined, undefined);
 // Test that ML-powered queries are run on non-Windows platforms running `security-extended` on
 // versions of the CodeQL CLI prior to 2.9.0.
@@ -2074,7 +2078,6 @@ test(
   "security-extended",
   "~0.4.0"
 );
-
 // Test that ML-powered queries are run on all platforms running `security-and-quality` on CodeQL
 // CLI 2.11.3+.
 test(
@@ -2085,6 +2088,16 @@ test(
   "security-and-quality",
   "~0.4.0"
 );
+// Test that ML-powered queries are run on all platforms running `security-experimental` on CodeQL
+// CLI 2.12.1+.
+test(
+  mlPoweredQueriesMacro,
+  "2.12.1",
+  true,
+  undefined,
+  "security-experimental",
+  "~0.4.0"
+);
 
 const calculateAugmentationMacro = test.macro({
   exec: async (
@@ -2268,8 +2281,8 @@ test("downloadPacks-no-registries", async (t) => {
         go: ["c", "d"],
         python: ["e", "f"],
       },
-      undefined, // registries
       sampleApiDetails,
+      undefined, // registriesAuthTokens
       tmpDir,
       logger
     );
@@ -2287,10 +2300,10 @@ test("downloadPacks-with-registries", async (t) => {
   // associated env vars
   return await util.withTmpDir(async (tmpDir) => {
     process.env.GITHUB_TOKEN = "not-a-token";
-    process.env.CODEQL_REGISTRIES_AUTH = "not-a-registries-auth";
+    process.env.CODEQL_REGISTRIES_AUTH = undefined;
     const logger = getRunnerLogger(true);
 
-    const registries = [
+    const registriesInput = yaml.dump([
       {
         // no slash
         url: "http://ghcr.io",
@@ -2303,9 +2316,12 @@ test("downloadPacks-with-registries", async (t) => {
         packages: "semmle/*",
         token: "still-not-a-token",
       },
-    ];
+    ]);
 
     // append a slash to the first url
+    const registries = yaml.load(
+      registriesInput
+    ) as configUtils.RegistryConfigWithCredentials[];
     const expectedRegistries = registries.map((r, i) => ({
       packages: r.packages,
       url: i === 0 ? `${r.url}/` : r.url,
@@ -2347,8 +2363,8 @@ test("downloadPacks-with-registries", async (t) => {
         go: ["c", "d"],
         python: ["e", "f"],
       },
-      registries,
       sampleApiDetails,
+      registriesInput,
       tmpDir,
       logger
     );
@@ -2366,7 +2382,7 @@ test("downloadPacks-with-registries", async (t) => {
 
     // Verify that the env vars were unset.
     t.deepEqual(process.env.GITHUB_TOKEN, "not-a-token");
-    t.deepEqual(process.env.CODEQL_REGISTRIES_AUTH, "not-a-registries-auth");
+    t.deepEqual(process.env.CODEQL_REGISTRIES_AUTH, undefined);
   });
 });
 
@@ -2378,7 +2394,7 @@ test("downloadPacks-with-registries fails on 2.10.3", async (t) => {
     process.env.CODEQL_REGISTRIES_AUTH = "not-a-registries-auth";
     const logger = getRunnerLogger(true);
 
-    const registries = [
+    const registriesInput = yaml.dump([
       {
         url: "http://ghcr.io",
         packages: ["codeql/*", "dsp-testing/*"],
@@ -2389,7 +2405,7 @@ test("downloadPacks-with-registries fails on 2.10.3", async (t) => {
         packages: "semmle/*",
         token: "still-not-a-token",
       },
-    ];
+    ]);
 
     const codeQL = setCodeQL({
       getVersion: () => Promise.resolve("2.10.3"),
@@ -2400,8 +2416,8 @@ test("downloadPacks-with-registries fails on 2.10.3", async (t) => {
           codeQL,
           [Language.javascript, Language.java, Language.python],
           {},
-          registries,
           sampleApiDetails,
+          registriesInput,
           tmpDir,
           logger
         );
@@ -2420,7 +2436,7 @@ test("downloadPacks-with-registries fails with invalid registries block", async
     process.env.CODEQL_REGISTRIES_AUTH = "not-a-registries-auth";
     const logger = getRunnerLogger(true);
 
-    const registries = [
+    const registriesInput = yaml.dump([
       {
         // missing url property
         packages: ["codeql/*", "dsp-testing/*"],
@@ -2431,7 +2447,7 @@ test("downloadPacks-with-registries fails with invalid registries block", async
         packages: "semmle/*",
         token: "still-not-a-token",
       },
-    ];
+    ]);
 
     const codeQL = setCodeQL({
       getVersion: () => Promise.resolve("2.10.4"),
@@ -2442,8 +2458,8 @@ test("downloadPacks-with-registries fails with invalid registries block", async
           codeQL,
           [Language.javascript, Language.java, Language.python],
           {},
-          registries as RegistryConfigWithCredentials[] | undefined,
           sampleApiDetails,
+          registriesInput,
           tmpDir,
           logger
         );
@@ -2454,6 +2470,85 @@ test("downloadPacks-with-registries fails with invalid registries block", async
   });
 });
 
+// the happy path for generateRegistries is already tested in downloadPacks.
+// these following tests are for the error cases and when nothing is generated.
+test("no generateRegistries when CLI is too old", async (t) => {
+  return await util.withTmpDir(async (tmpDir) => {
+    const registriesInput = yaml.dump([
+      {
+        // no slash
+        url: "http://ghcr.io",
+        packages: ["codeql/*", "dsp-testing/*"],
+        token: "not-a-token",
+      },
+    ]);
+    const codeQL = setCodeQL({
+      // Accepted CLI versions are 2.10.4 or higher
+      getVersion: () => Promise.resolve("2.10.3"),
+    });
+    const logger = getRunnerLogger(true);
+    await t.throwsAsync(
+      async () =>
+        await configUtils.generateRegistries(
+          registriesInput,
+          codeQL,
+          tmpDir,
+          logger
+        ),
+      undefined,
+      "'registries' input is not supported on CodeQL versions less than 2.10.4."
+    );
+  });
+});
+test("no generateRegistries when registries is undefined", async (t) => {
+  return await util.withTmpDir(async (tmpDir) => {
+    const registriesInput = undefined;
+    const codeQL = setCodeQL({
+      // Accepted CLI versions are 2.10.4 or higher
+      getVersion: () => Promise.resolve(CODEQL_VERSION_GHES_PACK_DOWNLOAD),
+    });
+    const logger = getRunnerLogger(true);
+    const { registriesAuthTokens, qlconfigFile } =
+      await configUtils.generateRegistries(
+        registriesInput,
+        codeQL,
+        tmpDir,
+        logger
+      );
+
+    t.is(registriesAuthTokens, undefined);
+    t.is(qlconfigFile, undefined);
+  });
+});
+
+test("generateRegistries prefers original CODEQL_REGISTRIES_AUTH", async (t) => {
+  return await util.withTmpDir(async (tmpDir) => {
+    process.env.CODEQL_REGISTRIES_AUTH = "original";
+    const registriesInput = yaml.dump([
+      {
+        url: "http://ghcr.io",
+        packages: ["codeql/*", "dsp-testing/*"],
+        token: "not-a-token",
+      },
+    ]);
+    const codeQL = setCodeQL({
+      // Accepted CLI versions are 2.10.4 or higher
+      getVersion: () => Promise.resolve(CODEQL_VERSION_GHES_PACK_DOWNLOAD),
+    });
+    const logger = getRunnerLogger(true);
+    const { registriesAuthTokens, qlconfigFile } =
+      await configUtils.generateRegistries(
+        registriesInput,
+        codeQL,
+        tmpDir,
+        logger
+      );
+
+    t.is(registriesAuthTokens, "original");
+    t.is(qlconfigFile, path.join(tmpDir, "qlconfig.yml"));
+  });
+});
+
 // getLanguages
 
 const mockRepositoryNwo = parseRepositoryNwo("owner/repo");

src/config-utils.ts

@@ -10,6 +10,7 @@ import {
   CodeQL,
   CODEQL_VERSION_GHES_PACK_DOWNLOAD,
   CODEQL_VERSION_ML_POWERED_QUERIES_WINDOWS,
+  CODEQL_VERSION_SECURITY_EXPERIMENTAL_SUITE,
   ResolveQueriesOutput,
 } from "./codeql";
 import * as externalQueries from "./external-queries";
@@ -380,7 +381,11 @@ async function addDefaultQueries(
 }
 
 // The set of acceptable values for built-in suites from the codeql bundle
-const builtinSuites = ["security-extended", "security-and-quality"] as const;
+const builtinSuites = [
+  "security-experimental",
+  "security-extended",
+  "security-and-quality",
+] as const;
 
 /**
  * Determine the set of queries associated with suiteName's suites and add them to resultMap.
@@ -401,6 +406,19 @@ async function addBuiltinSuiteQueries(
   if (!found) {
     throw new Error(getQueryUsesInvalid(configFile, suiteName));
   }
+  if (
+    suiteName === "security-experimental" &&
+    !(await codeQlVersionAbove(
+      codeQL,
+      CODEQL_VERSION_SECURITY_EXPERIMENTAL_SUITE
+    ))
+  ) {
+    throw new Error(
+      `The 'security-experimental' suite is not supported on CodeQL CLI versions earlier than
+      ${CODEQL_VERSION_SECURITY_EXPERIMENTAL_SUITE}. Please upgrade to CodeQL CLI version
+      ${CODEQL_VERSION_SECURITY_EXPERIMENTAL_SUITE} or later.`
+    );
+  }
 
   // If we're running the JavaScript security-extended analysis (or a superset of it), the repo is
   // opted into the ML-powered queries beta, and a user hasn't already added the ML-powered query
@@ -413,7 +431,9 @@ async function addBuiltinSuiteQueries(
         CODEQL_VERSION_ML_POWERED_QUERIES_WINDOWS
       ))) &&
     languages.includes("javascript") &&
-    (found === "security-extended" || found === "security-and-quality") &&
+    (found === "security-experimental" ||
+      found === "security-extended" ||
+      found === "security-and-quality") &&
     !packs.javascript?.some(isMlPoweredJsQueriesPack) &&
     (await featureEnablement.getValue(Feature.MlPoweredQueriesEnabled, codeQL))
   ) {
@@ -1383,7 +1403,7 @@ function parseQueriesFromInput(
 
   const trimmedInput = queriesInputCombines
     ? rawQueriesInput.trim().slice(1).trim()
-    : rawQueriesInput?.trim();
+    : rawQueriesInput?.trim() ?? "";
   if (queriesInputCombines && trimmedInput.length === 0) {
     throw new Error(
       getConfigFilePropertyError(
@@ -1630,7 +1650,8 @@ export function parsePacks(
  * Without a '+', an input value will override the corresponding value in the config file.
  *
  * @param inputValue The input value to process.
- * @returns true if the input value should replace the corresponding value in the config file, false if it should be appended.
+ * @returns true if the input value should replace the corresponding value in the config file,
+ *          false if it should be appended.
  */
 function shouldCombine(inputValue?: string): boolean {
   return !!inputValue?.trim().startsWith("+");
@@ -1748,13 +1769,12 @@ export async function initConfig(
       }
     }
 
-    const registries = parseRegistries(registriesInput);
     await downloadPacks(
       codeQL,
       config.languages,
       config.packs,
-      registries,
       apiDetails,
+      registriesInput,
       config.tempDir,
       logger
     );
@@ -1878,32 +1898,18 @@ export async function downloadPacks(
   codeQL: CodeQL,
   languages: Language[],
   packs: Packs,
-  registries: RegistryConfigWithCredentials[] | undefined,
   apiDetails: api.GitHubApiDetails,
-  tmpDir: string,
+  registriesInput: string | undefined,
+  tempDir: string,
   logger: Logger
 ) {
-  let qlconfigFile: string | undefined;
+  // This code path is only used when config parsing occurs in the Action.
-  let registriesAuthTokens: string | undefined;
+  const { registriesAuthTokens, qlconfigFile } = await generateRegistries(
-  if (registries) {
+    registriesInput,
-    if (
+    codeQL,
-      !(await codeQlVersionAbove(codeQL, CODEQL_VERSION_GHES_PACK_DOWNLOAD))
+    tempDir,
-    ) {
+    logger
-      throw new Error(
+  );
-        `'registries' input is not supported on CodeQL versions less than ${CODEQL_VERSION_GHES_PACK_DOWNLOAD}.`
-      );
-    }
-
-    // generate a qlconfig.yml file to hold the registry configs.
-    const qlconfig = createRegistriesBlock(registries);
-    qlconfigFile = path.join(tmpDir, "qlconfig.yml");
-    fs.writeFileSync(qlconfigFile, yaml.dump(qlconfig), "utf8");
-
-    registriesAuthTokens = registries
-      .map((registry) => `${registry.url}=${registry.token}`)
-      .join(",");
-  }
-
   await wrapEnvironment(
     {
       GITHUB_TOKEN: apiDetails.auth,
@@ -1942,6 +1948,63 @@ export async function downloadPacks(
   );
 }
 
+/**
+ * Generate a `qlconfig.yml` file from the `registries` input.
+ * This file is used by the CodeQL CLI to list the registries to use for each
+ * pack.
+ *
+ * @param registriesInput The value of the `registries` input.
+ * @param codeQL a codeQL object, used only for checking the version of CodeQL.
+ * @param tempDir a temporary directory to store the generated qlconfig.yml file.
+ * @param logger a logger object.
+ * @returns The path to the generated `qlconfig.yml` file and the auth tokens to
+ *        use for each registry.
+ */
+export async function generateRegistries(
+  registriesInput: string | undefined,
+  codeQL: CodeQL,
+  tempDir: string,
+  logger: Logger
+) {
+  const registries = parseRegistries(registriesInput);
+  let registriesAuthTokens: string | undefined;
+  let qlconfigFile: string | undefined;
+  if (registries) {
+    if (
+      !(await codeQlVersionAbove(codeQL, CODEQL_VERSION_GHES_PACK_DOWNLOAD))
+    ) {
+      throw new Error(
+        `The 'registries' input is not supported on CodeQL CLI versions earlier than ${CODEQL_VERSION_GHES_PACK_DOWNLOAD}. Please upgrade to CodeQL CLI version ${CODEQL_VERSION_GHES_PACK_DOWNLOAD} or later.`
+      );
+    }
+
+    // generate a qlconfig.yml file to hold the registry configs.
+    const qlconfig = createRegistriesBlock(registries);
+    qlconfigFile = path.join(tempDir, "qlconfig.yml");
+    const qlconfigContents = yaml.dump(qlconfig);
+    fs.writeFileSync(qlconfigFile, qlconfigContents, "utf8");
+
+    logger.debug("Generated qlconfig.yml:");
+    logger.debug(qlconfigContents);
+    registriesAuthTokens = registries
+      .map((registry) => `${registry.url}=${registry.token}`)
+      .join(",");
+  }
+
+  if (typeof process.env.CODEQL_REGISTRIES_AUTH === "string") {
+    logger.debug(
+      "Using CODEQL_REGISTRIES_AUTH environment variable to authenticate with registries."
+    );
+  }
+
+  return {
+    registriesAuthTokens:
+      // if the user has explicitly set the CODEQL_REGISTRIES_AUTH env var then use that
+      process.env.CODEQL_REGISTRIES_AUTH ?? registriesAuthTokens,
+    qlconfigFile,
+  };
+}
+
 function createRegistriesBlock(registries: RegistryConfigWithCredentials[]): {
   registries: RegistryConfigNoCredentials[];
 } {
@@ -1978,7 +2041,7 @@ function createRegistriesBlock(registries: RegistryConfigWithCredentials[]): {
  * @param env
  * @param operation
  */
-async function wrapEnvironment(
+export async function wrapEnvironment(
   env: Record<string, string | undefined>,
   operation: Function
 ) {

src/defaults.json

@@ -1,6 +1,6 @@
 {
-  "bundleVersion": "codeql-bundle-20230120",
+  "bundleVersion": "codeql-bundle-20230217",
-  "cliVersion": "2.12.1",
+  "cliVersion": "2.12.3",
-  "priorBundleVersion": "codeql-bundle-20230105",
+  "priorBundleVersion": "codeql-bundle-20230207",
-  "priorCliVersion": "2.12.0"
+  "priorCliVersion": "2.12.2"
 }

src/feature-flags.ts

@@ -34,12 +34,9 @@ export interface FeatureEnablement {
 }
 
 export enum Feature {
-  BypassToolcacheEnabled = "bypass_toolcache_enabled",
-  BypassToolcacheKotlinSwiftEnabled = "bypass_toolcache_kotlin_swift_enabled",
   CliConfigFileEnabled = "cli_config_file_enabled",
   DisableKotlinAnalysisEnabled = "disable_kotlin_analysis_enabled",
   MlPoweredQueriesEnabled = "ml_powered_queries_enabled",
-  TrapCachingEnabled = "trap_caching_enabled",
   UploadFailedSarifEnabled = "upload_failed_sarif_enabled",
 }
 
@@ -47,18 +44,6 @@ export const featureConfig: Record<
   Feature,
   { envVar: string; minimumVersion: string | undefined }
 > = {
-  [Feature.BypassToolcacheEnabled]: {
-    envVar: "CODEQL_BYPASS_TOOLCACHE",
-    // Cannot specify a minimum version because this flag is checked before we have
-    // access to the CodeQL instance.
-    minimumVersion: undefined,
-  },
-  [Feature.BypassToolcacheKotlinSwiftEnabled]: {
-    envVar: "CODEQL_BYPASS_TOOLCACHE_KOTLIN_SWIFT",
-    // Cannot specify a minimum version because this flag is checked before we have
-    // access to the CodeQL instance.
-    minimumVersion: undefined,
-  },
   [Feature.DisableKotlinAnalysisEnabled]: {
     envVar: "CODEQL_DISABLE_KOTLIN_ANALYSIS",
     minimumVersion: undefined,
@@ -71,10 +56,6 @@ export const featureConfig: Record<
     envVar: "CODEQL_ML_POWERED_QUERIES",
     minimumVersion: "2.7.5",
   },
-  [Feature.TrapCachingEnabled]: {
-    envVar: "CODEQL_TRAP_CACHING",
-    minimumVersion: undefined,
-  },
   [Feature.UploadFailedSarifEnabled]: {
     envVar: "CODEQL_ACTION_UPLOAD_FAILED_SARIF",
     minimumVersion: "2.11.3",
@@ -138,11 +119,6 @@ export class Features implements FeatureEnablement {
       );
     }
 
-    // Bypassing the toolcache is disabled in test mode.
-    if (feature === Feature.BypassToolcacheEnabled && util.isInTestMode()) {
-      return false;
-    }
-
     const envVar = (
       process.env[featureConfig[feature].envVar] || ""
     ).toLocaleLowerCase();
@@ -172,13 +148,17 @@ export class Features implements FeatureEnablement {
 class GitHubFeatureFlags implements FeatureEnablement {
   private cachedApiResponse: GitHubFeatureFlagsApiResponse | undefined;
 
+  // We cache whether the feature flags were accessed or not in order to accurately report whether flags were
+  // incorrectly configured vs. inaccessible in our telemetry.
+  private hasAccessedRemoteFeatureFlags: boolean;
+
   constructor(
     private readonly gitHubVersion: util.GitHubVersion,
     private readonly repositoryNwo: RepositoryNwo,
     private readonly featureFlagsFile: string,
     private readonly logger: Logger
   ) {
-    /**/
+    this.hasAccessedRemoteFeatureFlags = false; // Not accessed by default.
   }
 
   private getCliVersionFromFeatureFlag(f: string): string | undefined {
@@ -211,7 +191,9 @@ class GitHubFeatureFlags implements FeatureEnablement {
       const defaultDotComCliVersion = await this.getDefaultDotcomCliVersion();
       return {
         cliVersion: defaultDotComCliVersion.version,
-        toolsFeatureFlagsValid: defaultDotComCliVersion.toolsFeatureFlagsValid,
+        toolsFeatureFlagsValid: this.hasAccessedRemoteFeatureFlags
+          ? defaultDotComCliVersion.toolsFeatureFlagsValid
+          : undefined,
         variant,
       };
     }
@@ -224,7 +206,7 @@ class GitHubFeatureFlags implements FeatureEnablement {
 
   async getDefaultDotcomCliVersion(): Promise<{
     version: string;
-    toolsFeatureFlagsValid: boolean;
+    toolsFeatureFlagsValid: boolean | undefined;
   }> {
     const response = await this.getAllFeatures();
 
@@ -252,7 +234,9 @@ class GitHubFeatureFlags implements FeatureEnablement {
       );
       return {
         version: defaults.cliVersion,
-        toolsFeatureFlagsValid: false,
+        toolsFeatureFlagsValid: this.hasAccessedRemoteFeatureFlags
+          ? false
+          : undefined,
       };
     }
 
@@ -350,6 +334,7 @@ class GitHubFeatureFlags implements FeatureEnablement {
       this.logger.debug(
         "Not running against github.com. Disabling all toggleable features."
       );
+      this.hasAccessedRemoteFeatureFlags = false;
       return {};
     }
     try {
@@ -365,6 +350,7 @@ class GitHubFeatureFlags implements FeatureEnablement {
         "Loaded the following default values for the feature flags from the Code Scanning API: " +
           `${JSON.stringify(remoteFlags)}`
       );
+      this.hasAccessedRemoteFeatureFlags = true;
       return remoteFlags;
     } catch (e) {
       if (util.isHTTPError(e) && e.status === 403) {
@@ -374,6 +360,7 @@ class GitHubFeatureFlags implements FeatureEnablement {
             "This could be because the Action is running on a pull request from a fork. If not, " +
             `please ensure the Action has the 'security-events: write' permission. Details: ${e}`
         );
+        this.hasAccessedRemoteFeatureFlags = false;
         return {};
       } else {
         // Some features, such as `ml_powered_queries_enabled` affect the produced alerts.
@@ -385,6 +372,5 @@ class GitHubFeatureFlags implements FeatureEnablement {
         );
       }
     }
-    return {};
   }
 }

src/init-action.ts

@@ -16,7 +16,7 @@ import {
 import { getGitHubVersion } from "./api-client";
 import { CodeQL, CODEQL_VERSION_NEW_TRACING } from "./codeql";
 import * as configUtils from "./config-utils";
-import { Feature, FeatureEnablement, Features } from "./feature-flags";
+import { Feature, Features } from "./feature-flags";
 import {
   initCodeQL,
   initConfig,
@@ -43,7 +43,6 @@ import {
   GitHubVariant,
   initializeEnvironment,
   isHostedRunner,
-  shouldBypassToolcache,
 } from "./util";
 import { validateWorkflow } from "./workflow";
 
@@ -87,7 +86,9 @@ interface InitWithConfigStatusReport extends InitStatusReport {
 interface InitToolsDownloadFields {
   /** Time taken to download the bundle, in milliseconds. */
   tools_download_duration_ms?: number;
-  /** Whether the relevant tools dotcom feature flags have been misconfigured. Only populated if we attempt to determine the default version based on the dotcom feature flags. */
+  /**
+   * Whether the relevant tools dotcom feature flags have been misconfigured.
+   * Only populated if we attempt to determine the default version based on the dotcom feature flags. */
   tools_feature_flags_valid?: boolean;
 }
 
@@ -117,13 +118,14 @@ async function sendInitStatusReport(
     workflow_languages: workflowLanguages || "",
   };
 
-  let initToolsDownloadFields: InitToolsDownloadFields = {};
+  const initToolsDownloadFields: InitToolsDownloadFields = {};
 
-  if (toolsSource === ToolsSource.Download) {
+  if (toolsDownloadDurationMs !== undefined) {
-    initToolsDownloadFields = {
+    initToolsDownloadFields.tools_download_duration_ms =
-      tools_download_duration_ms: toolsDownloadDurationMs,
+      toolsDownloadDurationMs;
-      tools_feature_flags_valid: toolsFeatureFlagsValid,
+  }
-    };
+  if (toolsFeatureFlagsValid !== undefined) {
+    initToolsDownloadFields.tools_feature_flags_valid = toolsFeatureFlagsValid;
   }
 
   if (config !== undefined) {
@@ -202,6 +204,8 @@ async function run() {
     getRequiredEnvParam("GITHUB_REPOSITORY")
   );
 
+  const registriesInput = getOptionalInput("registries");
+
   const features = new Features(
     gitHubVersion,
     repositoryNwo,
@@ -236,13 +240,6 @@ async function run() {
       apiDetails,
       getTemporaryDirectory(),
       gitHubVersion.type,
-      await shouldBypassToolcache(
-        features,
-        getOptionalInput("tools"),
-        getOptionalInput("languages"),
-        repositoryNwo,
-        logger
-      ),
       codeQLDefaultVersionInfo,
       logger
     );
@@ -256,10 +253,10 @@ async function run() {
       getOptionalInput("languages"),
       getOptionalInput("queries"),
       getOptionalInput("packs"),
-      getOptionalInput("registries"),
+      registriesInput,
       getOptionalInput("config-file"),
       getOptionalInput("db-location"),
-      await getTrapCachingEnabled(features),
+      getTrapCachingEnabled(),
       // Debug mode is enabled if:
       // - The `init` Action is passed `debug: true`.
       // - Actions step debugging is enabled (e.g. by [enabling debug logging for a rerun](https://docs.github.com/en/actions/managing-workflow-runs/re-running-workflows-and-jobs#re-running-all-the-jobs-in-a-workflow),
@@ -340,7 +337,9 @@ async function run() {
       config,
       sourceRoot,
       "Runner.Worker.exe",
+      registriesInput,
       features,
+      apiDetails,
       logger
     );
     if (tracerConfig !== undefined) {
@@ -391,9 +390,7 @@ async function run() {
   );
 }
 
-async function getTrapCachingEnabled(
+function getTrapCachingEnabled(): boolean {
-  featureEnablement: FeatureEnablement
-): Promise<boolean> {
   // If the workflow specified something always respect that
   const trapCaching = getOptionalInput("trap-caching");
   if (trapCaching !== undefined) return trapCaching === "true";
@@ -401,8 +398,8 @@ async function getTrapCachingEnabled(
   // On self-hosted runners which may have slow network access, disable TRAP caching by default
   if (!isHostedRunner()) return false;
 
-  // On hosted runners, respect the feature flag
+  // On hosted runners, enable TRAP caching by default
-  return await featureEnablement.getValue(Feature.TrapCachingEnabled);
+  return true;
 }
 
 async function runWrapper() {

src/init.ts

@@ -27,7 +27,6 @@ export async function initCodeQL(
   apiDetails: GitHubApiDetails,
   tempDir: string,
   variant: util.GitHubVariant,
-  bypassToolcache: boolean,
   defaultCliVersion: CodeQLDefaultVersionInfo,
   logger: Logger
 ): Promise<{
@@ -43,7 +42,6 @@ export async function initCodeQL(
       apiDetails,
       tempDir,
       variant,
-      bypassToolcache,
       defaultCliVersion,
       logger,
       true
@@ -104,20 +102,46 @@ export async function runInit(
   config: configUtils.Config,
   sourceRoot: string,
   processName: string | undefined,
+  registriesInput: string | undefined,
   featureEnablement: FeatureEnablement,
+  apiDetails: GitHubApiCombinedDetails,
   logger: Logger
 ): Promise<TracerConfig | undefined> {
   fs.mkdirSync(config.dbLocation, { recursive: true });
 
   try {
     if (await codeQlVersionAbove(codeql, CODEQL_VERSION_NEW_TRACING)) {
-      // Init a database cluster
+      // When parsing the codeql config in the CLI, we have not yet created the qlconfig file.
-      await codeql.databaseInitCluster(
+      // So, create it now.
-        config,
+      // If we are parsing the config file in the Action, then the qlconfig file was already created
-        sourceRoot,
+      // before the `pack download` command was invoked. It is not required for the init command.
-        processName,
+      let registriesAuthTokens: string | undefined;
-        featureEnablement,
+      let qlconfigFile: string | undefined;
-        logger
+      if (await util.useCodeScanningConfigInCli(codeql, featureEnablement)) {
+        ({ registriesAuthTokens, qlconfigFile } =
+          await configUtils.generateRegistries(
+            registriesInput,
+            codeql,
+            config.tempDir,
+            logger
+          ));
+      }
+      await configUtils.wrapEnvironment(
+        {
+          GITHUB_TOKEN: apiDetails.auth,
+          CODEQL_REGISTRIES_AUTH: registriesAuthTokens,
+        },
+
+        // Init a database cluster
+        async () =>
+          await codeql.databaseInitCluster(
+            config,
+            sourceRoot,
+            processName,
+            featureEnablement,
+            qlconfigFile,
+            logger
+          )
       );
     } else {
       for (const language of config.languages) {

src/languages.ts

@@ -21,8 +21,6 @@ export const LANGUAGE_ALIASES: { [lang: string]: Language } = {
 
 export type LanguageOrAlias = Language | keyof typeof LANGUAGE_ALIASES;
 
-export const KOTLIN_SWIFT_BYPASS = ["kotlin", "swift"];
-
 export function resolveAlias(lang: LanguageOrAlias): Language {
   return LANGUAGE_ALIASES[lang] || lang;
 }

src/setup-codeql.ts

@@ -354,7 +354,6 @@ async function findOverridingToolsInCache(
 
 export async function getCodeQLSource(
   toolsInput: string | undefined,
-  bypassToolcache: boolean,
   defaultCliVersion: CodeQLDefaultVersionInfo,
   apiDetails: api.GitHubApiDetails,
   variant: util.GitHubVariant,
@@ -368,25 +367,18 @@ export async function getCodeQLSource(
     };
   }
 
-  /** The reason why the tools shipped with the Action have been forced. */
+  /**
-  const forceShippedToolsReason =
+   * Whether the tools shipped with the Action, i.e. those in `defaults.json`, have been forced.
-    // We use the special value of 'latest' to prioritize the version in the
+   *
-    // defaults over any pinned cached version.
+   * We use the special value of 'latest' to prioritize the version in `defaults.json` over the
-    toolsInput === "latest"
+   * version specified by the feature flags on Dotcom and over any pinned cached version on
-      ? '"tools: latest" was requested'
+   * Enterprise Server.
-      : // If the user hasn't requested a particular CodeQL version, then bypass
+   */
-      // the toolcache when the appropriate feature is enabled. This
+  const forceShippedTools = toolsInput === "latest";
-      // allows us to quickly rollback a broken bundle that has made its way
-      // into the toolcache.
-      toolsInput === undefined && bypassToolcache
-      ? "a specific version of the CodeQL tools was not requested and the bypass toolcache feature is enabled"
-      : undefined;
-  /** Whether the tools shipped with the Action, i.e. those in `defaults.json`, have been forced. */
-  const forceShippedTools = forceShippedToolsReason !== undefined;
   if (forceShippedTools) {
     logger.info(
       "Overriding the version of the CodeQL tools by the version shipped with the Action since " +
-        `${forceShippedToolsReason}.`
+        `"tools: latest" was requested.`
     );
   }
 
@@ -714,7 +706,6 @@ export function getCodeQLURLVersion(url: string): string {
  * @param apiDetails
  * @param tempDir
  * @param variant
- * @param bypassToolcache
  * @param defaultCliVersion
  * @param logger
  * @param checkVersion Whether to check that CodeQL CLI meets the minimum
@@ -726,7 +717,6 @@ export async function setupCodeQLBundle(
   apiDetails: api.GitHubApiDetails,
   tempDir: string,
   variant: util.GitHubVariant,
-  bypassToolcache: boolean,
   defaultCliVersion: CodeQLDefaultVersionInfo,
   logger: Logger
 ): Promise<{
@@ -737,7 +727,6 @@ export async function setupCodeQLBundle(
 }> {
   const source = await getCodeQLSource(
     toolsInput,
-    bypassToolcache,
     defaultCliVersion,
     apiDetails,
     variant,

src/upload-lib.ts

@@ -416,7 +416,8 @@ export async function waitForProcessing(
         statusCheckingStarted + STATUS_CHECK_TIMEOUT_MILLISECONDS
       ) {
         // If the analysis hasn't finished processing in the allotted time, we continue anyway rather than failing.
-        // It's possible the analysis will eventually finish processing, but it's not worth spending more Actions time waiting.
+        // It's possible the analysis will eventually finish processing, but it's not worth spending more
+        // Actions time waiting.
         logger.warning(
           "Timed out waiting for analysis to finish processing. Continuing."
         );
@@ -462,7 +463,9 @@ export async function waitForProcessing(
         util.assertNever(status);
       }
 
-      await util.delay(STATUS_CHECK_FREQUENCY_MILLISECONDS);
+      await util.delay(STATUS_CHECK_FREQUENCY_MILLISECONDS, {
+        allowProcessExit: false,
+      });
     }
   } finally {
     logger.endGroup();

src/util.test.ts

@@ -8,14 +8,8 @@ import * as sinon from "sinon";
 
 import * as api from "./api-client";
 import { Config } from "./config-utils";
-import { Feature } from "./feature-flags";
 import { getRunnerLogger } from "./logging";
-import { parseRepositoryNwo } from "./repository";
+import { setupTests } from "./testing-utils";
-import {
-  createFeatures,
-  mockLanguagesInRepo,
-  setupTests,
-} from "./testing-utils";
 import * as util from "./util";
 
 setupTests(test);
@@ -398,123 +392,3 @@ test("withTimeout doesn't call callback if promise resolves", async (t) => {
   t.deepEqual(shortTaskTimedOut, false);
   t.deepEqual(result, 99);
 });
-
-const mockRepositoryNwo = parseRepositoryNwo("owner/repo");
-// eslint-disable-next-line github/array-foreach
-[
-  {
-    name: "disabled",
-    features: [],
-    hasCustomCodeQL: false,
-    languagesInput: undefined,
-    languagesInRepository: [],
-    expected: false,
-    expectedApiCall: false,
-  },
-  {
-    name: "disabled even though swift kotlin bypassed",
-    features: [Feature.BypassToolcacheKotlinSwiftEnabled],
-    hasCustomCodeQL: false,
-    languagesInput: undefined,
-    languagesInRepository: [],
-    expected: false,
-    expectedApiCall: true,
-  },
-  {
-    name: "disabled even though swift kotlin analyzed",
-    features: [],
-    hasCustomCodeQL: false,
-    languagesInput: " sWiFt , KoTlIn ",
-    languagesInRepository: [],
-    expected: false,
-    expectedApiCall: false,
-  },
-  {
-    name: "toolcache bypass all",
-    features: [Feature.BypassToolcacheEnabled],
-    hasCustomCodeQL: false,
-    languagesInput: undefined,
-    languagesInRepository: [],
-    expected: true,
-    expectedApiCall: false,
-  },
-  {
-    name: "custom CodeQL",
-    features: [],
-    hasCustomCodeQL: true,
-    languagesInput: undefined,
-    languagesInRepository: [],
-    expected: true,
-    expectedApiCall: false,
-  },
-  {
-    name: "bypass swift",
-    features: [Feature.BypassToolcacheKotlinSwiftEnabled],
-    hasCustomCodeQL: false,
-    languagesInput: " sWiFt ,other",
-    languagesInRepository: [],
-    expected: true,
-    expectedApiCall: false,
-  },
-  {
-    name: "bypass kotlin",
-    features: [Feature.BypassToolcacheKotlinSwiftEnabled],
-    hasCustomCodeQL: false,
-    languagesInput: "other, KoTlIn ",
-    languagesInRepository: [],
-    expected: true,
-    expectedApiCall: false,
-  },
-  {
-    name: "bypass kotlin language from repository",
-    features: [Feature.BypassToolcacheKotlinSwiftEnabled],
-    hasCustomCodeQL: false,
-    languagesInput: "",
-    languagesInRepository: ["KoTlIn", "other"],
-    expected: true,
-    expectedApiCall: true,
-  },
-  {
-    name: "bypass swift language from repository",
-    features: [Feature.BypassToolcacheKotlinSwiftEnabled],
-    hasCustomCodeQL: false,
-    languagesInput: "",
-    languagesInRepository: ["SwiFt", "other"],
-    expected: true,
-    expectedApiCall: true,
-  },
-  {
-    name: "bypass java from input if there is kotlin in repository",
-    features: [Feature.BypassToolcacheKotlinSwiftEnabled],
-    hasCustomCodeQL: false,
-    languagesInput: "java",
-    languagesInRepository: ["kotlin", "other"],
-    expected: true,
-    expectedApiCall: true,
-  },
-  {
-    name: "don't bypass java from input if there is no kotlin in repository",
-    features: [Feature.BypassToolcacheKotlinSwiftEnabled],
-    hasCustomCodeQL: false,
-    languagesInput: "java",
-    languagesInRepository: ["java", "other"],
-    expected: false,
-    expectedApiCall: true,
-  },
-].forEach((args) => {
-  test(`shouldBypassToolcache: ${args.name}`, async (t) => {
-    const mockRequest = mockLanguagesInRepo(args.languagesInRepository);
-    const mockLogger = getRunnerLogger(true);
-    const featureEnablement = createFeatures(args.features);
-    const codeqlUrl = args.hasCustomCodeQL ? "custom-codeql-url" : undefined;
-    const actual = await util.shouldBypassToolcache(
-      featureEnablement,
-      codeqlUrl,
-      args.languagesInput,
-      mockRepositoryNwo,
-      mockLogger
-    );
-    t.deepEqual(actual, args.expected);
-    t.deepEqual(mockRequest.called, args.expectedApiCall);
-  });
-});

src/util.ts

@@ -13,15 +13,12 @@ import * as apiCompatibility from "./api-compatibility.json";
 import { CodeQL, CODEQL_VERSION_NEW_TRACING } from "./codeql";
 import {
   Config,
-  getLanguagesInRepo,
-  getRawLanguages,
   parsePacksSpecification,
   prettyPrintPack,
 } from "./config-utils";
 import { Feature, FeatureEnablement } from "./feature-flags";
-import { KOTLIN_SWIFT_BYPASS, Language } from "./languages";
+import { Language } from "./languages";
 import { Logger } from "./logging";
-import { RepositoryNwo } from "./repository";
 import { CODEQL_ACTION_TEST_MODE } from "./shared-environment";
 
 /**
@@ -551,16 +548,38 @@ export async function bundleDb(
   return databaseBundlePath;
 }
 
-export async function delay(milliseconds: number) {
+/**
-  // Immediately `unref` the timer such that it only prevents the process from exiting if the
+ * @param milliseconds time to delay
-  // surrounding promise is being awaited.
+ * @param opts options
-  return new Promise((resolve) => setTimeout(resolve, milliseconds).unref());
+ * @param opts.allowProcessExit if true, the timer will not prevent the process from exiting
+ */
+export async function delay(
+  milliseconds: number,
+  { allowProcessExit }: { allowProcessExit: boolean }
+) {
+  return new Promise((resolve) => {
+    const timer = setTimeout(resolve, milliseconds);
+    if (allowProcessExit) {
+      // Immediately `unref` the timer such that it only prevents the process from exiting if the
+      // surrounding promise is being awaited.
+      timer.unref();
+    }
+  });
 }
 
 export function isGoodVersion(versionSpec: string) {
   return !BROKEN_VERSIONS.includes(versionSpec);
 }
 
+/**
+ * Checks whether the CodeQL CLI supports the `--expect-discarded-cache` command-line flag.
+ */
+export async function supportExpectDiscardedCache(
+  codeQL: CodeQL
+): Promise<boolean> {
+  return codeQlVersionAbove(codeQL, "2.12.1");
+}
+
 export const ML_POWERED_JS_QUERIES_PACK_NAME =
   "codeql/javascript-experimental-atm-queries";
 
@@ -751,7 +770,7 @@ export async function withTimeout<T>(
     return result;
   };
   const timeoutTask = async () => {
-    await delay(timeoutMs);
+    await delay(timeoutMs, { allowProcessExit: true });
     if (!finished) {
       // Workaround: While the promise racing below will allow the main code
       // to continue, the process won't normally exit until the asynchronous
@@ -776,7 +795,7 @@ export async function checkForTimeout() {
     core.info(
       "A timeout occurred, force exiting the process after 30 seconds to prevent hanging."
     );
-    await delay(30_000);
+    await delay(30_000, { allowProcessExit: true });
     process.exit();
   }
 }
@@ -802,63 +821,6 @@ export function isHostedRunner() {
   );
 }
 
-/**
- *
- * @param featuresEnablement The features enabled for the current run
- * @param languagesInput Languages input from the workflow
- * @param repository The owner/name of the repository
- * @param logger A logger
- * @returns A boolean indicating whether or not the toolcache should be bypassed and the latest codeql should be downloaded.
- */
-export async function shouldBypassToolcache(
-  featuresEnablement: FeatureEnablement,
-  codeqlUrl: string | undefined,
-  languagesInput: string | undefined,
-  repository: RepositoryNwo,
-  logger: Logger
-): Promise<boolean> {
-  // An explicit codeql url is specified, that means the toolcache will not be used.
-  if (codeqlUrl) {
-    return true;
-  }
-
-  // Check if the toolcache is disabled for all languages
-  if (await featuresEnablement.getValue(Feature.BypassToolcacheEnabled)) {
-    return true;
-  }
-
-  // Check if the toolcache is disabled for kotlin and swift.
-  if (
-    !(await featuresEnablement.getValue(
-      Feature.BypassToolcacheKotlinSwiftEnabled
-    ))
-  ) {
-    return false;
-  }
-
-  // Now check to see if kotlin or swift is one of the languages being analyzed.
-  const { rawLanguages, autodetected } = await getRawLanguages(
-    languagesInput,
-    repository,
-    logger
-  );
-  let bypass = rawLanguages.some((lang) => KOTLIN_SWIFT_BYPASS.includes(lang));
-  if (bypass) {
-    logger.info(
-      `Bypassing toolcache for kotlin or swift. Languages: ${rawLanguages}`
-    );
-  } else if (!autodetected && rawLanguages.includes(Language.java)) {
-    // special case: java was explicitly specified, but there might be
-    // some kotlin in the repository, so we need to make a request for that.
-    const langsInRepo = await getLanguagesInRepo(repository, logger);
-    if (langsInRepo.includes("kotlin")) {
-      logger.info(`Bypassing toolcache for kotlin.`);
-      bypass = true;
-    }
-  }
-  return bypass;
-}
-
 export function parseMatrixInput(
   matrixInput: string | undefined
 ): { [key: string]: string } | undefined {