diff --git a/analyze/action.yml b/analyze/action.yml
index 9b950f6fa..7aaeeec2d 100644
--- a/analyze/action.yml
+++ b/analyze/action.yml
@@ -19,7 +19,6 @@ inputs:
   threads:
     description: The number of threads to be used by CodeQL.
     required: false
-    default: "1"
   checkout_path:
     description: "The path at which the analyzed repository was checked out. Used to relativeize any absolute paths in the uploaded SARIF file."
     required: false
diff --git a/lib/analysis-paths.test.js b/lib/analysis-paths.test.js
index c022e9b15..b3707e6be 100644
--- a/lib/analysis-paths.test.js
+++ b/lib/analysis-paths.test.js
@@ -13,31 +13,42 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const ava_1 = __importDefault(require("ava"));
 const analysisPaths = __importStar(require("./analysis-paths"));
 const testing_utils_1 = require("./testing-utils");
+const util = __importStar(require("./util"));
 testing_utils_1.setupTests(ava_1.default);
 ava_1.default("emptyPaths", async (t) => {
-    const config = {
-        languages: [],
-        queries: {},
-        pathsIgnore: [],
-        paths: [],
-        originalUserInput: {},
-    };
-    analysisPaths.includeAndExcludeAnalysisPaths(config);
-    t.is(process.env['LGTM_INDEX_INCLUDE'], undefined);
-    t.is(process.env['LGTM_INDEX_EXCLUDE'], undefined);
-    t.is(process.env['LGTM_INDEX_FILTERS'], undefined);
+    return await util.withTmpDir(async (tmpDir) => {
+        const config = {
+            languages: [],
+            queries: {},
+            pathsIgnore: [],
+            paths: [],
+            originalUserInput: {},
+            tempDir: tmpDir,
+            toolCacheDir: tmpDir,
+            codeQLCmd: '',
+        };
+        analysisPaths.includeAndExcludeAnalysisPaths(config);
+        t.is(process.env['LGTM_INDEX_INCLUDE'], undefined);
+        t.is(process.env['LGTM_INDEX_EXCLUDE'], undefined);
+        t.is(process.env['LGTM_INDEX_FILTERS'], undefined);
+    });
 });
 ava_1.default("nonEmptyPaths", async (t) => {
-    const config = {
-        languages: [],
-        queries: {},
-        paths: ['path1', 'path2', '**/path3'],
-        pathsIgnore: ['path4', 'path5', 'path6/**'],
-        originalUserInput: {},
-    };
-    analysisPaths.includeAndExcludeAnalysisPaths(config);
-    t.is(process.env['LGTM_INDEX_INCLUDE'], 'path1\npath2');
-    t.is(process.env['LGTM_INDEX_EXCLUDE'], 'path4\npath5');
-    t.is(process.env['LGTM_INDEX_FILTERS'], 'include:path1\ninclude:path2\ninclude:**/path3\nexclude:path4\nexclude:path5\nexclude:path6/**');
+    return await util.withTmpDir(async (tmpDir) => {
+        const config = {
+            languages: [],
+            queries: {},
+            paths: ['path1', 'path2', '**/path3'],
+            pathsIgnore: ['path4', 'path5', 'path6/**'],
+            originalUserInput: {},
+            tempDir: tmpDir,
+            toolCacheDir: tmpDir,
+            codeQLCmd: '',
+        };
+        analysisPaths.includeAndExcludeAnalysisPaths(config);
+        t.is(process.env['LGTM_INDEX_INCLUDE'], 'path1\npath2');
+        t.is(process.env['LGTM_INDEX_EXCLUDE'], 'path4\npath5');
+        t.is(process.env['LGTM_INDEX_FILTERS'], 'include:path1\ninclude:path2\ninclude:**/path3\nexclude:path4\nexclude:path5\nexclude:path6/**');
+    });
 });
 //# sourceMappingURL=analysis-paths.test.js.map
\ No newline at end of file
diff --git a/lib/analysis-paths.test.js.map b/lib/analysis-paths.test.js.map
index 8a8ea7c42..cf4958c1b 100644
--- a/lib/analysis-paths.test.js.map
+++ b/lib/analysis-paths.test.js.map
@@ -1 +1 @@
-{"version":3,"file":"analysis-paths.test.js","sourceRoot":"","sources":["../src/analysis-paths.test.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,8CAAuB;AAEvB,gEAAkD;AAClD,mDAA2C;AAE3C,0BAAU,CAAC,aAAI,CAAC,CAAC;AAEjB,aAAI,CAAC,YAAY,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IAC3B,MAAM,MAAM,GAAG;QACb,SAAS,EAAE,EAAE;QACb,OAAO,EAAE,EAAE;QACX,WAAW,EAAE,EAAE;QACf,KAAK,EAAE,EAAE;QACT,iBAAiB,EAAE,EAAE;KACtB,CAAC;IACF,aAAa,CAAC,8BAA8B,CAAC,MAAM,CAAC,CAAC;IACrD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,SAAS,CAAC,CAAC;IACnD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,SAAS,CAAC,CAAC;IACnD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,SAAS,CAAC,CAAC;AACrD,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,eAAe,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IAC9B,MAAM,MAAM,GAAG;QACb,SAAS,EAAE,EAAE;QACb,OAAO,EAAE,EAAE;QACX,KAAK,EAAE,CAAC,OAAO,EAAE,OAAO,EAAE,UAAU,CAAC;QACrC,WAAW,EAAE,CAAC,OAAO,EAAE,OAAO,EAAE,UAAU,CAAC;QAC3C,iBAAiB,EAAE,EAAE;KACtB,CAAC;IACF,aAAa,CAAC,8BAA8B,CAAC,MAAM,CAAC,CAAC;IACrD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,cAAc,CAAC,CAAC;IACxD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,cAAc,CAAC,CAAC;IACxD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,gGAAgG,CAAC,CAAC;AAC5I,CAAC,CAAC,CAAC"}
\ No newline at end of file
+{"version":3,"file":"analysis-paths.test.js","sourceRoot":"","sources":["../src/analysis-paths.test.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,8CAAuB;AAEvB,gEAAkD;AAClD,mDAA2C;AAC3C,6CAA+B;AAE/B,0BAAU,CAAC,aAAI,CAAC,CAAC;AAEjB,aAAI,CAAC,YAAY,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IAC3B,OAAO,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAC,MAAM,EAAC,EAAE;QAC1C,MAAM,MAAM,GAAG;YACb,SAAS,EAAE,EAAE;YACb,OAAO,EAAE,EAAE;YACX,WAAW,EAAE,EAAE;YACf,KAAK,EAAE,EAAE;YACT,iBAAiB,EAAE,EAAE;YACrB,OAAO,EAAE,MAAM;YACf,YAAY,EAAE,MAAM;YACpB,SAAS,EAAE,EAAE;SACd,CAAC;QACF,aAAa,CAAC,8BAA8B,CAAC,MAAM,CAAC,CAAC;QACrD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,SAAS,CAAC,CAAC;QACnD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,SAAS,CAAC,CAAC;QACnD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,SAAS,CAAC,CAAC;IACrD,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,eAAe,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IAC9B,OAAO,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAC,MAAM,EAAC,EAAE;QAC1C,MAAM,MAAM,GAAG;YACb,SAAS,EAAE,EAAE;YACb,OAAO,EAAE,EAAE;YACX,KAAK,EAAE,CAAC,OAAO,EAAE,OAAO,EAAE,UAAU,CAAC;YACrC,WAAW,EAAE,CAAC,OAAO,EAAE,OAAO,EAAE,UAAU,CAAC;YAC3C,iBAAiB,EAAE,EAAE;YACrB,OAAO,EAAE,MAAM;YACf,YAAY,EAAE,MAAM;YACpB,SAAS,EAAE,EAAE;SACd,CAAC;QACF,aAAa,CAAC,8BAA8B,CAAC,MAAM,CAAC,CAAC;QACrD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,cAAc,CAAC,CAAC;QACxD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,cAAc,CAAC,CAAC;QACxD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,gGAAgG,CAAC,CAAC;IAC5I,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}
\ No newline at end of file
diff --git a/lib/autobuild.js b/lib/autobuild.js
index a1b98ce61..9a7414723 100644
--- a/lib/autobuild.js
+++ b/lib/autobuild.js
@@ -10,6 +10,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const core = __importStar(require("@actions/core"));
 const codeql_1 = require("./codeql");
 const config_utils = __importStar(require("./config-utils"));
+const languages_1 = require("./languages");
 const util = __importStar(require("./util"));
 async function sendCompletedStatusReport(startedAt, allLanguages, failingLanguage, cause) {
     var _a, _b;
@@ -30,12 +31,12 @@ async function run() {
         if (!await util.sendStatusReport(await util.createStatusReportBase('autobuild', 'starting', startedAt), true)) {
             return;
         }
-        const config = await config_utils.getConfig();
+        const config = await config_utils.getConfig(util.getRequiredEnvParam('RUNNER_TEMP'));
         // Attempt to find a language to autobuild
         // We want pick the dominant language in the repo from the ones we're able to build
         // The languages are sorted in order specified by user or by lines of code if we got
         // them from the GitHub API, so try to build the first language on the list.
-        const autobuildLanguages = config.languages.filter(codeql_1.isTracedLanguage);
+        const autobuildLanguages = config.languages.filter(languages_1.isTracedLanguage);
         language = autobuildLanguages[0];
         if (!language) {
             core.info("None of the languages in this project require extra build steps");
@@ -46,7 +47,7 @@ async function run() {
             core.warning(`We will only automatically build ${language} code. If you wish to scan ${autobuildLanguages.slice(1).join(' and ')}, you must replace this block with custom build steps.`);
         }
         core.startGroup(`Attempting to automatically build ${language} code`);
-        const codeQL = codeql_1.getCodeQL();
+        const codeQL = codeql_1.getCodeQL(config.codeQLCmd);
         await codeQL.runAutobuild(language);
         core.endGroup();
     }
diff --git a/lib/autobuild.js.map b/lib/autobuild.js.map
index 701d0cda5..ae6f40580 100644
--- a/lib/autobuild.js.map
+++ b/lib/autobuild.js.map
@@ -1 +1 @@
-{"version":3,"file":"autobuild.js","sourceRoot":"","sources":["../src/autobuild.ts"],"names":[],"mappings":";;;;;;;;;AAAA,oDAAsC;AAEtC,qCAAuD;AACvD,6DAA+C;AAC/C,6CAA+B;AAS/B,KAAK,UAAU,yBAAyB,CACtC,SAAe,EACf,YAAsB,EACtB,eAAwB,EACxB,KAAa;;IAEb,MAAM,MAAM,GAAG,eAAe,KAAK,SAAS,IAAI,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC;IAC5F,MAAM,gBAAgB,GAAG,MAAM,IAAI,CAAC,sBAAsB,CACxD,WAAW,EACX,MAAM,EACN,SAAS,QACT,KAAK,0CAAE,OAAO,QACd,KAAK,0CAAE,KAAK,CAAC,CAAC;IAChB,MAAM,YAAY,GAA0B;QAC1C,GAAG,gBAAgB;QACnB,mBAAmB,EAAE,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC;QAC3C,iBAAiB,EAAE,eAAe;KACnC,CAAC;IACF,MAAM,IAAI,CAAC,gBAAgB,CAAC,YAAY,CAAC,CAAC;AAC5C,CAAC;AAED,KAAK,UAAU,GAAG;IAChB,MAAM,SAAS,GAAG,IAAI,IAAI,EAAE,CAAC;IAC7B,IAAI,QAAQ,CAAC;IACb,IAAI;QACF,IAAI,CAAC,0BAA0B,EAAE,CAAC;QAClC,IAAI,CAAC,MAAM,IAAI,CAAC,gBAAgB,CAAC,MAAM,IAAI,CAAC,sBAAsB,CAAC,WAAW,EAAE,UAAU,EAAE,SAAS,CAAC,EAAE,IAAI,CAAC,EAAE;YAC7G,OAAO;SACR;QAED,MAAM,MAAM,GAAG,MAAM,YAAY,CAAC,SAAS,EAAE,CAAC;QAE9C,0CAA0C;QAC1C,mFAAmF;QACnF,oFAAoF;QACpF,4EAA4E;QAC5E,MAAM,kBAAkB,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,yBAAgB,CAAC,CAAC;QACrE,QAAQ,GAAG,kBAAkB,CAAC,CAAC,CAAC,CAAC;QAEjC,IAAI,CAAC,QAAQ,EAAE;YACb,IAAI,CAAC,IAAI,CAAC,iEAAiE,CAAC,CAAC;YAC7E,OAAO;SACR;QAED,IAAI,CAAC,KAAK,CAAC,sCAAsC,QAAQ,EAAE,CAAC,CAAC;QAE7D,IAAI,kBAAkB,CAAC,MAAM,GAAG,CAAC,EAAE;YACjC,IAAI,CAAC,OAAO,CAAC,oCAAoC,QAAQ,8BAA8B,kBAAkB,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,wDAAwD,CAAC,CAAC;SAC3L;QAED,IAAI,CAAC,UAAU,CAAC,qCAAqC,QAAQ,OAAO,CAAC,CAAC;QACtE,MAAM,MAAM,GAAG,kBAAS,EAAE,CAAC;QAC3B,MAAM,MAAM,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC;QAEpC,IAAI,CAAC,QAAQ,EAAE,CAAC;KAEjB;IAAC,OAAO,KAAK,EAAE;QACd,IAAI,CAAC,SAAS,CAAC,kIAAkI,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC;QACnK,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;QACnB,MAAM,yBAAyB,CAAC,SAAS,EAAE,CAAC,QAAQ,CAAC,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC;QACxE,OAAO;KACR;IAED,MAAM,yBAAyB,CAAC,SAAS,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC;AACzD,CAAC;AAED,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;IACd,IAAI,CAAC,SAAS,CAAC,4BAA4B,GAAG,CAAC,CAAC,CAAC;IACjD,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;AACjB,CAAC,CAAC,CAAC"}
\ No newline at end of file
+{"version":3,"file":"autobuild.js","sourceRoot":"","sources":["../src/autobuild.ts"],"names":[],"mappings":";;;;;;;;;AAAA,oDAAsC;AAEtC,qCAAqC;AACrC,6DAA+C;AAC/C,2CAA+C;AAC/C,6CAA+B;AAS/B,KAAK,UAAU,yBAAyB,CACtC,SAAe,EACf,YAAsB,EACtB,eAAwB,EACxB,KAAa;;IAEb,MAAM,MAAM,GAAG,eAAe,KAAK,SAAS,IAAI,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC;IAC5F,MAAM,gBAAgB,GAAG,MAAM,IAAI,CAAC,sBAAsB,CACxD,WAAW,EACX,MAAM,EACN,SAAS,QACT,KAAK,0CAAE,OAAO,QACd,KAAK,0CAAE,KAAK,CAAC,CAAC;IAChB,MAAM,YAAY,GAA0B;QAC1C,GAAG,gBAAgB;QACnB,mBAAmB,EAAE,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC;QAC3C,iBAAiB,EAAE,eAAe;KACnC,CAAC;IACF,MAAM,IAAI,CAAC,gBAAgB,CAAC,YAAY,CAAC,CAAC;AAC5C,CAAC;AAED,KAAK,UAAU,GAAG;IAChB,MAAM,SAAS,GAAG,IAAI,IAAI,EAAE,CAAC;IAC7B,IAAI,QAAQ,CAAC;IACb,IAAI;QACF,IAAI,CAAC,0BAA0B,EAAE,CAAC;QAClC,IAAI,CAAC,MAAM,IAAI,CAAC,gBAAgB,CAAC,MAAM,IAAI,CAAC,sBAAsB,CAAC,WAAW,EAAE,UAAU,EAAE,SAAS,CAAC,EAAE,IAAI,CAAC,EAAE;YAC7G,OAAO;SACR;QAED,MAAM,MAAM,GAAG,MAAM,YAAY,CAAC,SAAS,CAAC,IAAI,CAAC,mBAAmB,CAAC,aAAa,CAAC,CAAC,CAAC;QAErF,0CAA0C;QAC1C,mFAAmF;QACnF,oFAAoF;QACpF,4EAA4E;QAC5E,MAAM,kBAAkB,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,4BAAgB,CAAC,CAAC;QACrE,QAAQ,GAAG,kBAAkB,CAAC,CAAC,CAAC,CAAC;QAEjC,IAAI,CAAC,QAAQ,EAAE;YACb,IAAI,CAAC,IAAI,CAAC,iEAAiE,CAAC,CAAC;YAC7E,OAAO;SACR;QAED,IAAI,CAAC,KAAK,CAAC,sCAAsC,QAAQ,EAAE,CAAC,CAAC;QAE7D,IAAI,kBAAkB,CAAC,MAAM,GAAG,CAAC,EAAE;YACjC,IAAI,CAAC,OAAO,CAAC,oCAAoC,QAAQ,8BAA8B,kBAAkB,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,wDAAwD,CAAC,CAAC;SAC3L;QAED,IAAI,CAAC,UAAU,CAAC,qCAAqC,QAAQ,OAAO,CAAC,CAAC;QACtE,MAAM,MAAM,GAAG,kBAAS,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;QAC3C,MAAM,MAAM,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC;QAEpC,IAAI,CAAC,QAAQ,EAAE,CAAC;KAEjB;IAAC,OAAO,KAAK,EAAE;QACd,IAAI,CAAC,SAAS,CAAC,kIAAkI,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC;QACnK,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC;QACnB,MAAM,yBAAyB,CAAC,SAAS,EAAE,CAAC,QAAQ,CAAC,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC;QACxE,OAAO;KACR;IAED,MAAM,yBAAyB,CAAC,SAAS,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC;AACzD,CAAC;AAED,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;IACd,IAAI,CAAC,SAAS,CAAC,4BAA4B,GAAG,CAAC,CAAC,CAAC;IACjD,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;AACjB,CAAC,CAAC,CAAC"}
\ No newline at end of file
diff --git a/lib/codeql.js b/lib/codeql.js
index c0586d9fa..3c7cf10c8 100644
--- a/lib/codeql.js
+++ b/lib/codeql.js
@@ -28,11 +28,6 @@ const util = __importStar(require("./util"));
  * Can be overridden in tests using `setCodeQL`.
  */
 let cachedCodeQL = undefined;
-/**
- * Environment variable used to store the location of the CodeQL CLI executable.
- * Value is set by setupCodeQL and read by getCodeQL.
- */
-const CODEQL_ACTION_CMD = "CODEQL_ACTION_CMD";
 const CODEQL_BUNDLE_VERSION = defaults.bundleVersion;
 const CODEQL_BUNDLE_NAME = "codeql-bundle.tar.gz";
 const CODEQL_DEFAULT_ACTION_REPOSITORY = "github/codeql-action";
@@ -143,7 +138,6 @@ async function setupCodeQL() {
             throw new Error("Unsupported platform: " + process.platform);
         }
         cachedCodeQL = getCodeQLForCmd(codeqlCmd);
-        core.exportVariable(CODEQL_ACTION_CMD, codeqlCmd);
         return cachedCodeQL;
     }
     catch (e) {
@@ -169,16 +163,21 @@ function getCodeQLURLVersion(url) {
     return s;
 }
 exports.getCodeQLURLVersion = getCodeQLURLVersion;
-function getCodeQL() {
+/**
+ * Use the CodeQL executable located at the given path.
+ */
+function getCodeQL(cmd) {
     if (cachedCodeQL === undefined) {
-        const codeqlCmd = util.getRequiredEnvParam(CODEQL_ACTION_CMD);
-        cachedCodeQL = getCodeQLForCmd(codeqlCmd);
+        cachedCodeQL = getCodeQLForCmd(cmd);
     }
     return cachedCodeQL;
 }
 exports.getCodeQL = getCodeQL;
-function resolveFunction(partialCodeql, methodName) {
+function resolveFunction(partialCodeql, methodName, defaultImplementation) {
     if (typeof partialCodeql[methodName] !== 'function') {
+        if (defaultImplementation !== undefined) {
+            return defaultImplementation;
+        }
         const dummyMethod = () => {
             throw new Error('CodeQL ' + methodName + ' method not correctly defined');
         };
@@ -194,7 +193,7 @@ function resolveFunction(partialCodeql, methodName) {
  */
 function setCodeQL(partialCodeql) {
     cachedCodeQL = {
-        getDir: resolveFunction(partialCodeql, 'getDir'),
+        getPath: resolveFunction(partialCodeql, 'getPath', () => '/tmp/dummy-path'),
         printVersion: resolveFunction(partialCodeql, 'printVersion'),
         getTracerEnv: resolveFunction(partialCodeql, 'getTracerEnv'),
         databaseInit: resolveFunction(partialCodeql, 'databaseInit'),
@@ -204,12 +203,27 @@ function setCodeQL(partialCodeql) {
         resolveQueries: resolveFunction(partialCodeql, 'resolveQueries'),
         databaseAnalyze: resolveFunction(partialCodeql, 'databaseAnalyze')
     };
+    return cachedCodeQL;
 }
 exports.setCodeQL = setCodeQL;
+/**
+ * Get the cached CodeQL object. Should only be used from tests.
+ *
+ * TODO: Work out a good way for tests to get this from the test context
+ * instead of having to have this method.
+ */
+function getCachedCodeQL() {
+    if (cachedCodeQL === undefined) {
+        // Should never happen as setCodeQL is called by testing-utils.setupTests
+        throw new Error('cachedCodeQL undefined');
+    }
+    return cachedCodeQL;
+}
+exports.getCachedCodeQL = getCachedCodeQL;
 function getCodeQLForCmd(cmd) {
     return {
-        getDir: function () {
-            return path.dirname(cmd);
+        getPath: function () {
+            return cmd;
         },
         printVersion: async function () {
             await exec.exec(cmd, [
@@ -225,6 +239,7 @@ function getCodeQLForCmd(cmd) {
                 'trace-command',
                 databasePath,
                 ...compilerSpecArg,
+                ...getExtraOptionsFromEnv(['database', 'trace-command']),
                 process.execPath,
                 path.resolve(__dirname, 'tracer-env.js'),
                 envFile
@@ -238,6 +253,7 @@ function getCodeQLForCmd(cmd) {
                 databasePath,
                 '--language=' + language,
                 '--source-root=' + sourceRoot,
+                ...getExtraOptionsFromEnv(['database', 'init']),
             ]);
         },
         runAutobuild: async function (language) {
@@ -259,7 +275,8 @@ function getCodeQLForCmd(cmd) {
                 'resolve',
                 'extractor',
                 '--format=json',
-                '--language=' + language
+                '--language=' + language,
+                ...getExtraOptionsFromEnv(['resolve', 'extractor']),
             ], {
                 silent: true,
                 listeners: {
@@ -274,6 +291,7 @@ function getCodeQLForCmd(cmd) {
             await exec.exec(cmd, [
                 'database',
                 'trace-command',
+                ...getExtraOptionsFromEnv(['database', 'trace-command']),
                 databasePath,
                 '--',
                 traceCommand
@@ -283,6 +301,7 @@ function getCodeQLForCmd(cmd) {
             await exec.exec(cmd, [
                 'database',
                 'finalize',
+                ...getExtraOptionsFromEnv(['database', 'finalize']),
                 databasePath
             ]);
         },
@@ -291,7 +310,8 @@ function getCodeQLForCmd(cmd) {
                 'resolve',
                 'queries',
                 ...queries,
-                '--format=bylanguage'
+                '--format=bylanguage',
+                ...getExtraOptionsFromEnv(['resolve', 'queries'])
             ];
             if (extraSearchPath !== undefined) {
                 codeqlArgs.push('--search-path', extraSearchPath);
@@ -316,17 +336,54 @@ function getCodeQLForCmd(cmd) {
                 '--format=sarif-latest',
                 '--output=' + sarifFile,
                 '--no-sarif-add-snippets',
+                ...getExtraOptionsFromEnv(['database', 'analyze']),
                 querySuite
             ]);
         }
     };
 }
-function isTracedLanguage(language) {
-    return ['cpp', 'java', 'csharp'].includes(language);
+/**
+ * Gets the options for `path` of `options` as an array of extra option strings.
+ */
+function getExtraOptionsFromEnv(path) {
+    let options = util.getExtraOptionsEnvParam();
+    return getExtraOptions(options, path, []);
 }
-exports.isTracedLanguage = isTracedLanguage;
-function isScannedLanguage(language) {
-    return !isTracedLanguage(language);
+/**
+ * Gets the options for `path` of `options` as an array of extra option strings.
+ *
+ * - the special terminal step name '*' in `options` matches all path steps
+ * - throws an exception if this conversion is impossible.
+ */
+function getExtraOptions(options, path, pathInfo) {
+    var _a, _b, _c;
+    /**
+     * Gets `options` as an array of extra option strings.
+     *
+     * - throws an exception mentioning `pathInfo` if this conversion is impossible.
+     */
+    function asExtraOptions(options, pathInfo) {
+        if (options === undefined) {
+            return [];
+        }
+        if (!Array.isArray(options)) {
+            const msg = `The extra options for '${pathInfo.join('.')}' ('${JSON.stringify(options)}') are not in an array.`;
+            throw new Error(msg);
+        }
+        return options.map(o => {
+            const t = typeof o;
+            if (t !== 'string' && t !== 'number' && t !== 'boolean') {
+                const msg = `The extra option for '${pathInfo.join('.')}' ('${JSON.stringify(o)}') is not a primitive value.`;
+                throw new Error(msg);
+            }
+            return o + '';
+        });
+    }
+    let all = asExtraOptions((_a = options) === null || _a === void 0 ? void 0 : _a['*'], pathInfo.concat('*'));
+    let specific = path.length === 0 ?
+        asExtraOptions(options, pathInfo) :
+        getExtraOptions((_b = options) === null || _b === void 0 ? void 0 : _b[path[0]], (_c = path) === null || _c === void 0 ? void 0 : _c.slice(1), pathInfo.concat(path[0]));
+    return all.concat(specific);
 }
-exports.isScannedLanguage = isScannedLanguage;
+exports.getExtraOptions = getExtraOptions;
 //# sourceMappingURL=codeql.js.map
\ No newline at end of file
diff --git a/lib/codeql.js.map b/lib/codeql.js.map
index 624d21ed9..9856e6957 100644
--- a/lib/codeql.js.map
+++ b/lib/codeql.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/lib/codeql.test.js b/lib/codeql.test.js
index d41fe0684..a36a8f616 100644
--- a/lib/codeql.test.js
+++ b/lib/codeql.test.js
@@ -57,4 +57,26 @@ ava_1.default('parse codeql bundle url version', t => {
         }
     }
 });
+ava_1.default('getExtraOptions works for explicit paths', t => {
+    t.deepEqual(codeql.getExtraOptions({}, ['foo'], []), []);
+    t.deepEqual(codeql.getExtraOptions({ foo: [42] }, ['foo'], []), ['42']);
+    t.deepEqual(codeql.getExtraOptions({ foo: { bar: [42] } }, ['foo', 'bar'], []), ['42']);
+});
+ava_1.default('getExtraOptions works for wildcards', t => {
+    t.deepEqual(codeql.getExtraOptions({ '*': [42] }, ['foo'], []), ['42']);
+});
+ava_1.default('getExtraOptions works for wildcards and explicit paths', t => {
+    let o1 = { '*': [42], foo: [87] };
+    t.deepEqual(codeql.getExtraOptions(o1, ['foo'], []), ['42', '87']);
+    let o2 = { '*': [42], foo: [87] };
+    t.deepEqual(codeql.getExtraOptions(o2, ['foo', 'bar'], []), ['42']);
+    let o3 = { '*': [42], foo: { '*': [87], bar: [99] } };
+    let p = ['foo', 'bar'];
+    t.deepEqual(codeql.getExtraOptions(o3, p, []), ['42', '87', '99']);
+});
+ava_1.default('getExtraOptions throws for bad content', t => {
+    t.throws(() => codeql.getExtraOptions({ '*': 42 }, ['foo'], []));
+    t.throws(() => codeql.getExtraOptions({ foo: 87 }, ['foo'], []));
+    t.throws(() => codeql.getExtraOptions({ '*': [42], foo: { '*': 87, bar: [99] } }, ['foo', 'bar'], []));
+});
 //# sourceMappingURL=codeql.test.js.map
\ No newline at end of file
diff --git a/lib/codeql.test.js.map b/lib/codeql.test.js.map
index 5034ca12d..949d4ce19 100644
--- a/lib/codeql.test.js.map
+++ b/lib/codeql.test.js.map
@@ -1 +1 @@
-{"version":3,"file":"codeql.test.js","sourceRoot":"","sources":["../src/codeql.test.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,+DAAiD;AACjD,8CAAuB;AACvB,gDAAwB;AACxB,2CAA6B;AAE7B,iDAAmC;AACnC,mDAA2C;AAC3C,6CAA+B;AAE/B,0BAAU,CAAC,aAAI,CAAC,CAAC;AAEjB,aAAI,CAAC,8BAA8B,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IAE7C,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAC,MAAM,EAAC,EAAE;QAEnC,OAAO,CAAC,GAAG,CAAC,kBAAkB,CAAC,GAAG,MAAM,CAAC;QAEzC,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QACvD,OAAO,CAAC,GAAG,CAAC,mBAAmB,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;QAE9D,MAAM,QAAQ,GAAG,CAAC,UAAU,EAAE,UAAU,CAAC,CAAC;QAE1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC;YAE5B,cAAI,CAAC,qBAAqB,CAAC;iBACxB,GAAG,CAAC,2BAA2B,OAAO,uBAAuB,CAAC;iBAC9D,aAAa,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,uCAAuC,CAAC,CAAC,CAAC;YAGrF,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,GAAG,8CAA8C,OAAO,uBAAuB,CAAC;YAE1G,MAAM,MAAM,CAAC,WAAW,EAAE,CAAC;YAE3B,CAAC,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,QAAQ,EAAE,SAAS,OAAO,EAAE,CAAC,CAAC,CAAC;SACxD;QAED,MAAM,cAAc,GAAG,SAAS,CAAC,eAAe,CAAC,QAAQ,CAAC,CAAC;QAE3D,CAAC,CAAC,EAAE,CAAC,cAAc,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC;IACjC,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,iCAAiC,EAAE,CAAC,CAAC,EAAE;IAE1C,MAAM,KAAK,GAAG;QACZ,UAAU,EAAE,gBAAgB;QAC5B,YAAY,EAAE,kBAAkB;QAChC,cAAc,EAAE,cAAc;QAC9B,OAAO,EAAE,OAAO;QAChB,aAAa,EAAE,aAAa;QAC5B,cAAc,EAAE,cAAc;KAC/B,CAAC;IAEF,KAAK,MAAM,CAAC,OAAO,EAAE,eAAe,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;QAC9D,MAAM,GAAG,GAAG,wCAAwC,OAAO,MAAM,CAAC;QAElE,IAAI;YACF,MAAM,aAAa,GAAG,MAAM,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAC;YACtD,CAAC,CAAC,SAAS,CAAC,aAAa,EAAE,eAAe,CAAC,CAAC;SAC7C;QAAC,OAAO,CAAC,EAAE;YACV,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC;SACnB;KACF;AACH,CAAC,CAAC,CAAC"}
\ No newline at end of file
+{"version":3,"file":"codeql.test.js","sourceRoot":"","sources":["../src/codeql.test.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,+DAAiD;AACjD,8CAAuB;AACvB,gDAAwB;AACxB,2CAA6B;AAE7B,iDAAmC;AACnC,mDAA2C;AAC3C,6CAA+B;AAE/B,0BAAU,CAAC,aAAI,CAAC,CAAC;AAEjB,aAAI,CAAC,8BAA8B,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IAE7C,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAC,MAAM,EAAC,EAAE;QAEnC,OAAO,CAAC,GAAG,CAAC,kBAAkB,CAAC,GAAG,MAAM,CAAC;QAEzC,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QACvD,OAAO,CAAC,GAAG,CAAC,mBAAmB,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;QAE9D,MAAM,QAAQ,GAAG,CAAC,UAAU,EAAE,UAAU,CAAC,CAAC;QAE1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC;YAE5B,cAAI,CAAC,qBAAqB,CAAC;iBACxB,GAAG,CAAC,2BAA2B,OAAO,uBAAuB,CAAC;iBAC9D,aAAa,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,uCAAuC,CAAC,CAAC,CAAC;YAGrF,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,GAAG,8CAA8C,OAAO,uBAAuB,CAAC;YAE1G,MAAM,MAAM,CAAC,WAAW,EAAE,CAAC;YAE3B,CAAC,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,QAAQ,EAAE,SAAS,OAAO,EAAE,CAAC,CAAC,CAAC;SACxD;QAED,MAAM,cAAc,GAAG,SAAS,CAAC,eAAe,CAAC,QAAQ,CAAC,CAAC;QAE3D,CAAC,CAAC,EAAE,CAAC,cAAc,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC;IACjC,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,iCAAiC,EAAE,CAAC,CAAC,EAAE;IAE1C,MAAM,KAAK,GAAG;QACZ,UAAU,EAAE,gBAAgB;QAC5B,YAAY,EAAE,kBAAkB;QAChC,cAAc,EAAE,cAAc;QAC9B,OAAO,EAAE,OAAO;QAChB,aAAa,EAAE,aAAa;QAC5B,cAAc,EAAE,cAAc;KAC/B,CAAC;IAEF,KAAK,MAAM,CAAC,OAAO,EAAE,eAAe,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;QAC9D,MAAM,GAAG,GAAG,wCAAwC,OAAO,MAAM,CAAC;QAElE,IAAI;YACF,MAAM,aAAa,GAAG,MAAM,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAC;YACtD,CAAC,CAAC,SAAS,CAAC,aAAa,EAAE,eAAe,CAAC,CAAC;SAC7C;QAAC,OAAO,CAAC,EAAE;YACV,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC;SACnB;KACF;AACH,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,0CAA0C,EAAE,CAAC,CAAC,EAAE;IACnD,CAAC,CAAC,SAAS,CAAC,MAAM,CAAC,eAAe,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC;IAEzD,CAAC,CAAC,SAAS,CAAC,MAAM,CAAC,eAAe,CAAC,EAAC,GAAG,EAAE,CAAC,EAAE,CAAC,EAAC,EAAE,CAAC,KAAK,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC;IAEtE,CAAC,CAAC,SAAS,CAAC,MAAM,CAAC,eAAe,CAAC,EAAC,GAAG,EAAE,EAAC,GAAG,EAAE,CAAC,EAAE,CAAC,EAAC,EAAC,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC;AACtF,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,qCAAqC,EAAE,CAAC,CAAC,EAAE;IAC9C,CAAC,CAAC,SAAS,CAAC,MAAM,CAAC,eAAe,CAAC,EAAC,GAAG,EAAE,CAAC,EAAE,CAAC,EAAC,EAAE,CAAC,KAAK,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC;AACxE,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,wDAAwD,EAAE,CAAC,CAAC,EAAE;IACjE,IAAI,EAAE,GAAG,EAAC,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC;IAChC,CAAC,CAAC,SAAS,CAAC,MAAM,CAAC,eAAe,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC,CAAC;IAEnE,IAAI,EAAE,GAAG,EAAC,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC;IAChC,CAAC,CAAC,SAAS,CAAC,MAAM,CAAC,eAAe,CAAC,EAAE,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC;IAEpE,IAAI,EAAE,GAAG,EAAC,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAC,EAAC,CAAC;IACnD,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;IACvB,CAAC,CAAC,SAAS,CAAC,MAAM,CAAC,eAAe,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC,CAAC;AACrE,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,wCAAwC,EAAE,CAAC,CAAC,EAAE;IACjD,CAAC,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,eAAe,CAAC,EAAC,GAAG,EAAE,EAAE,EAAC,EAAE,CAAC,KAAK,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;IAE/D,CAAC,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,eAAe,CAAC,EAAC,GAAG,EAAE,EAAE,EAAC,EAAE,CAAC,KAAK,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;IAE/D,CAAC,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,eAAe,CAAC,EAAC,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAC,EAAC,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;AACtG,CAAC,CAAC,CAAC"}
\ No newline at end of file
diff --git a/lib/config-utils.js b/lib/config-utils.js
index f3ef4843b..ef6829521 100644
--- a/lib/config-utils.js
+++ b/lib/config-utils.js
@@ -12,8 +12,8 @@ const fs = __importStar(require("fs"));
 const yaml = __importStar(require("js-yaml"));
 const path = __importStar(require("path"));
 const api = __importStar(require("./api-client"));
-const codeql_1 = require("./codeql");
 const externalQueries = __importStar(require("./external-queries"));
+const languages_1 = require("./languages");
 const util = __importStar(require("./util"));
 // Property names from the user-supplied config file.
 const NAME_PROPERTY = 'name';
@@ -22,13 +22,6 @@ const QUERIES_PROPERTY = 'queries';
 const QUERIES_USES_PROPERTY = 'uses';
 const PATHS_IGNORE_PROPERTY = 'paths-ignore';
 const PATHS_PROPERTY = 'paths';
-// All the languages supported by CodeQL
-const ALL_LANGUAGES = ['csharp', 'cpp', 'go', 'java', 'javascript', 'python'];
-// Some alternate names for languages
-const LANGUAGE_ALIASES = {
-    'c': 'cpp',
-    'typescript': 'javascript',
-};
 /**
  * A list of queries from https://github.com/github/codeql that
  * we don't want to run. Disabling them here is a quicker alternative to
@@ -71,9 +64,8 @@ function validateQueries(resolvedQueries) {
 /**
  * Run 'codeql resolve queries' and add the results to resultMap
  */
-async function runResolveQueries(resultMap, toResolve, extraSearchPath, errorOnInvalidQueries) {
-    const codeQl = codeql_1.getCodeQL();
-    const resolvedQueries = await codeQl.resolveQueries(toResolve, extraSearchPath);
+async function runResolveQueries(codeQL, resultMap, toResolve, extraSearchPath, errorOnInvalidQueries) {
+    const resolvedQueries = await codeQL.resolveQueries(toResolve, extraSearchPath);
     for (const [language, queries] of Object.entries(resolvedQueries.byLanguage)) {
         if (resultMap[language] === undefined) {
             resultMap[language] = [];
@@ -87,9 +79,9 @@ async function runResolveQueries(resultMap, toResolve, extraSearchPath, errorOnI
 /**
  * Get the set of queries included by default.
  */
-async function addDefaultQueries(languages, resultMap) {
+async function addDefaultQueries(codeQL, languages, resultMap) {
     const suites = languages.map(l => l + '-code-scanning.qls');
-    await runResolveQueries(resultMap, suites, undefined, false);
+    await runResolveQueries(codeQL, resultMap, suites, undefined, false);
 }
 // The set of acceptable values for built-in suites from the codeql bundle
 const builtinSuites = ['security-extended', 'security-and-quality'];
@@ -97,18 +89,18 @@ const builtinSuites = ['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.
  */
-async function addBuiltinSuiteQueries(configFile, languages, resultMap, suiteName) {
+async function addBuiltinSuiteQueries(configFile, languages, codeQL, resultMap, suiteName) {
     const suite = builtinSuites.find((suite) => suite === suiteName);
     if (!suite) {
         throw new Error(getQueryUsesInvalid(configFile, suiteName));
     }
     const suites = languages.map(l => l + '-' + suiteName + '.qls');
-    await runResolveQueries(resultMap, suites, undefined, false);
+    await runResolveQueries(codeQL, resultMap, suites, undefined, false);
 }
 /**
  * Retrieve the set of queries at localQueryPath and add them to resultMap.
  */
-async function addLocalQueries(configFile, resultMap, localQueryPath) {
+async function addLocalQueries(configFile, codeQL, resultMap, localQueryPath) {
     // Resolve the local path against the workspace so that when this is
     // passed to codeql it resolves to exactly the path we expect it to resolve to.
     const workspacePath = fs.realpathSync(util.getRequiredEnvParam('GITHUB_WORKSPACE'));
@@ -125,12 +117,12 @@ async function addLocalQueries(configFile, resultMap, localQueryPath) {
     }
     // Get the root of the current repo to use when resolving query dependencies
     const rootOfRepo = util.getRequiredEnvParam('GITHUB_WORKSPACE');
-    await runResolveQueries(resultMap, [absoluteQueryPath], rootOfRepo, true);
+    await runResolveQueries(codeQL, resultMap, [absoluteQueryPath], rootOfRepo, true);
 }
 /**
  * Retrieve the set of queries at the referenced remote repo and add them to resultMap.
  */
-async function addRemoteQueries(configFile, resultMap, queryUses) {
+async function addRemoteQueries(configFile, codeQL, resultMap, queryUses, tempDir) {
     let tok = queryUses.split('@');
     if (tok.length !== 2) {
         throw new Error(getQueryUsesInvalid(configFile, queryUses));
@@ -149,11 +141,11 @@ async function addRemoteQueries(configFile, resultMap, queryUses) {
     }
     const nwo = tok[0] + '/' + tok[1];
     // Checkout the external repository
-    const rootOfRepo = await externalQueries.checkoutExternalRepository(nwo, ref);
+    const rootOfRepo = await externalQueries.checkoutExternalRepository(nwo, ref, tempDir);
     const queryPath = tok.length > 2
         ? path.join(rootOfRepo, tok.slice(2).join('/'))
         : rootOfRepo;
-    await runResolveQueries(resultMap, [queryPath], rootOfRepo, true);
+    await runResolveQueries(codeQL, resultMap, [queryPath], rootOfRepo, true);
 }
 /**
  * Parse a query 'uses' field to a discrete set of query files and update resultMap.
@@ -163,23 +155,23 @@ async function addRemoteQueries(configFile, resultMap, queryUses) {
  * local paths starting with './', or references to remote repos, or
  * a finite set of hardcoded terms for builtin suites.
  */
-async function parseQueryUses(configFile, languages, resultMap, queryUses) {
+async function parseQueryUses(configFile, languages, codeQL, resultMap, queryUses, tempDir) {
     queryUses = queryUses.trim();
     if (queryUses === "") {
         throw new Error(getQueryUsesInvalid(configFile));
     }
     // Check for the local path case before we start trying to parse the repository name
     if (queryUses.startsWith("./")) {
-        await addLocalQueries(configFile, resultMap, queryUses.slice(2));
+        await addLocalQueries(configFile, codeQL, resultMap, queryUses.slice(2));
         return;
     }
     // Check for one of the builtin suites
     if (queryUses.indexOf('/') === -1 && queryUses.indexOf('@') === -1) {
-        await addBuiltinSuiteQueries(configFile, languages, resultMap, queryUses);
+        await addBuiltinSuiteQueries(configFile, languages, codeQL, resultMap, queryUses);
         return;
     }
     // Otherwise, must be a reference to another repo
-    await addRemoteQueries(configFile, resultMap, queryUses);
+    await addRemoteQueries(configFile, codeQL, resultMap, queryUses, tempDir);
 }
 // Regex validating stars in paths or paths-ignore entries.
 // The intention is to only allow ** to appear when immediately
@@ -300,17 +292,6 @@ exports.getUnknownLanguagesError = getUnknownLanguagesError;
  */
 async function getLanguagesInRepo() {
     var _a;
-    // Translate between GitHub's API names for languages and ours
-    const codeqlLanguages = {
-        'C': 'cpp',
-        'C++': 'cpp',
-        'C#': 'csharp',
-        'Go': 'go',
-        'Java': 'java',
-        'JavaScript': 'javascript',
-        'TypeScript': 'javascript',
-        'Python': 'python',
-    };
     let repo_nwo = (_a = process.env['GITHUB_REPOSITORY']) === null || _a === void 0 ? void 0 : _a.split("/");
     if (repo_nwo) {
         let owner = repo_nwo[0];
@@ -326,9 +307,10 @@ async function getLanguagesInRepo() {
         // Since sets in javascript maintain insertion order, using a set here and then splatting it
         // into an array gives us an array of languages ordered by popularity
         let languages = new Set();
-        for (let lang in response.data) {
-            if (lang in codeqlLanguages) {
-                languages.add(codeqlLanguages[lang]);
+        for (let lang of Object.keys(response.data)) {
+            let parsedLang = languages_1.parseLanguage(lang);
+            if (parsedLang !== undefined) {
+                languages.add(parsedLang);
             }
         }
         return [...languages];
@@ -365,48 +347,45 @@ async function getLanguages() {
         throw new Error(getNoLanguagesError());
     }
     // Make sure they are supported
-    const checkedLanguages = [];
+    const parsedLanguages = [];
     const unknownLanguages = [];
     for (let language of languages) {
-        // Normalise to lower case
-        language = language.toLowerCase();
-        // Resolve any known aliases
-        if (language in LANGUAGE_ALIASES) {
-            language = LANGUAGE_ALIASES[language];
-        }
-        const checkedLanguage = ALL_LANGUAGES.find(l => l === language);
-        if (checkedLanguage === undefined) {
+        const parsedLanguage = languages_1.parseLanguage(language);
+        if (parsedLanguage === undefined) {
             unknownLanguages.push(language);
         }
-        else if (checkedLanguages.indexOf(checkedLanguage) === -1) {
-            checkedLanguages.push(checkedLanguage);
+        else if (parsedLanguages.indexOf(parsedLanguage) === -1) {
+            parsedLanguages.push(parsedLanguage);
         }
     }
     if (unknownLanguages.length > 0) {
         throw new Error(getUnknownLanguagesError(unknownLanguages));
     }
-    return checkedLanguages;
+    return parsedLanguages;
 }
 /**
  * Get the default config for when the user has not supplied one.
  */
-async function getDefaultConfig() {
+async function getDefaultConfig(tempDir, toolCacheDir, codeQL) {
     const languages = await getLanguages();
     const queries = {};
-    await addDefaultQueries(languages, queries);
+    await addDefaultQueries(codeQL, languages, queries);
     return {
         languages: languages,
         queries: queries,
         pathsIgnore: [],
         paths: [],
         originalUserInput: {},
+        tempDir,
+        toolCacheDir,
+        codeQLCmd: codeQL.getPath(),
     };
 }
 exports.getDefaultConfig = getDefaultConfig;
 /**
  * Load the config from the given file.
  */
-async function loadConfig(configFile) {
+async function loadConfig(configFile, tempDir, toolCacheDir, codeQL) {
     let parsedYAML;
     if (isLocal(configFile)) {
         // Treat the config file as relative to the workspace
@@ -439,7 +418,7 @@ async function loadConfig(configFile) {
         disableDefaultQueries = parsedYAML[DISABLE_DEFAULT_QUERIES_PROPERTY];
     }
     if (!disableDefaultQueries) {
-        await addDefaultQueries(languages, queries);
+        await addDefaultQueries(codeQL, languages, queries);
     }
     if (QUERIES_PROPERTY in parsedYAML) {
         if (!(parsedYAML[QUERIES_PROPERTY] instanceof Array)) {
@@ -449,7 +428,7 @@ async function loadConfig(configFile) {
             if (!(QUERIES_USES_PROPERTY in query) || typeof query[QUERIES_USES_PROPERTY] !== "string") {
                 throw new Error(getQueryUsesInvalid(configFile));
             }
-            await parseQueryUses(configFile, languages, queries, query[QUERIES_USES_PROPERTY]);
+            await parseQueryUses(configFile, languages, codeQL, queries, query[QUERIES_USES_PROPERTY], tempDir);
         }
     }
     if (PATHS_IGNORE_PROPERTY in parsedYAML) {
@@ -487,7 +466,10 @@ async function loadConfig(configFile) {
         queries,
         pathsIgnore,
         paths,
-        originalUserInput: parsedYAML
+        originalUserInput: parsedYAML,
+        tempDir,
+        toolCacheDir,
+        codeQLCmd: codeQL.getPath(),
     };
 }
 /**
@@ -496,16 +478,16 @@ async function loadConfig(configFile) {
  * This will parse the config from the user input if present, or generate
  * a default config. The parsed config is then stored to a known location.
  */
-async function initConfig() {
+async function initConfig(tempDir, toolCacheDir, codeQL) {
     const configFile = core.getInput('config-file');
     let config;
     // If no config file was provided create an empty one
     if (configFile === '') {
         core.debug('No configuration file was provided');
-        config = await getDefaultConfig();
+        config = await getDefaultConfig(tempDir, toolCacheDir, codeQL);
     }
     else {
-        config = await loadConfig(configFile);
+        config = await loadConfig(configFile, tempDir, toolCacheDir, codeQL);
     }
     // Save the config so we can easily access it again in the future
     await saveConfig(config);
@@ -559,8 +541,8 @@ async function getRemoteConfig(configFile) {
 /**
  * Get the file path where the parsed config will be stored.
  */
-function getPathToParsedConfigFile() {
-    return path.join(util.getRequiredEnvParam('RUNNER_TEMP'), 'config');
+function getPathToParsedConfigFile(tempDir) {
+    return path.join(tempDir, 'config');
 }
 exports.getPathToParsedConfigFile = getPathToParsedConfigFile;
 /**
@@ -568,7 +550,7 @@ exports.getPathToParsedConfigFile = getPathToParsedConfigFile;
  */
 async function saveConfig(config) {
     const configString = JSON.stringify(config);
-    const configFile = getPathToParsedConfigFile();
+    const configFile = getPathToParsedConfigFile(config.tempDir);
     fs.mkdirSync(path.dirname(configFile), { recursive: true });
     fs.writeFileSync(configFile, configString, 'utf8');
     core.debug('Saved config:');
@@ -582,8 +564,8 @@ async function saveConfig(config) {
  * stored to a known location. On the second and further calls, this will
  * return the contents of the parsed config from the known location.
  */
-async function getConfig() {
-    const configFile = getPathToParsedConfigFile();
+async function getConfig(tempDir) {
+    const configFile = getPathToParsedConfigFile(tempDir);
     if (!fs.existsSync(configFile)) {
         throw new Error("Config file could not be found at expected location. Has the 'init' action been called?");
     }
diff --git a/lib/config-utils.js.map b/lib/config-utils.js.map
index bd318ae53..dd8364d75 100644
--- a/lib/config-utils.js.map
+++ b/lib/config-utils.js.map
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\ No newline at end of file
diff --git a/lib/config-utils.test.js b/lib/config-utils.test.js
index 97218aa64..0ae54f4b7 100644
--- a/lib/config-utils.test.js
+++ b/lib/config-utils.test.js
@@ -16,8 +16,9 @@ const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const sinon_1 = __importDefault(require("sinon"));
 const api = __importStar(require("./api-client"));
-const CodeQL = __importStar(require("./codeql"));
+const codeql_1 = require("./codeql");
 const configUtils = __importStar(require("./config-utils"));
+const languages_1 = require("./languages");
 const testing_utils_1 = require("./testing-utils");
 const util = __importStar(require("./util"));
 testing_utils_1.setupTests(ava_1.default);
@@ -60,7 +61,7 @@ ava_1.default("load empty config", async (t) => {
         process.env['GITHUB_WORKSPACE'] = tmpDir;
         setInput('config-file', undefined);
         setInput('languages', 'javascript,python');
-        CodeQL.setCodeQL({
+        const codeQL = codeql_1.setCodeQL({
             resolveQueries: async function () {
                 return {
                     byLanguage: {},
@@ -69,8 +70,8 @@ ava_1.default("load empty config", async (t) => {
                 };
             },
         });
-        const config = await configUtils.initConfig();
-        t.deepEqual(config, await configUtils.getDefaultConfig());
+        const config = await configUtils.initConfig(tmpDir, tmpDir, codeQL);
+        t.deepEqual(config, await configUtils.getDefaultConfig(tmpDir, tmpDir, codeQL));
     });
 });
 ava_1.default("loading config saves config", async (t) => {
@@ -79,7 +80,7 @@ ava_1.default("loading config saves config", async (t) => {
         process.env['GITHUB_WORKSPACE'] = tmpDir;
         setInput('config-file', undefined);
         setInput('languages', 'javascript,python');
-        CodeQL.setCodeQL({
+        const codeQL = codeql_1.setCodeQL({
             resolveQueries: async function () {
                 return {
                     byLanguage: {},
@@ -89,14 +90,14 @@ ava_1.default("loading config saves config", async (t) => {
             },
         });
         // Sanity check the saved config file does not already exist
-        t.false(fs.existsSync(configUtils.getPathToParsedConfigFile()));
+        t.false(fs.existsSync(configUtils.getPathToParsedConfigFile(tmpDir)));
         // Sanity check that getConfig throws before we have called initConfig
-        await t.throwsAsync(configUtils.getConfig);
-        const config1 = await configUtils.initConfig();
+        await t.throwsAsync(() => configUtils.getConfig(tmpDir));
+        const config1 = await configUtils.initConfig(tmpDir, tmpDir, codeQL);
         // The saved config file should now exist
-        t.true(fs.existsSync(configUtils.getPathToParsedConfigFile()));
+        t.true(fs.existsSync(configUtils.getPathToParsedConfigFile(tmpDir)));
         // And that same newly-initialised config should now be returned by getConfig
-        const config2 = await configUtils.getConfig();
+        const config2 = await configUtils.getConfig(tmpDir);
         t.deepEqual(config1, config2);
     });
 });
@@ -106,7 +107,7 @@ ava_1.default("load input outside of workspace", async (t) => {
         process.env['GITHUB_WORKSPACE'] = tmpDir;
         setInput('config-file', '../input');
         try {
-            await configUtils.initConfig();
+            await configUtils.initConfig(tmpDir, tmpDir, codeql_1.getCachedCodeQL());
             throw new Error('initConfig did not throw error');
         }
         catch (err) {
@@ -121,7 +122,7 @@ ava_1.default("load non-local input with invalid repo syntax", async (t) => {
         // no filename given, just a repo
         setInput('config-file', 'octo-org/codeql-config@main');
         try {
-            await configUtils.initConfig();
+            await configUtils.initConfig(tmpDir, tmpDir, codeql_1.getCachedCodeQL());
             throw new Error('initConfig did not throw error');
         }
         catch (err) {
@@ -137,7 +138,7 @@ ava_1.default("load non-existent input", async (t) => {
         setInput('config-file', 'input');
         setInput('languages', 'javascript');
         try {
-            await configUtils.initConfig();
+            await configUtils.initConfig(tmpDir, tmpDir, codeql_1.getCachedCodeQL());
             throw new Error('initConfig did not throw error');
         }
         catch (err) {
@@ -149,7 +150,7 @@ ava_1.default("load non-empty input", async (t) => {
     return await util.withTmpDir(async (tmpDir) => {
         process.env['RUNNER_TEMP'] = tmpDir;
         process.env['GITHUB_WORKSPACE'] = tmpDir;
-        CodeQL.setCodeQL({
+        const codeQL = codeql_1.setCodeQL({
             resolveQueries: async function () {
                 return {
                     byLanguage: {
@@ -177,7 +178,7 @@ ava_1.default("load non-empty input", async (t) => {
         fs.mkdirSync(path.join(tmpDir, 'foo'));
         // And the config we expect it to parse to
         const expectedConfig = {
-            languages: ['javascript'],
+            languages: [languages_1.Language.javascript],
             queries: { 'javascript': ['/foo/a.ql', '/bar/b.ql'] },
             pathsIgnore: ['a', 'b'],
             paths: ['c/d'],
@@ -188,11 +189,14 @@ ava_1.default("load non-empty input", async (t) => {
                 'paths-ignore': ['a', 'b'],
                 paths: ['c/d'],
             },
+            tempDir: tmpDir,
+            toolCacheDir: tmpDir,
+            codeQLCmd: codeQL.getPath(),
         };
         fs.writeFileSync(path.join(tmpDir, 'input'), inputFileContents, 'utf8');
         setInput('config-file', 'input');
         setInput('languages', 'javascript');
-        const actualConfig = await configUtils.initConfig();
+        const actualConfig = await configUtils.initConfig(tmpDir, tmpDir, codeQL);
         // Should exactly equal the object we constructed earlier
         t.deepEqual(actualConfig, expectedConfig);
     });
@@ -207,7 +211,7 @@ ava_1.default("default queries are used", async (t) => {
         // We determine this by whether CodeQL.resolveQueries is called
         // with the correct arguments.
         const resolveQueriesArgs = [];
-        CodeQL.setCodeQL({
+        const codeQL = codeql_1.setCodeQL({
             resolveQueries: async function (queries, extraSearchPath) {
                 resolveQueriesArgs.push({ queries, extraSearchPath });
                 return {
@@ -231,7 +235,7 @@ ava_1.default("default queries are used", async (t) => {
         fs.writeFileSync(path.join(tmpDir, 'input'), inputFileContents, 'utf8');
         setInput('config-file', 'input');
         setInput('languages', 'javascript');
-        await configUtils.initConfig();
+        await configUtils.initConfig(tmpDir, tmpDir, codeQL);
         // Check resolve queries was called correctly
         t.deepEqual(resolveQueriesArgs.length, 1);
         t.deepEqual(resolveQueriesArgs[0].queries, ['javascript-code-scanning.qls']);
@@ -242,7 +246,7 @@ ava_1.default("API client used when reading remote config", async (t) => {
     return await util.withTmpDir(async (tmpDir) => {
         process.env['RUNNER_TEMP'] = tmpDir;
         process.env['GITHUB_WORKSPACE'] = tmpDir;
-        CodeQL.setCodeQL({
+        const codeQL = codeql_1.setCodeQL({
             resolveQueries: async function () {
                 return {
                     byLanguage: {
@@ -275,7 +279,7 @@ ava_1.default("API client used when reading remote config", async (t) => {
         fs.mkdirSync(path.join(tmpDir, 'foo/bar'), { recursive: true });
         setInput('config-file', 'octo-org/codeql-config/config.yaml@main');
         setInput('languages', 'javascript');
-        await configUtils.initConfig();
+        await configUtils.initConfig(tmpDir, tmpDir, codeQL);
         t.assert(spyGetContents.called);
     });
 });
@@ -288,7 +292,7 @@ ava_1.default("Remote config handles the case where a directory is provided", as
         const repoReference = 'octo-org/codeql-config/config.yaml@main';
         setInput('config-file', repoReference);
         try {
-            await configUtils.initConfig();
+            await configUtils.initConfig(tmpDir, tmpDir, codeql_1.getCachedCodeQL());
             throw new Error('initConfig did not throw error');
         }
         catch (err) {
@@ -307,7 +311,7 @@ ava_1.default("Invalid format of remote config handled correctly", async (t) =>
         const repoReference = 'octo-org/codeql-config/config.yaml@main';
         setInput('config-file', repoReference);
         try {
-            await configUtils.initConfig();
+            await configUtils.initConfig(tmpDir, tmpDir, codeql_1.getCachedCodeQL());
             throw new Error('initConfig did not throw error');
         }
         catch (err) {
@@ -321,7 +325,7 @@ ava_1.default("No detected languages", async (t) => {
         process.env['GITHUB_WORKSPACE'] = tmpDir;
         mockListLanguages([]);
         try {
-            await configUtils.initConfig();
+            await configUtils.initConfig(tmpDir, tmpDir, codeql_1.getCachedCodeQL());
             throw new Error('initConfig did not throw error');
         }
         catch (err) {
@@ -335,7 +339,7 @@ ava_1.default("Unknown languages", async (t) => {
         process.env['GITHUB_WORKSPACE'] = tmpDir;
         setInput('languages', 'ruby,english');
         try {
-            await configUtils.initConfig();
+            await configUtils.initConfig(tmpDir, tmpDir, codeql_1.getCachedCodeQL());
             throw new Error('initConfig did not throw error');
         }
         catch (err) {
@@ -348,7 +352,7 @@ function doInvalidInputTest(testName, inputFileContents, expectedErrorMessageGen
         return await util.withTmpDir(async (tmpDir) => {
             process.env['RUNNER_TEMP'] = tmpDir;
             process.env['GITHUB_WORKSPACE'] = tmpDir;
-            CodeQL.setCodeQL({
+            const codeQL = codeql_1.setCodeQL({
                 resolveQueries: async function () {
                     return {
                         byLanguage: {},
@@ -362,7 +366,7 @@ function doInvalidInputTest(testName, inputFileContents, expectedErrorMessageGen
             setInput('config-file', 'input');
             setInput('languages', 'javascript');
             try {
-                await configUtils.initConfig();
+                await configUtils.initConfig(tmpDir, tmpDir, codeQL);
                 throw new Error('initConfig did not throw error');
             }
             catch (err) {
diff --git a/lib/config-utils.test.js.map b/lib/config-utils.test.js.map
index 6a6a82faf..a5d19654f 100644
--- a/lib/config-utils.test.js.map
+++ b/lib/config-utils.test.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/lib/external-queries.js b/lib/external-queries.js
index f15a49685..fa660dfb5 100644
--- a/lib/external-queries.js
+++ b/lib/external-queries.js
@@ -11,14 +11,12 @@ const core = __importStar(require("@actions/core"));
 const exec = __importStar(require("@actions/exec"));
 const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
-const util = __importStar(require("./util"));
 /**
  * Check out repository at the given ref, and return the directory of the checkout.
  */
-async function checkoutExternalRepository(repository, ref) {
-    const folder = util.getRequiredEnvParam('RUNNER_TEMP');
+async function checkoutExternalRepository(repository, ref, tempDir) {
     core.info('Checking out ' + repository);
-    const checkoutLocation = path.join(folder, repository);
+    const checkoutLocation = path.join(tempDir, repository);
     if (!fs.existsSync(checkoutLocation)) {
         const repoURL = 'https://github.com/' + repository + '.git';
         await exec.exec('git', ['clone', repoURL, checkoutLocation]);
diff --git a/lib/external-queries.js.map b/lib/external-queries.js.map
index 0a190c616..8a94b633e 100644
--- a/lib/external-queries.js.map
+++ b/lib/external-queries.js.map
@@ -1 +1 @@
-{"version":3,"file":"external-queries.js","sourceRoot":"","sources":["../src/external-queries.ts"],"names":[],"mappings":";;;;;;;;;AAAA,oDAAsC;AACtC,oDAAsC;AACtC,uCAAyB;AACzB,2CAA6B;AAE7B,6CAA+B;AAE/B;;GAEG;AACI,KAAK,UAAU,0BAA0B,CAAC,UAAkB,EAAE,GAAW;IAC9E,MAAM,MAAM,GAAG,IAAI,CAAC,mBAAmB,CAAC,aAAa,CAAC,CAAC;IAEvD,IAAI,CAAC,IAAI,CAAC,eAAe,GAAG,UAAU,CAAC,CAAC;IAExC,MAAM,gBAAgB,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;IACvD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,gBAAgB,CAAC,EAAE;QACpC,MAAM,OAAO,GAAG,qBAAqB,GAAG,UAAU,GAAG,MAAM,CAAC;QAC5D,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,OAAO,EAAE,OAAO,EAAE,gBAAgB,CAAC,CAAC,CAAC;QAC7D,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE;YACrB,cAAc,GAAG,gBAAgB;YACjC,YAAY,GAAG,gBAAgB,GAAG,OAAO;YACzC,UAAU,EAAE,GAAG;SAChB,CAAC,CAAC;KACJ;IAED,OAAO,gBAAgB,CAAC;AAC1B,CAAC;AAjBD,gEAiBC"}
\ No newline at end of file
+{"version":3,"file":"external-queries.js","sourceRoot":"","sources":["../src/external-queries.ts"],"names":[],"mappings":";;;;;;;;;AAAA,oDAAsC;AACtC,oDAAsC;AACtC,uCAAyB;AACzB,2CAA6B;AAE7B;;GAEG;AACI,KAAK,UAAU,0BAA0B,CAAC,UAAkB,EAAE,GAAW,EAAE,OAAe;IAC/F,IAAI,CAAC,IAAI,CAAC,eAAe,GAAG,UAAU,CAAC,CAAC;IAExC,MAAM,gBAAgB,GAAG,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC;IACxD,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,gBAAgB,CAAC,EAAE;QACpC,MAAM,OAAO,GAAG,qBAAqB,GAAG,UAAU,GAAG,MAAM,CAAC;QAC5D,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC,OAAO,EAAE,OAAO,EAAE,gBAAgB,CAAC,CAAC,CAAC;QAC7D,MAAM,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE;YACrB,cAAc,GAAG,gBAAgB;YACjC,YAAY,GAAG,gBAAgB,GAAG,OAAO;YACzC,UAAU,EAAE,GAAG;SAChB,CAAC,CAAC;KACJ;IAED,OAAO,gBAAgB,CAAC;AAC1B,CAAC;AAfD,gEAeC"}
\ No newline at end of file
diff --git a/lib/external-queries.test.js b/lib/external-queries.test.js
index d66d82432..06d9d2f84 100644
--- a/lib/external-queries.test.js
+++ b/lib/external-queries.test.js
@@ -19,8 +19,7 @@ const util = __importStar(require("./util"));
 testing_utils_1.setupTests(ava_1.default);
 ava_1.default("checkoutExternalQueries", async (t) => {
     await util.withTmpDir(async (tmpDir) => {
-        process.env["RUNNER_TEMP"] = tmpDir;
-        await externalQueries.checkoutExternalRepository("github/codeql-go", "df4c6869212341b601005567381944ed90906b6b");
+        await externalQueries.checkoutExternalRepository("github/codeql-go", "df4c6869212341b601005567381944ed90906b6b", tmpDir);
         // COPYRIGHT file existed in df4c6869212341b601005567381944ed90906b6b but not in the default branch
         t.true(fs.existsSync(path.join(tmpDir, "github", "codeql-go", "COPYRIGHT")));
     });
diff --git a/lib/external-queries.test.js.map b/lib/external-queries.test.js.map
index ad9fd4805..2181cea69 100644
--- a/lib/external-queries.test.js.map
+++ b/lib/external-queries.test.js.map
@@ -1 +1 @@
-{"version":3,"file":"external-queries.test.js","sourceRoot":"","sources":["../src/external-queries.test.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,8CAAuB;AACvB,uCAAyB;AACzB,2CAA6B;AAE7B,oEAAsD;AACtD,mDAA2C;AAC3C,6CAA+B;AAE/B,0BAAU,CAAC,aAAI,CAAC,CAAC;AAEjB,aAAI,CAAC,yBAAyB,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IACxC,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAC,MAAM,EAAC,EAAE;QACnC,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,GAAG,MAAM,CAAC;QACpC,MAAM,eAAe,CAAC,0BAA0B,CAAC,kBAAkB,EAAE,0CAA0C,CAAC,CAAC;QAEjH,mGAAmG;QACnG,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC;IAC/E,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}
\ No newline at end of file
+{"version":3,"file":"external-queries.test.js","sourceRoot":"","sources":["../src/external-queries.test.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,8CAAuB;AACvB,uCAAyB;AACzB,2CAA6B;AAE7B,oEAAsD;AACtD,mDAA2C;AAC3C,6CAA+B;AAE/B,0BAAU,CAAC,aAAI,CAAC,CAAC;AAEjB,aAAI,CAAC,yBAAyB,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IACxC,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAC,MAAM,EAAC,EAAE;QACnC,MAAM,eAAe,CAAC,0BAA0B,CAC9C,kBAAkB,EAClB,0CAA0C,EAC1C,MAAM,CAAC,CAAC;QAEV,mGAAmG;QACnG,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,QAAQ,EAAE,WAAW,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC;IAC/E,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}
\ No newline at end of file
diff --git a/lib/finalize-db.js b/lib/finalize-db.js
index b0bf4e9e8..ff0803255 100644
--- a/lib/finalize-db.js
+++ b/lib/finalize-db.js
@@ -12,6 +12,7 @@ const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const codeql_1 = require("./codeql");
 const configUtils = __importStar(require("./config-utils"));
+const languages_1 = require("./languages");
 const logging_1 = require("./logging");
 const repository_1 = require("./repository");
 const sharedEnv = __importStar(require("./shared-environment"));
@@ -29,9 +30,9 @@ async function sendStatusReport(startedAt, queriesStats, uploadStats, error) {
     await util.sendStatusReport(statusReport);
 }
 async function createdDBForScannedLanguages(databaseFolder, config) {
-    const codeql = codeql_1.getCodeQL();
+    const codeql = codeql_1.getCodeQL(config.codeQLCmd);
     for (const language of config.languages) {
-        if (codeql_1.isScannedLanguage(language)) {
+        if (languages_1.isScannedLanguage(language)) {
             core.startGroup('Extracting ' + language);
             await codeql.extractScannedLanguage(path.join(databaseFolder, language), language);
             core.endGroup();
@@ -40,7 +41,7 @@ async function createdDBForScannedLanguages(databaseFolder, config) {
 }
 async function finalizeDatabaseCreation(databaseFolder, config) {
     await createdDBForScannedLanguages(databaseFolder, config);
-    const codeql = codeql_1.getCodeQL();
+    const codeql = codeql_1.getCodeQL(config.codeQLCmd);
     for (const language of config.languages) {
         core.startGroup('Finalizing ' + language);
         await codeql.finalizeDatabase(path.join(databaseFolder, language));
@@ -49,7 +50,7 @@ async function finalizeDatabaseCreation(databaseFolder, config) {
 }
 // Runs queries and creates sarif files in the given folder
 async function runQueries(databaseFolder, sarifFolder, config) {
-    const codeql = codeql_1.getCodeQL();
+    const codeql = codeql_1.getCodeQL(config.codeQLCmd);
     for (let language of fs.readdirSync(databaseFolder)) {
         core.startGroup('Analyzing ' + language);
         const queries = config.queries[language] || [];
@@ -86,10 +87,10 @@ async function run() {
         if (!await util.sendStatusReport(await util.createStatusReportBase('finish', 'starting', startedAt), true)) {
             return;
         }
-        const config = await configUtils.getConfig();
+        const config = await configUtils.getConfig(util.getRequiredEnvParam('RUNNER_TEMP'));
         core.exportVariable(sharedEnv.ODASA_TRACER_CONFIGURATION, '');
         delete process.env[sharedEnv.ODASA_TRACER_CONFIGURATION];
-        const databaseFolder = util.getCodeQLDatabasesDir();
+        const databaseFolder = util.getCodeQLDatabasesDir(config.tempDir);
         const sarifFolder = core.getInput('output');
         fs.mkdirSync(sarifFolder, { recursive: true });
         core.info('Finalizing database creation');
diff --git a/lib/finalize-db.js.map b/lib/finalize-db.js.map
index 1921ec524..033de3812 100644
--- a/lib/finalize-db.js.map
+++ b/lib/finalize-db.js.map
@@ -1 +1 @@
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diff --git a/lib/fingerprints.js b/lib/fingerprints.js
index d9a1e3b27..f5a8d2217 100644
--- a/lib/fingerprints.js
+++ b/lib/fingerprints.js
@@ -10,7 +10,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const core = __importStar(require("@actions/core"));
 const fs = __importStar(require("fs"));
 const long_1 = __importDefault(require("long"));
 const tab = '\t'.charCodeAt(0);
@@ -122,7 +121,7 @@ function hash(callback, input) {
 exports.hash = hash;
 // Generate a hash callback function that updates the given result in-place
 // when it recieves a hash for the correct line number. Ignores hashes for other lines.
-function locationUpdateCallback(result, location) {
+function locationUpdateCallback(result, location, logger) {
     var _a, _b;
     let locationStartLine = (_b = (_a = location.physicalLocation) === null || _a === void 0 ? void 0 : _a.region) === null || _b === void 0 ? void 0 : _b.startLine;
     if (locationStartLine === undefined) {
@@ -146,7 +145,7 @@ function locationUpdateCallback(result, location) {
             result.partialFingerprints.primaryLocationLineHash = hash;
         }
         else if (existingFingerprint !== hash) {
-            core.warning('Calculated fingerprint of ' + hash +
+            logger.warning('Calculated fingerprint of ' + hash +
                 ' for file ' + location.physicalLocation.artifactLocation.uri +
                 ' line ' + lineNumber +
                 ', but found existing inconsistent fingerprint value ' + existingFingerprint);
@@ -157,21 +156,21 @@ function locationUpdateCallback(result, location) {
 // the source file so we can hash it.
 // If possible returns a absolute file path for the source file,
 // or if not possible then returns undefined.
-function resolveUriToFile(location, artifacts) {
+function resolveUriToFile(location, artifacts, logger) {
     // This may be referencing an artifact
     if (!location.uri && location.index !== undefined) {
         if (typeof location.index !== 'number' ||
             location.index < 0 ||
             location.index >= artifacts.length ||
             typeof artifacts[location.index].location !== 'object') {
-            core.debug(`Ignoring location as URI "${location.index}" is invalid`);
+            logger.debug(`Ignoring location as URI "${location.index}" is invalid`);
             return undefined;
         }
         location = artifacts[location.index].location;
     }
     // Get the URI and decode
     if (typeof location.uri !== 'string') {
-        core.debug(`Ignoring location as index "${location.uri}" is invalid`);
+        logger.debug(`Ignoring location as index "${location.uri}" is invalid`);
         return undefined;
     }
     let uri = decodeURIComponent(location.uri);
@@ -181,13 +180,13 @@ function resolveUriToFile(location, artifacts) {
         uri = uri.substring(fileUriPrefix.length);
     }
     if (uri.indexOf('://') !== -1) {
-        core.debug(`Ignoring location URI "${uri}" as the scheme is not recognised`);
+        logger.debug(`Ignoring location URI "${uri}" as the scheme is not recognised`);
         return undefined;
     }
     // Discard any absolute paths that aren't in the src root
     const srcRootPrefix = process.env['GITHUB_WORKSPACE'] + '/';
     if (uri.startsWith('/') && !uri.startsWith(srcRootPrefix)) {
-        core.debug(`Ignoring location URI "${uri}" as it is outside of the src root`);
+        logger.debug(`Ignoring location URI "${uri}" as it is outside of the src root`);
         return undefined;
     }
     // Just assume a relative path is relative to the src root.
@@ -198,7 +197,7 @@ function resolveUriToFile(location, artifacts) {
     }
     // Check the file exists
     if (!fs.existsSync(uri)) {
-        core.debug(`Unable to compute fingerprint for non-existent file: ${uri}`);
+        logger.debug(`Unable to compute fingerprint for non-existent file: ${uri}`);
         return undefined;
     }
     return uri;
@@ -206,7 +205,7 @@ function resolveUriToFile(location, artifacts) {
 exports.resolveUriToFile = resolveUriToFile;
 // Compute fingerprints for results in the given sarif file
 // and return an updated sarif file contents.
-function addFingerprints(sarifContents) {
+function addFingerprints(sarifContents, logger) {
     var _a, _b;
     let sarif = JSON.parse(sarifContents);
     // Gather together results for the same file and construct
@@ -219,17 +218,17 @@ function addFingerprints(sarifContents) {
             // Check the primary location is defined correctly and is in the src root
             const primaryLocation = (result.locations || [])[0];
             if (!((_b = (_a = primaryLocation) === null || _a === void 0 ? void 0 : _a.physicalLocation) === null || _b === void 0 ? void 0 : _b.artifactLocation)) {
-                core.debug(`Unable to compute fingerprint for invalid location: ${JSON.stringify(primaryLocation)}`);
+                logger.debug(`Unable to compute fingerprint for invalid location: ${JSON.stringify(primaryLocation)}`);
                 continue;
             }
-            const filepath = resolveUriToFile(primaryLocation.physicalLocation.artifactLocation, artifacts);
+            const filepath = resolveUriToFile(primaryLocation.physicalLocation.artifactLocation, artifacts, logger);
             if (!filepath) {
                 continue;
             }
             if (!callbacksByFile[filepath]) {
                 callbacksByFile[filepath] = [];
             }
-            callbacksByFile[filepath].push(locationUpdateCallback(result, primaryLocation));
+            callbacksByFile[filepath].push(locationUpdateCallback(result, primaryLocation, logger));
         }
     }
     // Now hash each file that was found
diff --git a/lib/fingerprints.js.map b/lib/fingerprints.js.map
index 3b8064b84..eec4a3b97 100644
--- a/lib/fingerprints.js.map
+++ b/lib/fingerprints.js.map
@@ -1 +1 @@
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\ No newline at end of file
+{"version":3,"file":"fingerprints.js","sourceRoot":"","sources":["../src/fingerprints.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,uCAAyB;AACzB,gDAAwB;AAIxB,MAAM,GAAG,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC;AAC/B,MAAM,KAAK,GAAG,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC;AAChC,MAAM,EAAE,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC;AAC9B,MAAM,EAAE,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC;AAC9B,MAAM,UAAU,GAAG,GAAG,CAAC;AACvB,MAAM,GAAG,GAAG,cAAI,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI;AAElC,8CAA8C;AAC9C,SAAS,eAAe;IACtB,IAAI,QAAQ,GAAG,cAAI,CAAC,GAAG,CAAC,CAAC,IAAI;IAC7B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE;QACnC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC;KACnC;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAMD;;;;;;;;;;;GAWG;AACH,SAAgB,IAAI,CAAC,QAAsB,EAAE,KAAa;IACxD,iCAAiC;IACjC,MAAM,MAAM,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAEzC,4DAA4D;IAC5D,sDAAsD;IACtD,wDAAwD;IACxD,MAAM,WAAW,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;IAE/C,4DAA4D;IAC5D,IAAI,IAAI,GAAG,cAAI,CAAC,IAAI,CAAC;IACrB,IAAI,QAAQ,GAAG,eAAe,EAAE,CAAC;IAEjC,qFAAqF;IACrF,IAAI,KAAK,GAAG,CAAC,CAAC;IACd,8EAA8E;IAC9E,IAAI,UAAU,GAAG,CAAC,CAAC;IACnB,2DAA2D;IAC3D,IAAI,SAAS,GAAG,IAAI,CAAC;IACrB,oDAAoD;IACpD,IAAI,MAAM,GAAG,KAAK,CAAC;IACnB,wDAAwD;IACxD,0CAA0C;IAC1C,MAAM,UAAU,GAAoC,EAAE,CAAC;IAEvD,mEAAmE;IACnE,MAAM,UAAU,GAAG;QACjB,IAAI,SAAS,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC;QAC/C,IAAI,CAAC,UAAU,CAAC,SAAS,CAAC,EAAE;YAC1B,UAAU,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC;SAC3B;QACD,UAAU,CAAC,SAAS,CAAC,EAAE,CAAC;QACxB,QAAQ,CAAC,WAAW,CAAC,KAAK,CAAC,EAAE,SAAS,GAAG,GAAG,GAAG,UAAU,CAAC,SAAS,CAAC,CAAC,CAAC;QACtE,WAAW,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC;IAC1B,CAAC,CAAC;IAEF,sEAAsE;IACtE,MAAM,UAAU,GAAG,UAAU,OAAe;QAC1C,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;QAC5B,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAC;QACxB,IAAI,GAAG,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC;aACtB,GAAG,CAAC,cAAI,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;aAC1B,QAAQ,CAAC,QAAQ,CAAC,QAAQ,CAAC,cAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;QAEpD,KAAK,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,UAAU,CAAC;IACnC,CAAC,CAAC;IAEF,gFAAgF;IAChF,2EAA2E;IAC3E,8EAA8E;IAC9E,wEAAwE;IACxE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,EAAE;QACjD,IAAI,OAAO,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC;QACtD,+EAA+E;QAC/E,IAAI,OAAO,KAAK,KAAK,IAAI,OAAO,KAAK,GAAG,IAAI,CAAC,MAAM,IAAI,OAAO,KAAK,EAAE,CAAC,EAAE;YACtE,MAAM,GAAG,KAAK,CAAC;YACf,SAAS;SACV;QACD,qBAAqB;QACrB,IAAI,OAAO,KAAK,EAAE,EAAE;YAClB,OAAO,GAAG,EAAE,CAAC;YACb,MAAM,GAAG,IAAI,CAAC;SACf;aAAM;YACL,MAAM,GAAG,KAAK,CAAC;SAChB;QACD,IAAI,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE;YAC7B,UAAU,EAAE,CAAC;SACd;QACD,IAAI,SAAS,EAAE;YACb,SAAS,GAAG,KAAK,CAAC;YAClB,UAAU,EAAE,CAAC;YACb,WAAW,CAAC,KAAK,CAAC,GAAG,UAAU,CAAC;SACjC;QACD,IAAI,OAAO,KAAK,EAAE,EAAE;YAClB,SAAS,GAAG,IAAI,CAAC;SAClB;QACD,UAAU,CAAC,OAAO,CAAC,CAAC;KACrB;IAED,4BAA4B;IAC5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE;QACnC,IAAI,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE;YAC7B,UAAU,EAAE,CAAC;SACd;QACD,UAAU,CAAC,CAAC,CAAC,CAAC;KACf;AACH,CAAC;AAtFD,oBAsFC;AAED,2EAA2E;AAC3E,uFAAuF;AACvF,SAAS,sBAAsB,CAAC,MAAW,EAAE,QAAa,EAAE,MAAc;;IACxE,IAAI,iBAAiB,eAAG,QAAQ,CAAC,gBAAgB,0CAAE,MAAM,0CAAE,SAAS,CAAC;IACrE,IAAI,iBAAiB,KAAK,SAAS,EAAE;QACnC,0EAA0E;QAC1E,8EAA8E;QAC9E,gDAAgD;QAChD,iBAAiB,GAAG,CAAC,CAAC;KACvB;IACD,OAAO,UAAU,UAAkB,EAAE,IAAY;QAC/C,gDAAgD;QAChD,IAAI,iBAAiB,KAAK,UAAU,EAAE;YACpC,OAAO;SACR;QAED,IAAI,CAAC,MAAM,CAAC,mBAAmB,EAAE;YAC/B,MAAM,CAAC,mBAAmB,GAAG,EAAE,CAAC;SACjC;QACD,MAAM,mBAAmB,GAAG,MAAM,CAAC,mBAAmB,CAAC,uBAAuB,CAAC;QAE/E,0DAA0D;QAC1D,2CAA2C;QAC3C,IAAI,CAAC,mBAAmB,EAAE;YACxB,MAAM,CAAC,mBAAmB,CAAC,uBAAuB,GAAG,IAAI,CAAC;SAC3D;aAAM,IAAI,mBAAmB,KAAK,IAAI,EAAE;YACvC,MAAM,CAAC,OAAO,CAAC,4BAA4B,GAAG,IAAI;gBAChD,YAAY,GAAG,QAAQ,CAAC,gBAAgB,CAAC,gBAAgB,CAAC,GAAG;gBAC7D,QAAQ,GAAG,UAAU;gBACrB,sDAAsD,GAAG,mBAAmB,CAAC,CAAC;SACjF;IACH,CAAC,CAAC;AACJ,CAAC;AAED,iEAAiE;AACjE,qCAAqC;AACrC,gEAAgE;AAChE,6CAA6C;AAC7C,SAAgB,gBAAgB,CAAC,QAAa,EAAE,SAAgB,EAAE,MAAc;IAC9E,sCAAsC;IACtC,IAAI,CAAC,QAAQ,CAAC,GAAG,IAAI,QAAQ,CAAC,KAAK,KAAK,SAAS,EAAE;QACjD,IAAI,OAAO,QAAQ,CAAC,KAAK,KAAK,QAAQ;YACpC,QAAQ,CAAC,KAAK,GAAG,CAAC;YAClB,QAAQ,CAAC,KAAK,IAAI,SAAS,CAAC,MAAM;YAClC,OAAO,SAAS,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,QAAQ,KAAK,QAAQ,EAAE;YACxD,MAAM,CAAC,KAAK,CAAC,6BAA6B,QAAQ,CAAC,KAAK,cAAc,CAAC,CAAC;YACxE,OAAO,SAAS,CAAC;SAClB;QACD,QAAQ,GAAG,SAAS,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC;KAC/C;IAED,yBAAyB;IACzB,IAAI,OAAO,QAAQ,CAAC,GAAG,KAAK,QAAQ,EAAE;QACpC,MAAM,CAAC,KAAK,CAAC,+BAA+B,QAAQ,CAAC,GAAG,cAAc,CAAC,CAAC;QACxE,OAAO,SAAS,CAAC;KAClB;IACD,IAAI,GAAG,GAAG,kBAAkB,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC;IAE3C,iEAAiE;IACjE,MAAM,aAAa,GAAG,SAAS,CAAC;IAChC,IAAI,GAAG,CAAC,UAAU,CAAC,aAAa,CAAC,EAAE;QACjC,GAAG,GAAG,GAAG,CAAC,SAAS,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC;KAC3C;IACD,IAAI,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE;QAC7B,MAAM,CAAC,KAAK,CAAC,0BAA0B,GAAG,mCAAmC,CAAC,CAAC;QAC/E,OAAO,SAAS,CAAC;KAClB;IAED,yDAAyD;IACzD,MAAM,aAAa,GAAG,OAAO,CAAC,GAAG,CAAC,kBAAkB,CAAC,GAAG,GAAG,CAAC;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\ No newline at end of file
diff --git a/lib/fingerprints.test.js b/lib/fingerprints.test.js
index 01b867866..11951a512 100644
--- a/lib/fingerprints.test.js
+++ b/lib/fingerprints.test.js
@@ -14,6 +14,7 @@ const ava_1 = __importDefault(require("ava"));
 const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const fingerprints = __importStar(require("./fingerprints"));
+const logging_1 = require("./logging");
 const testing_utils_1 = require("./testing-utils");
 testing_utils_1.setupTests(ava_1.default);
 function testHash(t, input, expectedHashes) {
@@ -98,7 +99,7 @@ ava_1.default('hash', (t) => {
 function testResolveUriToFile(uri, index, artifactsURIs) {
     const location = { "uri": uri, "index": index };
     const artifacts = artifactsURIs.map(uri => ({ "location": { "uri": uri } }));
-    return fingerprints.resolveUriToFile(location, artifacts);
+    return fingerprints.resolveUriToFile(location, artifacts, logging_1.getCLILogger());
 }
 ava_1.default('resolveUriToFile', t => {
     // The resolveUriToFile method checks that the file exists and is in the right directory
@@ -143,7 +144,7 @@ ava_1.default('addFingerprints', t => {
     expected = JSON.stringify(JSON.parse(expected));
     // The URIs in the SARIF files resolve to files in the testdata directory
     process.env['GITHUB_WORKSPACE'] = path.normalize(__dirname + '/../src/testdata');
-    t.deepEqual(fingerprints.addFingerprints(input), expected);
+    t.deepEqual(fingerprints.addFingerprints(input, logging_1.getCLILogger()), expected);
 });
 ava_1.default('missingRegions', t => {
     // Run an end-to-end test on a test file
@@ -154,6 +155,6 @@ ava_1.default('missingRegions', t => {
     expected = JSON.stringify(JSON.parse(expected));
     // The URIs in the SARIF files resolve to files in the testdata directory
     process.env['GITHUB_WORKSPACE'] = path.normalize(__dirname + '/../src/testdata');
-    t.deepEqual(fingerprints.addFingerprints(input), expected);
+    t.deepEqual(fingerprints.addFingerprints(input, logging_1.getCLILogger()), expected);
 });
 //# sourceMappingURL=fingerprints.test.js.map
\ No newline at end of file
diff --git a/lib/fingerprints.test.js.map b/lib/fingerprints.test.js.map
index a6becd3c2..09047973d 100644
--- a/lib/fingerprints.test.js.map
+++ b/lib/fingerprints.test.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/lib/languages.js b/lib/languages.js
new file mode 100644
index 000000000..2e839b098
--- /dev/null
+++ b/lib/languages.js
@@ -0,0 +1,43 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+// All the languages supported by CodeQL
+var Language;
+(function (Language) {
+    Language["csharp"] = "csharp";
+    Language["cpp"] = "cpp";
+    Language["go"] = "go";
+    Language["java"] = "java";
+    Language["javascript"] = "javascript";
+    Language["python"] = "python";
+})(Language = exports.Language || (exports.Language = {}));
+// Additional names for languages
+const LANGUAGE_ALIASES = {
+    'c': Language.cpp,
+    'c++': Language.cpp,
+    'c#': Language.csharp,
+    'typescript': Language.javascript,
+};
+// Translate from user input or GitHub's API names for languages to CodeQL's names for languages
+function parseLanguage(language) {
+    // Normalise to lower case
+    language = language.toLowerCase();
+    // See if it's an exact match
+    if (language in Language) {
+        return language;
+    }
+    // Check language aliases
+    if (language in LANGUAGE_ALIASES) {
+        return LANGUAGE_ALIASES[language];
+    }
+    return undefined;
+}
+exports.parseLanguage = parseLanguage;
+function isTracedLanguage(language) {
+    return ['cpp', 'java', 'csharp'].includes(language);
+}
+exports.isTracedLanguage = isTracedLanguage;
+function isScannedLanguage(language) {
+    return !isTracedLanguage(language);
+}
+exports.isScannedLanguage = isScannedLanguage;
+//# sourceMappingURL=languages.js.map
\ No newline at end of file
diff --git a/lib/languages.js.map b/lib/languages.js.map
new file mode 100644
index 000000000..8cb6df90a
--- /dev/null
+++ b/lib/languages.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"languages.js","sourceRoot":"","sources":["../src/languages.ts"],"names":[],"mappings":";;AAAA,wCAAwC;AACxC,IAAY,QAOX;AAPD,WAAY,QAAQ;IAClB,6BAAiB,CAAA;IACjB,uBAAW,CAAA;IACX,qBAAS,CAAA;IACT,yBAAa,CAAA;IACb,qCAAyB,CAAA;IACzB,6BAAiB,CAAA;AACnB,CAAC,EAPW,QAAQ,GAAR,gBAAQ,KAAR,gBAAQ,QAOnB;AAED,iCAAiC;AACjC,MAAM,gBAAgB,GAA+B;IACnD,GAAG,EAAE,QAAQ,CAAC,GAAG;IACjB,KAAK,EAAE,QAAQ,CAAC,GAAG;IACnB,IAAI,EAAE,QAAQ,CAAC,MAAM;IACrB,YAAY,EAAE,QAAQ,CAAC,UAAU;CAClC,CAAC;AAEF,gGAAgG;AAChG,SAAgB,aAAa,CAAC,QAAgB;IAC5C,0BAA0B;IAC1B,QAAQ,GAAG,QAAQ,CAAC,WAAW,EAAE,CAAC;IAElC,6BAA6B;IAC7B,IAAI,QAAQ,IAAI,QAAQ,EAAE;QACxB,OAAO,QAAoB,CAAC;KAC7B;IAED,yBAAyB;IACzB,IAAI,QAAQ,IAAI,gBAAgB,EAAE;QAChC,OAAO,gBAAgB,CAAC,QAAQ,CAAC,CAAC;KACnC;IAED,OAAO,SAAS,CAAC;AACnB,CAAC;AAfD,sCAeC;AAGD,SAAgB,gBAAgB,CAAC,QAAkB;IACjD,OAAO,CAAC,KAAK,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;AACtD,CAAC;AAFD,4CAEC;AAED,SAAgB,iBAAiB,CAAC,QAAkB;IAClD,OAAO,CAAC,gBAAgB,CAAC,QAAQ,CAAC,CAAC;AACrC,CAAC;AAFD,8CAEC"}
\ No newline at end of file
diff --git a/lib/languages.test.js b/lib/languages.test.js
new file mode 100644
index 000000000..9de8b4173
--- /dev/null
+++ b/lib/languages.test.js
@@ -0,0 +1,44 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const ava_1 = __importDefault(require("ava"));
+const languages_1 = require("./languages");
+const testing_utils_1 = require("./testing-utils");
+testing_utils_1.setupTests(ava_1.default);
+ava_1.default('parseLangauge', async (t) => {
+    // Exact matches
+    t.deepEqual(languages_1.parseLanguage('csharp'), languages_1.Language.csharp);
+    t.deepEqual(languages_1.parseLanguage('cpp'), languages_1.Language.cpp);
+    t.deepEqual(languages_1.parseLanguage('go'), languages_1.Language.go);
+    t.deepEqual(languages_1.parseLanguage('java'), languages_1.Language.java);
+    t.deepEqual(languages_1.parseLanguage('javascript'), languages_1.Language.javascript);
+    t.deepEqual(languages_1.parseLanguage('python'), languages_1.Language.python);
+    // Aliases
+    t.deepEqual(languages_1.parseLanguage('c'), languages_1.Language.cpp);
+    t.deepEqual(languages_1.parseLanguage('c++'), languages_1.Language.cpp);
+    t.deepEqual(languages_1.parseLanguage('c#'), languages_1.Language.csharp);
+    t.deepEqual(languages_1.parseLanguage('typescript'), languages_1.Language.javascript);
+    // Not matches
+    t.deepEqual(languages_1.parseLanguage('foo'), undefined);
+    t.deepEqual(languages_1.parseLanguage(' '), undefined);
+    t.deepEqual(languages_1.parseLanguage(''), undefined);
+});
+ava_1.default('isTracedLanguage', async (t) => {
+    t.true(languages_1.isTracedLanguage(languages_1.Language.cpp));
+    t.true(languages_1.isTracedLanguage(languages_1.Language.java));
+    t.true(languages_1.isTracedLanguage(languages_1.Language.csharp));
+    t.false(languages_1.isTracedLanguage(languages_1.Language.go));
+    t.false(languages_1.isTracedLanguage(languages_1.Language.javascript));
+    t.false(languages_1.isTracedLanguage(languages_1.Language.python));
+});
+ava_1.default('isScannedLanguage', async (t) => {
+    t.false(languages_1.isScannedLanguage(languages_1.Language.cpp));
+    t.false(languages_1.isScannedLanguage(languages_1.Language.java));
+    t.false(languages_1.isScannedLanguage(languages_1.Language.csharp));
+    t.true(languages_1.isScannedLanguage(languages_1.Language.go));
+    t.true(languages_1.isScannedLanguage(languages_1.Language.javascript));
+    t.true(languages_1.isScannedLanguage(languages_1.Language.python));
+});
+//# sourceMappingURL=languages.test.js.map
\ No newline at end of file
diff --git a/lib/languages.test.js.map b/lib/languages.test.js.map
new file mode 100644
index 000000000..e732925fe
--- /dev/null
+++ b/lib/languages.test.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"languages.test.js","sourceRoot":"","sources":["../src/languages.test.ts"],"names":[],"mappings":";;;;;AAAA,8CAAuB;AAEvB,2CAAyF;AACzF,mDAA2C;AAE3C,0BAAU,CAAC,aAAI,CAAC,CAAC;AAEjB,aAAI,CAAC,eAAe,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IAC9B,gBAAgB;IAChB,CAAC,CAAC,SAAS,CAAC,yBAAa,CAAC,QAAQ,CAAC,EAAE,oBAAQ,CAAC,MAAM,CAAC,CAAC;IACtD,CAAC,CAAC,SAAS,CAAC,yBAAa,CAAC,KAAK,CAAC,EAAE,oBAAQ,CAAC,GAAG,CAAC,CAAC;IAChD,CAAC,CAAC,SAAS,CAAC,yBAAa,CAAC,IAAI,CAAC,EAAE,oBAAQ,CAAC,EAAE,CAAC,CAAC;IAC9C,CAAC,CAAC,SAAS,CAAC,yBAAa,CAAC,MAAM,CAAC,EAAE,oBAAQ,CAAC,IAAI,CAAC,CAAC;IAClD,CAAC,CAAC,SAAS,CAAC,yBAAa,CAAC,YAAY,CAAC,EAAE,oBAAQ,CAAC,UAAU,CAAC,CAAC;IAC9D,CAAC,CAAC,SAAS,CAAC,yBAAa,CAAC,QAAQ,CAAC,EAAE,oBAAQ,CAAC,MAAM,CAAC,CAAC;IAEtD,UAAU;IACV,CAAC,CAAC,SAAS,CAAC,yBAAa,CAAC,GAAG,CAAC,EAAE,oBAAQ,CAAC,GAAG,CAAC,CAAC;IAC9C,CAAC,CAAC,SAAS,CAAC,yBAAa,CAAC,KAAK,CAAC,EAAE,oBAAQ,CAAC,GAAG,CAAC,CAAC;IAChD,CAAC,CAAC,SAAS,CAAC,yBAAa,CAAC,IAAI,CAAC,EAAE,oBAAQ,CAAC,MAAM,CAAC,CAAC;IAClD,CAAC,CAAC,SAAS,CAAC,yBAAa,CAAC,YAAY,CAAC,EAAE,oBAAQ,CAAC,UAAU,CAAC,CAAC;IAE9D,cAAc;IACd,CAAC,CAAC,SAAS,CAAC,yBAAa,CAAC,KAAK,CAAC,EAAE,SAAS,CAAC,CAAC;IAC7C,CAAC,CAAC,SAAS,CAAC,yBAAa,CAAC,GAAG,CAAC,EAAE,SAAS,CAAC,CAAC;IAC3C,CAAC,CAAC,SAAS,CAAC,yBAAa,CAAC,EAAE,CAAC,EAAE,SAAS,CAAC,CAAC;AAC5C,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,kBAAkB,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IACjC,CAAC,CAAC,IAAI,CAAC,4BAAgB,CAAC,oBAAQ,CAAC,GAAG,CAAC,CAAC,CAAC;IACvC,CAAC,CAAC,IAAI,CAAC,4BAAgB,CAAC,oBAAQ,CAAC,IAAI,CAAC,CAAC,CAAC;IACxC,CAAC,CAAC,IAAI,CAAC,4BAAgB,CAAC,oBAAQ,CAAC,MAAM,CAAC,CAAC,CAAC;IAE1C,CAAC,CAAC,KAAK,CAAC,4BAAgB,CAAC,oBAAQ,CAAC,EAAE,CAAC,CAAC,CAAC;IACvC,CAAC,CAAC,KAAK,CAAC,4BAAgB,CAAC,oBAAQ,CAAC,UAAU,CAAC,CAAC,CAAC;IAC/C,CAAC,CAAC,KAAK,CAAC,4BAAgB,CAAC,oBAAQ,CAAC,MAAM,CAAC,CAAC,CAAC;AAC7C,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,mBAAmB,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;IAClC,CAAC,CAAC,KAAK,CAAC,6BAAiB,CAAC,oBAAQ,CAAC,GAAG,CAAC,CAAC,CAAC;IACzC,CAAC,CAAC,KAAK,CAAC,6BAAiB,CAAC,oBAAQ,CAAC,IAAI,CAAC,CAAC,CAAC;IAC1C,CAAC,CAAC,KAAK,CAAC,6BAAiB,CAAC,oBAAQ,CAAC,MAAM,CAAC,CAAC,CAAC;IAE5C,CAAC,CAAC,IAAI,CAAC,6BAAiB,CAAC,oBAAQ,CAAC,EAAE,CAAC,CAAC,CAAC;IACvC,CAAC,CAAC,IAAI,CAAC,6BAAiB,CAAC,oBAAQ,CAAC,UAAU,CAAC,CAAC,CAAC;IAC/C,CAAC,CAAC,IAAI,CAAC,6BAAiB,CAAC,oBAAQ,CAAC,MAAM,CAAC,CAAC,CAAC;AAC7C,CAAC,CAAC,CAAC"}
\ No newline at end of file
diff --git a/lib/setup-tracer.js b/lib/setup-tracer.js
index 762a41653..4fe76b086 100644
--- a/lib/setup-tracer.js
+++ b/lib/setup-tracer.js
@@ -14,6 +14,7 @@ const path = __importStar(require("path"));
 const analysisPaths = __importStar(require("./analysis-paths"));
 const codeql_1 = require("./codeql");
 const configUtils = __importStar(require("./config-utils"));
+const languages_1 = require("./languages");
 const util = __importStar(require("./util"));
 const CRITICAL_TRACER_VARS = new Set(['SEMMLE_PRELOAD_libtrace',
     ,
@@ -49,14 +50,14 @@ async function tracerConfig(codeql, database, compilerSpec) {
     }
     return info;
 }
-function concatTracerConfigs(configs) {
+function concatTracerConfigs(tracerConfigs, config) {
     // A tracer config is a map containing additional environment variables and a tracer 'spec' file.
     // A tracer 'spec' file has the following format [log_file, number_of_blocks, blocks_text]
     // Merge the environments
     const env = {};
     let copyExecutables = false;
     let envSize = 0;
-    for (const v of configs) {
+    for (const v of tracerConfigs) {
         for (let e of Object.entries(v.env)) {
             const name = e[0];
             const value = e[1];
@@ -77,7 +78,7 @@ function concatTracerConfigs(configs) {
         }
     }
     // Concatenate spec files into a new spec file
-    let languages = Object.keys(configs);
+    let languages = Object.keys(tracerConfigs);
     const cppIndex = languages.indexOf('cpp');
     // Make sure cpp is the last language, if it's present since it must be concatenated last
     if (cppIndex !== -1) {
@@ -88,15 +89,14 @@ function concatTracerConfigs(configs) {
     let totalLines = [];
     let totalCount = 0;
     for (let lang of languages) {
-        const lines = fs.readFileSync(configs[lang].spec, 'utf8').split(/\r?\n/);
+        const lines = fs.readFileSync(tracerConfigs[lang].spec, 'utf8').split(/\r?\n/);
         const count = parseInt(lines[1], 10);
         totalCount += count;
         totalLines.push(...lines.slice(2));
     }
-    const tempFolder = util.getRequiredEnvParam('RUNNER_TEMP');
-    const newLogFilePath = path.resolve(tempFolder, 'compound-build-tracer.log');
-    const spec = path.resolve(tempFolder, 'compound-spec');
-    const compoundTempFolder = path.resolve(tempFolder, 'compound-temp');
+    const newLogFilePath = path.resolve(config.tempDir, 'compound-build-tracer.log');
+    const spec = path.resolve(config.tempDir, 'compound-spec');
+    const compoundTempFolder = path.resolve(config.tempDir, 'compound-temp');
     const newSpecContent = [newLogFilePath, totalCount.toString(10), ...totalLines];
     if (copyExecutables) {
         env['SEMMLE_COPY_EXECUTABLES_ROOT'] = compoundTempFolder;
@@ -152,7 +152,7 @@ async function run() {
         await codeql.printVersion();
         core.endGroup();
         core.startGroup('Load language configuration');
-        config = await configUtils.initConfig();
+        config = await configUtils.initConfig(util.getRequiredEnvParam('RUNNER_TEMP'), util.getRequiredEnvParam('RUNNER_TOOL_CACHE'), codeql);
         analysisPaths.includeAndExcludeAnalysisPaths(config);
         core.endGroup();
     }
@@ -173,7 +173,7 @@ async function run() {
         // Setup CODEQL_RAM flag (todo improve this https://github.com/github/dsp-code-scanning/issues/935)
         const codeqlRam = process.env['CODEQL_RAM'] || '6500';
         core.exportVariable('CODEQL_RAM', codeqlRam);
-        const databaseFolder = util.getCodeQLDatabasesDir();
+        const databaseFolder = util.getCodeQLDatabasesDir(config.tempDir);
         fs.mkdirSync(databaseFolder, { recursive: true });
         let tracedLanguageConfigs = [];
         // TODO: replace this code once CodeQL supports multi-language tracing
@@ -182,29 +182,30 @@ async function run() {
             // Init language database
             await codeql.databaseInit(languageDatabase, language, sourceRoot);
             // TODO: add better detection of 'traced languages' instead of using a hard coded list
-            if (codeql_1.isTracedLanguage(language)) {
+            if (languages_1.isTracedLanguage(language)) {
                 const config = await tracerConfig(codeql, languageDatabase);
                 tracedLanguageConfigs.push(config);
             }
         }
         if (tracedLanguageConfigs.length > 0) {
-            const mainTracerConfig = concatTracerConfigs(tracedLanguageConfigs);
+            const mainTracerConfig = concatTracerConfigs(tracedLanguageConfigs, config);
             if (mainTracerConfig.spec) {
                 for (let entry of Object.entries(mainTracerConfig.env)) {
                     core.exportVariable(entry[0], entry[1]);
                 }
                 core.exportVariable('ODASA_TRACER_CONFIGURATION', mainTracerConfig.spec);
+                const codeQLDir = path.dirname(codeql.getPath());
                 if (process.platform === 'darwin') {
-                    core.exportVariable('DYLD_INSERT_LIBRARIES', path.join(codeql.getDir(), 'tools', 'osx64', 'libtrace.dylib'));
+                    core.exportVariable('DYLD_INSERT_LIBRARIES', path.join(codeQLDir, 'tools', 'osx64', 'libtrace.dylib'));
                 }
                 else if (process.platform === 'win32') {
                     await exec.exec('powershell', [
                         path.resolve(__dirname, '..', 'src', 'inject-tracer.ps1'),
-                        path.resolve(codeql.getDir(), 'tools', 'win64', 'tracer.exe'),
+                        path.resolve(codeQLDir, 'tools', 'win64', 'tracer.exe'),
                     ], { env: { 'ODASA_TRACER_CONFIGURATION': mainTracerConfig.spec } });
                 }
                 else {
-                    core.exportVariable('LD_PRELOAD', path.join(codeql.getDir(), 'tools', 'linux64', '${LIB}trace.so'));
+                    core.exportVariable('LD_PRELOAD', path.join(codeQLDir, 'tools', 'linux64', '${LIB}trace.so'));
                 }
             }
         }
diff --git a/lib/setup-tracer.js.map b/lib/setup-tracer.js.map
index 5c2dfb171..4259b1744 100644
--- a/lib/setup-tracer.js.map
+++ b/lib/setup-tracer.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/lib/upload-lib.js b/lib/upload-lib.js
index c7e4bfb62..5798aa004 100644
--- a/lib/upload-lib.js
+++ b/lib/upload-lib.js
@@ -166,7 +166,7 @@ async function uploadFiles(sarifFiles, repositoryNwo, commitOid, ref, analysisKe
         validateSarifFileSchema(file, logger);
     }
     let sarifPayload = combineSarifFiles(sarifFiles);
-    sarifPayload = fingerprints.addFingerprints(sarifPayload);
+    sarifPayload = fingerprints.addFingerprints(sarifPayload, logger);
     const zipped_sarif = zlib_1.default.gzipSync(sarifPayload).toString('base64');
     let checkoutURI = file_url_1.default(checkoutPath);
     const toolNames = util.getToolNames(sarifPayload);
diff --git a/lib/upload-lib.js.map b/lib/upload-lib.js.map
index bb0a8102b..43c7378e3 100644
--- a/lib/upload-lib.js.map
+++ b/lib/upload-lib.js.map
@@ -1 +1 @@
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\ No newline at end of file
+{"version":3,"file":"upload-lib.js","sourceRoot":"","sources":["../src/upload-lib.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,oDAAsC;AACtC,wDAA+B;AAC/B,uCAAyB;AACzB,uDAAyC;AACzC,2CAA6B;AAC7B,gDAAwB;AAExB,kDAAoC;AACpC,6DAA+C;AAG/C,gEAAkD;AAClD,6CAA+B;AAI/B,mEAAmE;AACnE,qDAAqD;AACrD,SAAgB,iBAAiB,CAAC,UAAoB;IACpD,IAAI,aAAa,GAAG;QAClB,OAAO,EAAE,IAAI;QACb,IAAI,EAAE,EAAW;KAClB,CAAC;IAEF,KAAK,IAAI,SAAS,IAAI,UAAU,EAAE;QAChC,IAAI,WAAW,GAAG,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,YAAY,CAAC,SAAS,EAAE,MAAM,CAAC,CAAC,CAAC;QACjE,sBAAsB;QACtB,IAAI,aAAa,CAAC,OAAO,KAAK,IAAI,EAAE;YAClC,aAAa,CAAC,OAAO,GAAG,WAAW,CAAC,OAAO,CAAC;SAC7C;aAAM,IAAI,aAAa,CAAC,OAAO,KAAK,WAAW,CAAC,OAAO,EAAE;YACxD,MAAM,wCAAwC,GAAG,aAAa,CAAC,OAAO,GAAG,OAAO,GAAG,WAAW,CAAC,OAAO,CAAC;SACxG;QAED,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC,IAAI,CAAC,CAAC;KAC9C;IAED,OAAO,IAAI,CAAC,SAAS,CAAC,aAAa,CAAC,CAAC;AACvC,CAAC;AAnBD,8CAmBC;AAED,4BAA4B;AAC5B,qEAAqE;AACrE,KAAK,UAAU,aAAa,CAC1B,OAAY,EACZ,aAA4B,EAC5B,UAAkB,EAClB,YAAoB,EACpB,IAAgB,EAChB,MAAc;IAEd,MAAM,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC;IAEjC,sDAAsD;IACtD,MAAM,QAAQ,GAAG,OAAO,CAAC,GAAG,CAAC,WAAW,CAAC,KAAK,MAAM,IAAI,KAAK,CAAC;IAC9D,IAAI,QAAQ,EAAE;QACZ,OAAO;KACR;IAED,uDAAuD;IACvD,0CAA0C;IAC1C,4DAA4D;IAC5D,2DAA2D;IAC3D,MAAM,cAAc,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC;IAElC,MAAM,MAAM,GAAG,GAAG,CAAC,YAAY,CAAC,UAAU,EAAE,YAAY,CAAC,CAAC;IAE1D,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,IAAI,cAAc,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE;QACjE,MAAM,MAAM,GAAG,IAAI,KAAK,SAAS;YAC/B,CAAC,CAAC,gDAAgD;YAClD,CAAC,CAAC,+CAA+C,CAAC;QACpD,MAAM,QAAQ,GAAG,MAAM,MAAM,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YAC7C,KAAK,EAAE,aAAa,CAAC,KAAK;YAC1B,IAAI,EAAE,aAAa,CAAC,IAAI;YACxB,IAAI,EAAE,OAAO;SACd,CAAC,CAAC,CAAC;QAEJ,MAAM,CAAC,KAAK,CAAC,mBAAmB,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC;QAEpD,MAAM,UAAU,GAAG,QAAQ,CAAC,MAAM,CAAC;QACnC,IAAI,UAAU,KAAK,GAAG,EAAE;YACtB,MAAM,CAAC,IAAI,CAAC,+BAA+B,CAAC,CAAC;YAC7C,OAAO;SACR;QAED,MAAM,SAAS,GAAG,QAAQ,CAAC,OAAO,CAAC,qBAAqB,CAAC,CAAC;QAE1D,oEAAoE;QACpE,IAAI,CAAC,UAAU,IAAI,UAAU,GAAG,GAAG,IAAI,UAAU,IAAI,GAAG,EAAE;YACxD,MAAM,IAAI,KAAK,CAAC,iBAAiB,GAAG,SAAS,GAAG,MAAM,GAAG,UAAU,GAAG,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC;SAC7G;QAED,gDAAgD;QAChD,IAAI,OAAO,GAAG,cAAc,CAAC,MAAM,EAAE;YACnC,uEAAuE;YACvE,MAAM,CAAC,OAAO,CAAC,kBAAkB,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC,GAAG,MAAM,GAAG,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC;gBACtF,YAAY,GAAG,SAAS,GAAG,iBAAiB,GAAG,cAAc,CAAC,OAAO,CAAC;gBACtE,aAAa,GAAG,UAAU,GAAG,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC;YACrE,+BAA+B;YAC/B,MAAM,IAAI,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,UAAU,CAAC,CAAC,EAAE,cAAc,CAAC,OAAO,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC;YACtE,SAAS;SAEV;aAAM;YACL,wEAAwE;YACxE,wDAAwD;YACxD,qEAAqE;YACrE,MAAM,IAAI,KAAK,CAAC,iBAAiB,GAAG,SAAS,GAAG,MAAM,GAAG,UAAU,GAAG,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC;SAC7G;KACF;IAED,qEAAqE;IACrE,yDAAyD;IACzD,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAC;AACnC,CAAC;AAWD,4DAA4D;AAC5D,kDAAkD;AAClD,qDAAqD;AAC9C,KAAK,UAAU,MAAM,CAC1B,SAAiB,EACjB,aAA4B,EAC5B,SAAiB,EACjB,GAAW,EACX,WAA+B,EAC/B,YAAgC,EAChC,aAAiC,EACjC,YAAoB,EACpB,WAA+B,EAC/B,UAAkB,EAClB,YAAoB,EACpB,IAAgB,EAChB,MAAc;IAEd,MAAM,UAAU,GAAa,EAAE,CAAC;IAChC,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,SAAS,CAAC,EAAE;QAC7B,MAAM,IAAI,KAAK,CAAC,wBAAwB,SAAS,EAAE,CAAC,CAAC;KACtD;IACD,IAAI,EAAE,CAAC,SAAS,CAAC,SAAS,CAAC,CAAC,WAAW,EAAE,EAAE;QACzC,EAAE,CAAC,WAAW,CAAC,SAAS,CAAC;aACtB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;aACjC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC;aACpC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;QACpC,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,EAAE;YAC3B,MAAM,IAAI,KAAK,CAAC,sCAAsC,GAAG,SAAS,GAAG,KAAK,CAAC,CAAC;SAC7E;KACF;SAAM;QACL,UAAU,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;KAC5B;IAED,OAAO,MAAM,WAAW,CACtB,UAAU,EACV,aAAa,EACb,SAAS,EACT,GAAG,EACH,WAAW,EACX,YAAY,EACZ,aAAa,EACb,YAAY,EACZ,WAAW,EACX,UAAU,EACV,YAAY,EACZ,IAAI,EACJ,MAAM,CAAC,CAAC;AACZ,CAAC;AA7CD,wBA6CC;AAED,uDAAuD;AACvD,SAAgB,mBAAmB,CAAC,KAAa;IAC/C,IAAI,UAAU,GAAG,CAAC,CAAC;IACnB,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,EAAE;QACxC,UAAU,IAAI,GAAG,CAAC,OAAO,CAAC,MAAM,CAAC;KAClC;IACD,OAAO,UAAU,CAAC;AACpB,CAAC;AAND,kDAMC;AAED,mEAAmE;AACnE,0CAA0C;AAC1C,SAAgB,uBAAuB,CAAC,aAAqB,EAAE,MAAc;IAC3E,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,YAAY,CAAC,aAAa,EAAE,MAAM,CAAC,CAAC,CAAC;IACjE,MAAM,MAAM,GAAG,OAAO,CAAC,iCAAiC,CAAC,CAAC;IAE1D,MAAM,MAAM,GAAG,IAAI,UAAU,CAAC,SAAS,EAAE,CAAC,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;IAClE,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE;QACjB,+EAA+E;QAC/E,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,MAAM,EAAE;YACjC,MAAM,CAAC,UAAU,CAAC,iBAAiB,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC;YACnD,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;YAC5C,MAAM,CAAC,QAAQ,EAAE,CAAC;SACnB;QAED,8DAA8D;QAC9D,iFAAiF;QACjF,MAAM,WAAW,GAAG,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC;QAC3D,MAAM,IAAI,KAAK,CAAC,qBAAqB,GAAG,aAAa,GAAG,gCAAgC,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;KACpH;AACH,CAAC;AAlBD,0DAkBC;AAED,wCAAwC;AACxC,qDAAqD;AACrD,KAAK,UAAU,WAAW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\ No newline at end of file
diff --git a/lib/util.js b/lib/util.js
index 45b5b39e5..a0e2d76bd 100644
--- a/lib/util.js
+++ b/lib/util.js
@@ -45,6 +45,25 @@ function getRequiredEnvParam(paramName) {
     return value;
 }
 exports.getRequiredEnvParam = getRequiredEnvParam;
+/**
+ * Get the extra options for the codeql commands.
+ */
+function getExtraOptionsEnvParam() {
+    const varName = 'CODEQL_ACTION_EXTRA_OPTIONS';
+    const raw = process.env[varName];
+    if (raw === undefined || raw.length === 0) {
+        return {};
+    }
+    try {
+        return JSON.parse(raw);
+    }
+    catch (e) {
+        throw new Error(varName +
+            ' environment variable is set, but does not contain valid JSON: ' +
+            e.message);
+    }
+}
+exports.getExtraOptionsEnvParam = getExtraOptionsEnvParam;
 function isLocalRun() {
     return !!process.env.CODEQL_LOCAL_RUN
         && process.env.CODEQL_LOCAL_RUN !== 'false'
@@ -319,36 +338,44 @@ function getMemoryFlag() {
 }
 exports.getMemoryFlag = getMemoryFlag;
 /**
- * Get the codeql `--threads` value specified for the `threads` input. The value
- * defaults to 1. The value will be capped to the number of available CPUs.
+ * Get the codeql `--threads` value specified for the `threads` input.
+ * If not value was specified, all available threads will be used.
+ *
+ * The value will be capped to the number of available CPUs.
  *
  * @returns string
  */
 function getThreadsFlag() {
-    let numThreads = 1;
+    let numThreads;
     const numThreadsString = core.getInput("threads");
+    const maxThreads = os.cpus().length;
     if (numThreadsString) {
         numThreads = Number(numThreadsString);
         if (Number.isNaN(numThreads)) {
             throw new Error(`Invalid threads setting "${numThreadsString}", specified.`);
         }
-        const maxThreads = os.cpus().length;
         if (numThreads > maxThreads) {
+            core.info(`Clamping desired number of threads (${numThreads}) to max available (${maxThreads}).`);
             numThreads = maxThreads;
         }
         const minThreads = -maxThreads;
         if (numThreads < minThreads) {
+            core.info(`Clamping desired number of free threads (${numThreads}) to max available (${minThreads}).`);
             numThreads = minThreads;
         }
     }
+    else {
+        // Default to using all threads
+        numThreads = maxThreads;
+    }
     return `--threads=${numThreads}`;
 }
 exports.getThreadsFlag = getThreadsFlag;
 /**
  * Get the directory where CodeQL databases should be placed.
  */
-function getCodeQLDatabasesDir() {
-    return path.resolve(getRequiredEnvParam('RUNNER_TEMP'), 'codeql_databases');
+function getCodeQLDatabasesDir(tempDir) {
+    return path.resolve(tempDir, 'codeql_databases');
 }
 exports.getCodeQLDatabasesDir = getCodeQLDatabasesDir;
 //# sourceMappingURL=util.js.map
\ No newline at end of file
diff --git a/lib/util.js.map b/lib/util.js.map
index 320b90fcf..3f1dd0676 100644
--- a/lib/util.js.map
+++ b/lib/util.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/lib/util.test.js b/lib/util.test.js
index c92cd72a4..b5f4161a2 100644
--- a/lib/util.test.js
+++ b/lib/util.test.js
@@ -92,4 +92,25 @@ ava_1.default('prepareEnvironment() when a local run', t => {
     t.deepEqual(process.env.GITHUB_JOB, 'UNKNOWN-JOB');
     process.env.CODEQL_LOCAL_RUN = origLocalRun;
 });
+ava_1.default('getExtraOptionsEnvParam() succeeds on valid JSON with invalid options (for now)', t => {
+    const origExtraOptions = process.env.CODEQL_ACTION_EXTRA_OPTIONS;
+    const options = { foo: 42 };
+    process.env.CODEQL_ACTION_EXTRA_OPTIONS = JSON.stringify(options);
+    t.deepEqual(util.getExtraOptionsEnvParam(), options);
+    process.env.CODEQL_ACTION_EXTRA_OPTIONS = origExtraOptions;
+});
+ava_1.default('getExtraOptionsEnvParam() succeeds on valid options', t => {
+    const origExtraOptions = process.env.CODEQL_ACTION_EXTRA_OPTIONS;
+    const options = { database: { init: ["--debug"] } };
+    process.env.CODEQL_ACTION_EXTRA_OPTIONS =
+        JSON.stringify(options);
+    t.deepEqual(util.getExtraOptionsEnvParam(), options);
+    process.env.CODEQL_ACTION_EXTRA_OPTIONS = origExtraOptions;
+});
+ava_1.default('getExtraOptionsEnvParam() fails on invalid JSON', t => {
+    const origExtraOptions = process.env.CODEQL_ACTION_EXTRA_OPTIONS;
+    process.env.CODEQL_ACTION_EXTRA_OPTIONS = "{{invalid-json}}";
+    t.throws(util.getExtraOptionsEnvParam);
+    process.env.CODEQL_ACTION_EXTRA_OPTIONS = origExtraOptions;
+});
 //# sourceMappingURL=util.test.js.map
\ No newline at end of file
diff --git a/lib/util.test.js.map b/lib/util.test.js.map
index df299e559..9f2eb61f9 100644
--- a/lib/util.test.js.map
+++ b/lib/util.test.js.map
@@ -1 +1 @@
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\ No newline at end of file
+{"version":3,"file":"util.test.js","sourceRoot":"","sources":["../src/util.test.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,8CAAuB;AACvB,uCAAyB;AACzB,uCAAyB;AAEzB,mDAA2C;AAC3C,6CAA+B;AAE/B,0BAAU,CAAC,aAAI,CAAC,CAAC;AAEjB,aAAI,CAAC,cAAc,EAAE,CAAC,CAAC,EAAE;IACvB,MAAM,KAAK,GAAG,EAAE,CAAC,YAAY,CAAC,SAAS,GAAG,mCAAmC,EAAE,MAAM,CAAC,CAAC;IACvF,MAAM,SAAS,GAAG,IAAI,CAAC,YAAY,CAAC,KAAK,CAAC,CAAC;IAC3C,CAAC,CAAC,SAAS,CAAC,SAAS,EAAE,CAAC,+BAA+B,EAAE,QAAQ,CAAC,CAAC,CAAC;AACtE,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,sDAAsD,EAAE,CAAC,CAAC,EAAE;IAE/D,MAAM,QAAQ,GAAG,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,QAAQ,EAAE,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC;IAE3D,MAAM,KAAK,GAAG;QACZ,EAAE,EAAE,SAAS,QAAQ,GAAG,GAAG,EAAE;QAC7B,KAAK,EAAE,WAAW;KACnB,CAAC;IAEF,KAAK,MAAM,CAAC,KAAK,EAAE,YAAY,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;QAEzD,OAAO,CAAC,GAAG,CAAC,WAAW,CAAC,GAAG,KAAK,CAAC;QAEjC,MAAM,IAAI,GAAG,IAAI,CAAC,aAAa,EAAE,CAAC;QAClC,CAAC,CAAC,SAAS,CAAC,IAAI,EAAE,YAAY,CAAC,CAAC;KACjC;AACH,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,uDAAuD,EAAE,CAAC,CAAC,EAAE;IAChE,KAAK,MAAM,KAAK,IAAI,CAAC,IAAI,EAAE,QAAQ,CAAC,EAAE;QACpC,OAAO,CAAC,GAAG,CAAC,WAAW,CAAC,GAAG,KAAK,CAAC;QACjC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC;KAC9B;AACH,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,2DAA2D,EAAE,CAAC,CAAC,EAAE;IAEpE,MAAM,OAAO,GAAG,EAAE,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC;IAEjC,MAAM,KAAK,GAAG;QACZ,GAAG,EAAE,aAAa;QAClB,GAAG,EAAE,aAAa;QAClB,CAAC,GAAG,OAAO,GAAG,CAAC,EAAE,CAAC,EAAE,aAAa,OAAO,EAAE;QAC1C,CAAC,GAAG,CAAC,OAAO,GAAG,CAAC,EAAE,CAAC,EAAE,aAAa,CAAC,OAAO,EAAE;KAC7C,CAAC;IAEF,KAAK,MAAM,CAAC,KAAK,EAAE,YAAY,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;QAEzD,OAAO,CAAC,GAAG,CAAC,eAAe,CAAC,GAAG,KAAK,CAAC;QAErC,MAAM,IAAI,GAAG,IAAI,CAAC,cAAc,EAAE,CAAC;QACnC,CAAC,CAAC,SAAS,CAAC,IAAI,EAAE,YAAY,CAAC,CAAC;KACjC;AACH,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,gEAAgE,EAAE,CAAC,CAAC,EAAE;IACzE,OAAO,CAAC,GAAG,CAAC,eAAe,CAAC,GAAG,QAAQ,CAAC;IACxC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;AAChC,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,qCAAqC,EAAE,CAAC,CAAC,EAAE;IAC9C,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,GAAG,EAAE,CAAC;IAC/B,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;AACxB,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,6BAA6B,EAAE,CAAC,CAAC,EAAE;IACtC,MAAM,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC;IAElD,OAAO,CAAC,GAAG,CAAC,gBAAgB,GAAG,EAAE,CAAC;IAClC,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC;IAE7B,OAAO,CAAC,GAAG,CAAC,gBAAgB,GAAG,OAAO,CAAC;IACvC,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC;IAE7B,OAAO,CAAC,GAAG,CAAC,gBAAgB,GAAG,GAAG,CAAC;IACnC,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC;IAE7B,OAAO,CAAC,GAAG,CAAC,gBAAgB,GAAG,MAAM,CAAC;IACtC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC;IAE5B,OAAO,CAAC,GAAG,CAAC,gBAAgB,GAAG,SAAS,CAAC;IACzC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC;IAE5B,OAAO,CAAC,GAAG,CAAC,gBAAgB,GAAG,YAAY,CAAC;AAC9C,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,uCAAuC,EAAE,CAAC,CAAC,EAAE;IAChD,MAAM,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC;IAElD,OAAO,CAAC,GAAG,CAAC,gBAAgB,GAAG,OAAO,CAAC;IACvC,OAAO,CAAC,GAAG,CAAC,UAAU,GAAG,KAAK,CAAC;IAE/B,IAAI,CAAC,0BAA0B,EAAE,CAAC;IAElC,YAAY;IACZ,CAAC,CAAC,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,UAAU,EAAE,KAAK,CAAC,CAAC;IAE3C,OAAO,CAAC,GAAG,CAAC,gBAAgB,GAAG,MAAM,CAAC;IAEtC,IAAI,CAAC,0BAA0B,EAAE,CAAC;IAElC,YAAY;IACZ,CAAC,CAAC,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,UAAU,EAAE,KAAK,CAAC,CAAC;IAE3C,OAAO,CAAC,GAAG,CAAC,UAAU,GAAG,EAAE,CAAC;IAE5B,IAAI,CAAC,0BAA0B,EAAE,CAAC;IAElC,UAAU;IACV,CAAC,CAAC,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,UAAU,EAAE,aAAa,CAAC,CAAC;IAEnD,OAAO,CAAC,GAAG,CAAC,gBAAgB,GAAG,YAAY,CAAC;AAC9C,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,iFAAiF,EAAE,CAAC,CAAC,EAAE;IAC1F,MAAM,gBAAgB,GAAG,OAAO,CAAC,GAAG,CAAC,2BAA2B,CAAC;IAEjE,MAAM,OAAO,GAAG,EAAC,GAAG,EAAE,EAAE,EAAC,CAAC;IAE1B,OAAO,CAAC,GAAG,CAAC,2BAA2B,GAAG,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC;IAElE,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,uBAAuB,EAAE,EAAO,OAAO,CAAC,CAAC;IAE1D,OAAO,CAAC,GAAG,CAAC,2BAA2B,GAAG,gBAAgB,CAAC;AAC7D,CAAC,CAAC,CAAC;AAGH,aAAI,CAAC,qDAAqD,EAAE,CAAC,CAAC,EAAE;IAC9D,MAAM,gBAAgB,GAAG,OAAO,CAAC,GAAG,CAAC,2BAA2B,CAAC;IAEjE,MAAM,OAAO,GAAG,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,CAAC,SAAS,CAAC,EAAE,EAAE,CAAC;IACpD,OAAO,CAAC,GAAG,CAAC,2BAA2B;QACrC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC;IAE1B,CAAC,CAAC,SAAS,CAAC,IAAI,CAAC,uBAAuB,EAAE,EAAE,OAAO,CAAC,CAAC;IAErD,OAAO,CAAC,GAAG,CAAC,2BAA2B,GAAG,gBAAgB,CAAC;AAC7D,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,iDAAiD,EAAE,CAAC,CAAC,EAAE;IAC1D,MAAM,gBAAgB,GAAG,OAAO,CAAC,GAAG,CAAC,2BAA2B,CAAC;IAEjE,OAAO,CAAC,GAAG,CAAC,2BAA2B,GAAG,kBAAkB,CAAC;IAC7D,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC;IAEvC,OAAO,CAAC,GAAG,CAAC,2BAA2B,GAAG,gBAAgB,CAAC;AAC7D,CAAC,CAAC,CAAC"}
\ No newline at end of file
diff --git a/queries/unguarded-action-lib.ql b/queries/unguarded-action-lib.ql
new file mode 100644
index 000000000..c7c872214
--- /dev/null
+++ b/queries/unguarded-action-lib.ql
@@ -0,0 +1,108 @@
+/**
+ * @name Unguarded actions library use
+ * @description Code that runs outside of GitHub Actions tries to use a library that should only be used when running on actions.
+ * @kind problem
+ * @problem.severity error
+ * @id javascript/codeql-action/unguarded-action-lib
+ */
+
+import javascript
+
+/**
+ * An import from a library that is meant for GitHub Actions and
+ * we do not want to be using outside of actions.
+ */
+class ActionsLibImport extends ImportDeclaration {
+  ActionsLibImport() {
+    getImportedPath().getValue().matches("@actions/%")
+  }
+
+  string getName() {
+    result = getImportedPath().getValue()
+  }
+
+  Variable getAProvidedVariable() {
+    result = getASpecifier().getLocal().getVariable()
+  }
+}
+
+/**
+ * An entrypoint to the CLI.
+ */
+class ClIEntrypoint extends Function {
+  ClIEntrypoint() {
+    getFile().getAbsolutePath().matches("%/cli.ts")
+  }
+}
+
+/**
+ * A check of whether we are in actions mode or CLI mode.
+ */
+class ModeGuard extends IfStmt {
+  ModeGuard() {
+    getCondition().(EqualityTest).getAnOperand().(StringLiteral).getValue() = "actions" or
+    getCondition().(EqualityTest).getAnOperand().(StringLiteral).getValue() = "cli"
+  }
+
+  string getOperand() {
+    result = getCondition().(EqualityTest).getAnOperand().(StringLiteral).getValue()
+  }
+
+  predicate isPositive() {
+    getCondition().(EqualityTest).getPolarity() = true
+  }
+
+  /**
+   * Get the then or else block that is the "actions" path.
+   */
+  Stmt getActionsBlock() {
+    (getOperand() = "actions" and isPositive() and result = getThen())
+    or
+    (getOperand() = "cli" and not isPositive() and result = getThen())
+    or
+    (getOperand() = "actions" and not isPositive() and result = getElse())
+    or
+    (getOperand() = "cli" and isPositive() and result = getElse())
+  }
+
+  /**
+   * Get an expr that is only executed on actions
+   */
+  Expr getAnActionsExpr() {
+    getActionsBlock().getAChildStmt*().getAChildExpr*() = result
+  }
+}
+
+/**
+ * Any expr that is a transitive child of the given function
+ * and is not only called on actions.
+ */
+Expr getAFunctionChildExpr(Function f) {
+  not exists(ModeGuard guard | guard.getAnActionsExpr() = result) and
+  result.getContainer() = f
+}
+
+/*
+ * Result is a function that is called from the body of the given function `f`
+ * and is not only called on actions.
+ */
+Function calledBy(Function f) {
+  exists(InvokeExpr invokeExpr |
+    invokeExpr = getAFunctionChildExpr(f) and
+    invokeExpr.getResolvedCallee() = result and
+    not exists(ModeGuard guard | guard.getAnActionsExpr() = invokeExpr)
+  )
+  or
+  // Assume outer function causes inner function to be called
+  (result instanceof Expr and
+  result.getEnclosingContainer() = f and
+  not exists(ModeGuard guard | guard.getAnActionsExpr() = result))
+}
+
+from VarAccess v, ActionsLibImport actionsLib, ClIEntrypoint cliEntry 
+where actionsLib.getAProvidedVariable() = v.getVariable()
+  and getAFunctionChildExpr(calledBy*(cliEntry)) = v
+select v, "$@ is imported from $@ and this code can be called from $@",
+  v, v.getName(),
+  actionsLib, actionsLib.getName(),
+  cliEntry, "the CLI"
diff --git a/src/analysis-paths.test.ts b/src/analysis-paths.test.ts
index 7579fd782..2b830a154 100644
--- a/src/analysis-paths.test.ts
+++ b/src/analysis-paths.test.ts
@@ -2,33 +2,44 @@ import test from 'ava';
 
 import * as analysisPaths from './analysis-paths';
 import {setupTests} from './testing-utils';
+import * as util from './util';
 
 setupTests(test);
 
 test("emptyPaths", async t => {
-  const config = {
-    languages: [],
-    queries: {},
-    pathsIgnore: [],
-    paths: [],
-    originalUserInput: {},
-  };
-  analysisPaths.includeAndExcludeAnalysisPaths(config);
-  t.is(process.env['LGTM_INDEX_INCLUDE'], undefined);
-  t.is(process.env['LGTM_INDEX_EXCLUDE'], undefined);
-  t.is(process.env['LGTM_INDEX_FILTERS'], undefined);
+  return await util.withTmpDir(async tmpDir => {
+    const config = {
+      languages: [],
+      queries: {},
+      pathsIgnore: [],
+      paths: [],
+      originalUserInput: {},
+      tempDir: tmpDir,
+      toolCacheDir: tmpDir,
+      codeQLCmd: '',
+    };
+    analysisPaths.includeAndExcludeAnalysisPaths(config);
+    t.is(process.env['LGTM_INDEX_INCLUDE'], undefined);
+    t.is(process.env['LGTM_INDEX_EXCLUDE'], undefined);
+    t.is(process.env['LGTM_INDEX_FILTERS'], undefined);
+  });
 });
 
 test("nonEmptyPaths", async t => {
-  const config = {
-    languages: [],
-    queries: {},
-    paths: ['path1', 'path2', '**/path3'],
-    pathsIgnore: ['path4', 'path5', 'path6/**'],
-    originalUserInput: {},
-  };
-  analysisPaths.includeAndExcludeAnalysisPaths(config);
-  t.is(process.env['LGTM_INDEX_INCLUDE'], 'path1\npath2');
-  t.is(process.env['LGTM_INDEX_EXCLUDE'], 'path4\npath5');
-  t.is(process.env['LGTM_INDEX_FILTERS'], 'include:path1\ninclude:path2\ninclude:**/path3\nexclude:path4\nexclude:path5\nexclude:path6/**');
+  return await util.withTmpDir(async tmpDir => {
+    const config = {
+      languages: [],
+      queries: {},
+      paths: ['path1', 'path2', '**/path3'],
+      pathsIgnore: ['path4', 'path5', 'path6/**'],
+      originalUserInput: {},
+      tempDir: tmpDir,
+      toolCacheDir: tmpDir,
+      codeQLCmd: '',
+    };
+    analysisPaths.includeAndExcludeAnalysisPaths(config);
+    t.is(process.env['LGTM_INDEX_INCLUDE'], 'path1\npath2');
+    t.is(process.env['LGTM_INDEX_EXCLUDE'], 'path4\npath5');
+    t.is(process.env['LGTM_INDEX_FILTERS'], 'include:path1\ninclude:path2\ninclude:**/path3\nexclude:path4\nexclude:path5\nexclude:path6/**');
+  });
 });
diff --git a/src/autobuild.ts b/src/autobuild.ts
index 5c611499a..e1ca5e8b3 100644
--- a/src/autobuild.ts
+++ b/src/autobuild.ts
@@ -1,7 +1,8 @@
 import * as core from '@actions/core';
 
-import { getCodeQL, isTracedLanguage } from './codeql';
+import { getCodeQL } from './codeql';
 import * as config_utils from './config-utils';
+import { isTracedLanguage } from './languages';
 import * as util from './util';
 
 interface AutobuildStatusReport extends util.StatusReportBase {
@@ -41,7 +42,7 @@ async function run() {
       return;
     }
 
-    const config = await config_utils.getConfig();
+    const config = await config_utils.getConfig(util.getRequiredEnvParam('RUNNER_TEMP'));
 
     // Attempt to find a language to autobuild
     // We want pick the dominant language in the repo from the ones we're able to build
@@ -62,7 +63,7 @@ async function run() {
     }
 
     core.startGroup(`Attempting to automatically build ${language} code`);
-    const codeQL = getCodeQL();
+    const codeQL = getCodeQL(config.codeQLCmd);
     await codeQL.runAutobuild(language);
 
     core.endGroup();
diff --git a/src/codeql.test.ts b/src/codeql.test.ts
index 2d665b5a3..0db008fb2 100644
--- a/src/codeql.test.ts
+++ b/src/codeql.test.ts
@@ -63,3 +63,35 @@ test('parse codeql bundle url version', t => {
     }
   }
 });
+
+test('getExtraOptions works for explicit paths', t => {
+  t.deepEqual(codeql.getExtraOptions({}, ['foo'], []), []);
+
+  t.deepEqual(codeql.getExtraOptions({foo: [42]}, ['foo'], []), ['42']);
+
+  t.deepEqual(codeql.getExtraOptions({foo: {bar: [42]}}, ['foo', 'bar'], []), ['42']);
+});
+
+test('getExtraOptions works for wildcards', t => {
+  t.deepEqual(codeql.getExtraOptions({'*': [42]}, ['foo'], []), ['42']);
+});
+
+test('getExtraOptions works for wildcards and explicit paths', t => {
+  let o1 = {'*': [42], foo: [87]};
+  t.deepEqual(codeql.getExtraOptions(o1, ['foo'], []), ['42', '87']);
+
+  let o2 = {'*': [42], foo: [87]};
+  t.deepEqual(codeql.getExtraOptions(o2, ['foo', 'bar'], []), ['42']);
+
+  let o3 = {'*': [42], foo: { '*': [87], bar: [99]}};
+  let p = ['foo', 'bar'];
+  t.deepEqual(codeql.getExtraOptions(o3, p, []), ['42', '87', '99']);
+});
+
+test('getExtraOptions throws for bad content', t => {
+  t.throws(() => codeql.getExtraOptions({'*': 42}, ['foo'], []));
+
+  t.throws(() => codeql.getExtraOptions({foo: 87}, ['foo'], []));
+
+  t.throws(() => codeql.getExtraOptions({'*': [42], foo: { '*': 87, bar: [99]}}, ['foo', 'bar'], []));
+});
diff --git a/src/codeql.ts b/src/codeql.ts
index 0e081a80f..ddf93aed8 100644
--- a/src/codeql.ts
+++ b/src/codeql.ts
@@ -12,13 +12,35 @@ import uuidV4 from 'uuid/v4';
 
 import * as api from './api-client';
 import * as defaults from './defaults.json'; // Referenced from codeql-action-sync-tool!
+import { Language } from './languages';
 import * as util from './util';
 
+type Options = (string|number|boolean)[];
+
+/**
+ * Extra command line options for the codeql commands.
+ */
+interface ExtraOptions {
+  '*'?: Options;
+  database?: {
+    '*'?: Options,
+    init?: Options,
+    'trace-command'?: Options,
+    analyze?: Options,
+    finalize?: Options
+  };
+  resolve?: {
+    '*'?: Options,
+    extractor?: Options,
+    queries?: Options
+  };
+}
+
 export interface CodeQL {
   /**
-   * Get the directory where the CodeQL executable is located.
+   * Get the path of the CodeQL executable.
    */
-  getDir(): string;
+  getPath(): string;
   /**
    * Print version information about CodeQL.
    */
@@ -31,16 +53,16 @@ export interface CodeQL {
   /**
    * Run 'codeql database init'.
    */
-  databaseInit(databasePath: string, language: string, sourceRoot: string): Promise<void>;
+  databaseInit(databasePath: string, language: Language, sourceRoot: string): Promise<void>;
   /**
    * Runs the autobuilder for the given language.
    */
-  runAutobuild(language: string): Promise<void>;
+  runAutobuild(language: Language): Promise<void>;
   /**
    * Extract code for a scanned language using 'codeql database trace-command'
    * and running the language extracter.
    */
-  extractScannedLanguage(database: string, language: string): Promise<void>;
+  extractScannedLanguage(database: string, language: Language): Promise<void>;
   /**
    * Finalize a database using 'codeql database finalize'.
    */
@@ -75,12 +97,6 @@ export interface ResolveQueriesOutput {
  */
 let cachedCodeQL: CodeQL | undefined = undefined;
 
-/**
- * Environment variable used to store the location of the CodeQL CLI executable.
- * Value is set by setupCodeQL and read by getCodeQL.
- */
-const CODEQL_ACTION_CMD = "CODEQL_ACTION_CMD";
-
 const CODEQL_BUNDLE_VERSION = defaults.bundleVersion;
 const CODEQL_BUNDLE_NAME = "codeql-bundle.tar.gz";
 const CODEQL_DEFAULT_ACTION_REPOSITORY = "github/codeql-action";
@@ -198,7 +214,6 @@ export async function setupCodeQL(): Promise<CodeQL> {
     }
 
     cachedCodeQL = getCodeQLForCmd(codeqlCmd);
-    core.exportVariable(CODEQL_ACTION_CMD, codeqlCmd);
     return cachedCodeQL;
 
   } catch (e) {
@@ -229,16 +244,24 @@ export function getCodeQLURLVersion(url: string): string {
   return s;
 }
 
-export function getCodeQL(): CodeQL {
+/**
+ * Use the CodeQL executable located at the given path.
+ */
+export function getCodeQL(cmd: string): CodeQL {
   if (cachedCodeQL === undefined) {
-    const codeqlCmd = util.getRequiredEnvParam(CODEQL_ACTION_CMD);
-    cachedCodeQL = getCodeQLForCmd(codeqlCmd);
+    cachedCodeQL = getCodeQLForCmd(cmd);
   }
   return cachedCodeQL;
 }
 
-function resolveFunction<T>(partialCodeql: Partial<CodeQL>, methodName: string): T {
+function resolveFunction<T>(
+  partialCodeql: Partial<CodeQL>,
+  methodName: string,
+  defaultImplementation?: T): T {
   if (typeof partialCodeql[methodName] !== 'function') {
+    if (defaultImplementation !== undefined) {
+      return defaultImplementation;
+    }
     const dummyMethod = () => {
       throw new Error('CodeQL ' + methodName + ' method not correctly defined');
     };
@@ -253,9 +276,9 @@ function resolveFunction<T>(partialCodeql: Partial<CodeQL>, methodName: string):
  * Accepts a partial object and any undefined methods will be implemented
  * to immediately throw an exception indicating which method is missing.
  */
-export function setCodeQL(partialCodeql: Partial<CodeQL>) {
+export function setCodeQL(partialCodeql: Partial<CodeQL>): CodeQL {
   cachedCodeQL = {
-    getDir: resolveFunction(partialCodeql, 'getDir'),
+    getPath: resolveFunction(partialCodeql, 'getPath', () => '/tmp/dummy-path'),
     printVersion: resolveFunction(partialCodeql, 'printVersion'),
     getTracerEnv: resolveFunction(partialCodeql, 'getTracerEnv'),
     databaseInit: resolveFunction(partialCodeql, 'databaseInit'),
@@ -265,12 +288,27 @@ export function setCodeQL(partialCodeql: Partial<CodeQL>) {
     resolveQueries: resolveFunction(partialCodeql, 'resolveQueries'),
     databaseAnalyze: resolveFunction(partialCodeql, 'databaseAnalyze')
   };
+  return cachedCodeQL;
+}
+
+/**
+ * Get the cached CodeQL object. Should only be used from tests.
+ *
+ * TODO: Work out a good way for tests to get this from the test context
+ * instead of having to have this method.
+ */
+export function getCachedCodeQL(): CodeQL {
+  if (cachedCodeQL === undefined) {
+    // Should never happen as setCodeQL is called by testing-utils.setupTests
+    throw new Error('cachedCodeQL undefined');
+  }
+  return cachedCodeQL;
 }
 
 function getCodeQLForCmd(cmd: string): CodeQL {
   return {
-    getDir: function() {
-      return path.dirname(cmd);
+    getPath: function() {
+      return cmd;
     },
     printVersion: async function() {
       await exec.exec(cmd, [
@@ -286,22 +324,24 @@ function getCodeQLForCmd(cmd: string): CodeQL {
         'trace-command',
         databasePath,
         ...compilerSpecArg,
+        ...getExtraOptionsFromEnv(['database', 'trace-command']),
         process.execPath,
         path.resolve(__dirname, 'tracer-env.js'),
         envFile
       ]);
       return JSON.parse(fs.readFileSync(envFile, 'utf-8'));
     },
-    databaseInit: async function(databasePath: string, language: string, sourceRoot: string) {
+    databaseInit: async function(databasePath: string, language: Language, sourceRoot: string) {
       await exec.exec(cmd, [
         'database',
         'init',
         databasePath,
         '--language=' + language,
         '--source-root=' + sourceRoot,
+        ...getExtraOptionsFromEnv(['database', 'init']),
       ]);
     },
-    runAutobuild: async function(language: string) {
+    runAutobuild: async function(language: Language) {
       const cmdName = process.platform === 'win32' ? 'autobuild.cmd' : 'autobuild.sh';
       const autobuildCmd = path.join(path.dirname(cmd), language, 'tools', cmdName);
 
@@ -315,7 +355,7 @@ function getCodeQLForCmd(cmd: string): CodeQL {
 
       await exec.exec(autobuildCmd);
     },
-    extractScannedLanguage: async function(databasePath: string, language: string) {
+    extractScannedLanguage: async function(databasePath: string, language: Language) {
       // Get extractor location
       let extractorPath = '';
       await exec.exec(
@@ -324,7 +364,8 @@ function getCodeQLForCmd(cmd: string): CodeQL {
           'resolve',
           'extractor',
           '--format=json',
-          '--language=' + language
+          '--language=' + language,
+          ...getExtraOptionsFromEnv(['resolve', 'extractor']),
         ],
         {
           silent: true,
@@ -342,6 +383,7 @@ function getCodeQLForCmd(cmd: string): CodeQL {
       await exec.exec(cmd, [
         'database',
         'trace-command',
+        ...getExtraOptionsFromEnv(['database', 'trace-command']),
         databasePath,
         '--',
         traceCommand
@@ -351,6 +393,7 @@ function getCodeQLForCmd(cmd: string): CodeQL {
       await exec.exec(cmd, [
         'database',
         'finalize',
+        ...getExtraOptionsFromEnv(['database', 'finalize']),
         databasePath
       ]);
     },
@@ -359,7 +402,8 @@ function getCodeQLForCmd(cmd: string): CodeQL {
         'resolve',
         'queries',
         ...queries,
-        '--format=bylanguage'
+        '--format=bylanguage',
+        ...getExtraOptionsFromEnv(['resolve', 'queries'])
       ];
       if (extraSearchPath !== undefined) {
         codeqlArgs.push('--search-path', extraSearchPath);
@@ -385,16 +429,58 @@ function getCodeQLForCmd(cmd: string): CodeQL {
         '--format=sarif-latest',
         '--output=' + sarifFile,
         '--no-sarif-add-snippets',
+        ...getExtraOptionsFromEnv(['database', 'analyze']),
         querySuite
       ]);
     }
   };
 }
 
-export function isTracedLanguage(language: string): boolean {
-  return ['cpp', 'java', 'csharp'].includes(language);
+/**
+ * Gets the options for `path` of `options` as an array of extra option strings.
+ */
+function getExtraOptionsFromEnv(path: string[]) {
+  let options: ExtraOptions = util.getExtraOptionsEnvParam();
+  return getExtraOptions(options, path, []);
 }
 
-export function isScannedLanguage(language: string): boolean {
-  return !isTracedLanguage(language);
+/**
+ * Gets the options for `path` of `options` as an array of extra option strings.
+ *
+ * - the special terminal step name '*' in `options` matches all path steps
+ * - throws an exception if this conversion is impossible.
+ */
+export /* exported for testing */ function getExtraOptions(
+  options: any,
+  path: string[],
+  pathInfo: string[]): string[] {
+  /**
+   * Gets `options` as an array of extra option strings.
+   *
+   * - throws an exception mentioning `pathInfo` if this conversion is impossible.
+   */
+  function asExtraOptions(options: any, pathInfo: string[]): string[] {
+    if (options === undefined) {
+      return [];
+    }
+    if (!Array.isArray(options)) {
+      const msg =
+        `The extra options for '${pathInfo.join('.')}' ('${JSON.stringify(options)}') are not in an array.`;
+      throw new Error(msg);
+    }
+    return options.map(o => {
+      const t = typeof o;
+      if (t !== 'string' && t !== 'number' && t !== 'boolean') {
+        const msg =
+          `The extra option for '${pathInfo.join('.')}' ('${JSON.stringify(o)}') is not a primitive value.`;
+        throw new Error(msg);
+      }
+      return o + '';
+    });
+  }
+  let all = asExtraOptions(options?.['*'], pathInfo.concat('*'));
+  let specific = path.length === 0 ?
+    asExtraOptions(options, pathInfo) :
+    getExtraOptions(options?.[path[0]], path?.slice(1), pathInfo.concat(path[0]));
+  return all.concat(specific);
 }
diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index 25cf6fd46..0c1e48693 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -5,8 +5,9 @@ import * as path from 'path';
 import sinon from 'sinon';
 
 import * as api from './api-client';
-import * as CodeQL from './codeql';
+import { getCachedCodeQL, setCodeQL } from './codeql';
 import * as configUtils from './config-utils';
+import { Language } from "./languages";
 import {setupTests} from './testing-utils';
 import * as util from './util';
 
@@ -57,7 +58,7 @@ test("load empty config", async t => {
     setInput('config-file', undefined);
     setInput('languages', 'javascript,python');
 
-    CodeQL.setCodeQL({
+    const codeQL = setCodeQL({
       resolveQueries: async function() {
         return {
           byLanguage: {},
@@ -67,9 +68,9 @@ test("load empty config", async t => {
       },
     });
 
-    const config = await configUtils.initConfig();
+    const config = await configUtils.initConfig(tmpDir, tmpDir, codeQL);
 
-    t.deepEqual(config, await configUtils.getDefaultConfig());
+    t.deepEqual(config, await configUtils.getDefaultConfig(tmpDir, tmpDir, codeQL));
   });
 });
 
@@ -81,7 +82,7 @@ test("loading config saves config", async t => {
     setInput('config-file', undefined);
     setInput('languages', 'javascript,python');
 
-    CodeQL.setCodeQL({
+    const codeQL = setCodeQL({
       resolveQueries: async function() {
         return {
           byLanguage: {},
@@ -93,18 +94,18 @@ test("loading config saves config", async t => {
 
 
     // Sanity check the saved config file does not already exist
-    t.false(fs.existsSync(configUtils.getPathToParsedConfigFile()));
+    t.false(fs.existsSync(configUtils.getPathToParsedConfigFile(tmpDir)));
 
     // Sanity check that getConfig throws before we have called initConfig
-    await t.throwsAsync(configUtils.getConfig);
+    await t.throwsAsync(() => configUtils.getConfig(tmpDir));
 
-    const config1 = await configUtils.initConfig();
+    const config1 = await configUtils.initConfig(tmpDir, tmpDir, codeQL);
 
     // The saved config file should now exist
-    t.true(fs.existsSync(configUtils.getPathToParsedConfigFile()));
+    t.true(fs.existsSync(configUtils.getPathToParsedConfigFile(tmpDir)));
 
     // And that same newly-initialised config should now be returned by getConfig
-    const config2 = await configUtils.getConfig();
+    const config2 = await configUtils.getConfig(tmpDir);
     t.deepEqual(config1, config2);
   });
 });
@@ -117,7 +118,7 @@ test("load input outside of workspace", async t => {
     setInput('config-file', '../input');
 
     try {
-      await configUtils.initConfig();
+      await configUtils.initConfig(tmpDir, tmpDir, getCachedCodeQL());
       throw new Error('initConfig did not throw error');
     } catch (err) {
       t.deepEqual(err, new Error(configUtils.getConfigFileOutsideWorkspaceErrorMessage(path.join(tmpDir, '../input'))));
@@ -134,7 +135,7 @@ test("load non-local input with invalid repo syntax", async t => {
     setInput('config-file', 'octo-org/codeql-config@main');
 
     try {
-      await configUtils.initConfig();
+      await configUtils.initConfig(tmpDir, tmpDir, getCachedCodeQL());
       throw new Error('initConfig did not throw error');
     } catch (err) {
       t.deepEqual(err, new Error(configUtils.getConfigFileRepoFormatInvalidMessage('octo-org/codeql-config@main')));
@@ -152,7 +153,7 @@ test("load non-existent input", async t => {
     setInput('languages', 'javascript');
 
     try {
-      await configUtils.initConfig();
+      await configUtils.initConfig(tmpDir, tmpDir, getCachedCodeQL());
       throw new Error('initConfig did not throw error');
     } catch (err) {
       t.deepEqual(err, new Error(configUtils.getConfigFileDoesNotExistErrorMessage(path.join(tmpDir, 'input'))));
@@ -165,7 +166,7 @@ test("load non-empty input", async t => {
     process.env['RUNNER_TEMP'] = tmpDir;
     process.env['GITHUB_WORKSPACE'] = tmpDir;
 
-    CodeQL.setCodeQL({
+    const codeQL = setCodeQL({
       resolveQueries: async function() {
         return {
           byLanguage: {
@@ -196,7 +197,7 @@ test("load non-empty input", async t => {
 
     // And the config we expect it to parse to
     const expectedConfig: configUtils.Config = {
-      languages: ['javascript'],
+      languages: [Language.javascript],
       queries: {'javascript': ['/foo/a.ql', '/bar/b.ql']},
       pathsIgnore: ['a', 'b'],
       paths: ['c/d'],
@@ -207,13 +208,16 @@ test("load non-empty input", async t => {
         'paths-ignore': ['a', 'b'],
         paths: ['c/d'],
       },
+      tempDir: tmpDir,
+      toolCacheDir: tmpDir,
+      codeQLCmd: codeQL.getPath(),
     };
 
     fs.writeFileSync(path.join(tmpDir, 'input'), inputFileContents, 'utf8');
     setInput('config-file', 'input');
     setInput('languages', 'javascript');
 
-    const actualConfig = await configUtils.initConfig();
+    const actualConfig = await configUtils.initConfig(tmpDir, tmpDir, codeQL);
 
     // Should exactly equal the object we constructed earlier
     t.deepEqual(actualConfig, expectedConfig);
@@ -232,7 +236,7 @@ test("default queries are used", async t => {
     // with the correct arguments.
 
     const resolveQueriesArgs: {queries: string[], extraSearchPath: string | undefined}[] = [];
-    CodeQL.setCodeQL({
+    const codeQL = setCodeQL({
       resolveQueries: async function(queries: string[], extraSearchPath: string | undefined) {
         resolveQueriesArgs.push({queries, extraSearchPath});
         return {
@@ -260,7 +264,7 @@ test("default queries are used", async t => {
     setInput('config-file', 'input');
     setInput('languages', 'javascript');
 
-    await configUtils.initConfig();
+    await configUtils.initConfig(tmpDir, tmpDir, codeQL);
 
     // Check resolve queries was called correctly
     t.deepEqual(resolveQueriesArgs.length, 1);
@@ -274,7 +278,7 @@ test("API client used when reading remote config", async t => {
     process.env['RUNNER_TEMP'] = tmpDir;
     process.env['GITHUB_WORKSPACE'] = tmpDir;
 
-    CodeQL.setCodeQL({
+    const codeQL = setCodeQL({
       resolveQueries: async function() {
         return {
           byLanguage: {
@@ -311,7 +315,7 @@ test("API client used when reading remote config", async t => {
     setInput('config-file', 'octo-org/codeql-config/config.yaml@main');
     setInput('languages', 'javascript');
 
-    await configUtils.initConfig();
+    await configUtils.initConfig(tmpDir, tmpDir, codeQL);
     t.assert(spyGetContents.called);
   });
 });
@@ -327,7 +331,7 @@ test("Remote config handles the case where a directory is provided", async t =>
     const repoReference = 'octo-org/codeql-config/config.yaml@main';
     setInput('config-file', repoReference);
     try {
-      await configUtils.initConfig();
+      await configUtils.initConfig(tmpDir, tmpDir, getCachedCodeQL());
       throw new Error('initConfig did not throw error');
     } catch (err) {
       t.deepEqual(err, new Error(configUtils.getConfigFileDirectoryGivenMessage(repoReference)));
@@ -348,7 +352,7 @@ test("Invalid format of remote config handled correctly", async t => {
     const repoReference = 'octo-org/codeql-config/config.yaml@main';
     setInput('config-file', repoReference);
     try {
-      await configUtils.initConfig();
+      await configUtils.initConfig(tmpDir, tmpDir, getCachedCodeQL());
       throw new Error('initConfig did not throw error');
     } catch (err) {
       t.deepEqual(err, new Error(configUtils.getConfigFileFormatInvalidMessage(repoReference)));
@@ -364,7 +368,7 @@ test("No detected languages", async t => {
     mockListLanguages([]);
 
     try {
-      await configUtils.initConfig();
+      await configUtils.initConfig(tmpDir, tmpDir, getCachedCodeQL());
       throw new Error('initConfig did not throw error');
     } catch (err) {
       t.deepEqual(err, new Error(configUtils.getNoLanguagesError()));
@@ -380,7 +384,7 @@ test("Unknown languages", async t => {
     setInput('languages', 'ruby,english');
 
     try {
-      await configUtils.initConfig();
+      await configUtils.initConfig(tmpDir, tmpDir, getCachedCodeQL());
       throw new Error('initConfig did not throw error');
     } catch (err) {
       t.deepEqual(err, new Error(configUtils.getUnknownLanguagesError(['ruby', 'english'])));
@@ -398,7 +402,7 @@ function doInvalidInputTest(
       process.env['RUNNER_TEMP'] = tmpDir;
       process.env['GITHUB_WORKSPACE'] = tmpDir;
 
-      CodeQL.setCodeQL({
+      const codeQL = setCodeQL({
         resolveQueries: async function() {
           return {
             byLanguage: {},
@@ -414,7 +418,7 @@ function doInvalidInputTest(
       setInput('languages', 'javascript');
 
       try {
-        await configUtils.initConfig();
+        await configUtils.initConfig(tmpDir, tmpDir, codeQL);
         throw new Error('initConfig did not throw error');
       } catch (err) {
         t.deepEqual(err, new Error(expectedErrorMessageGenerator(inputFile)));
diff --git a/src/config-utils.ts b/src/config-utils.ts
index b886806d3..643bddb82 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -4,8 +4,9 @@ import * as yaml from 'js-yaml';
 import * as path from 'path';
 
 import * as api from './api-client';
-import { getCodeQL, ResolveQueriesOutput } from './codeql';
+import { CodeQL, ResolveQueriesOutput } from './codeql';
 import * as externalQueries from "./external-queries";
+import { Language, parseLanguage } from "./languages";
 import * as util from './util';
 
 // Property names from the user-supplied config file.
@@ -16,16 +17,6 @@ const QUERIES_USES_PROPERTY = 'uses';
 const PATHS_IGNORE_PROPERTY = 'paths-ignore';
 const PATHS_PROPERTY = 'paths';
 
-// All the languages supported by CodeQL
-const ALL_LANGUAGES = ['csharp', 'cpp', 'go', 'java', 'javascript', 'python'] as const;
-type Language = (typeof ALL_LANGUAGES)[number];
-
-// Some alternate names for languages
-const LANGUAGE_ALIASES: {[name: string]: Language} = {
-  'c': 'cpp',
-  'typescript': 'javascript',
-};
-
 /**
  * Format of the config file supplied by the user.
  */
@@ -70,6 +61,20 @@ export interface Config {
    * top-level field above.
    */
   originalUserInput: UserConfig;
+  /**
+   * Directory to use for temporary files that should be
+   * deleted at the end of the job.
+   */
+  tempDir: string;
+  /**
+   * Directory to use for the tool cache.
+   * This may be persisted between jobs but this is not guaranteed.
+   */
+  toolCacheDir: string;
+  /**
+   * Path of the CodeQL executable.
+   */
+  codeQLCmd: string;
 }
 
 /**
@@ -119,13 +124,13 @@ function validateQueries(resolvedQueries: ResolveQueriesOutput) {
  * Run 'codeql resolve queries' and add the results to resultMap
  */
 async function runResolveQueries(
+  codeQL: CodeQL,
   resultMap: { [language: string]: string[] },
   toResolve: string[],
   extraSearchPath: string | undefined,
   errorOnInvalidQueries: boolean) {
 
-  const codeQl = getCodeQL();
-  const resolvedQueries = await codeQl.resolveQueries(toResolve, extraSearchPath);
+  const resolvedQueries = await codeQL.resolveQueries(toResolve, extraSearchPath);
 
   for (const [language, queries] of Object.entries(resolvedQueries.byLanguage)) {
     if (resultMap[language] === undefined) {
@@ -142,9 +147,9 @@ async function runResolveQueries(
 /**
  * Get the set of queries included by default.
  */
-async function addDefaultQueries(languages: string[], resultMap: { [language: string]: string[] }) {
+async function addDefaultQueries(codeQL: CodeQL, languages: string[], resultMap: { [language: string]: string[] }) {
   const suites = languages.map(l => l + '-code-scanning.qls');
-  await runResolveQueries(resultMap, suites, undefined, false);
+  await runResolveQueries(codeQL, resultMap, suites, undefined, false);
 }
 
 // The set of acceptable values for built-in suites from the codeql bundle
@@ -157,6 +162,7 @@ const builtinSuites = ['security-extended', 'security-and-quality'] as const;
 async function addBuiltinSuiteQueries(
   configFile: string,
   languages: string[],
+  codeQL: CodeQL,
   resultMap: { [language: string]: string[] },
   suiteName: string) {
 
@@ -166,7 +172,7 @@ async function addBuiltinSuiteQueries(
   }
 
   const suites = languages.map(l => l + '-' + suiteName + '.qls');
-  await runResolveQueries(resultMap, suites, undefined, false);
+  await runResolveQueries(codeQL, resultMap, suites, undefined, false);
 }
 
 /**
@@ -174,6 +180,7 @@ async function addBuiltinSuiteQueries(
  */
 async function addLocalQueries(
   configFile: string,
+  codeQL: CodeQL,
   resultMap: { [language: string]: string[] },
   localQueryPath: string) {
 
@@ -198,13 +205,19 @@ async function addLocalQueries(
   // Get the root of the current repo to use when resolving query dependencies
   const rootOfRepo = util.getRequiredEnvParam('GITHUB_WORKSPACE');
 
-  await runResolveQueries(resultMap, [absoluteQueryPath], rootOfRepo, true);
+  await runResolveQueries(codeQL, resultMap, [absoluteQueryPath], rootOfRepo, true);
 }
 
 /**
  * Retrieve the set of queries at the referenced remote repo and add them to resultMap.
  */
-async function addRemoteQueries(configFile: string, resultMap: { [language: string]: string[] }, queryUses: string) {
+async function addRemoteQueries(
+  configFile: string,
+  codeQL: CodeQL,
+  resultMap: { [language: string]: string[] },
+  queryUses: string,
+  tempDir: string) {
+
   let tok = queryUses.split('@');
   if (tok.length !== 2) {
     throw new Error(getQueryUsesInvalid(configFile, queryUses));
@@ -226,13 +239,13 @@ async function addRemoteQueries(configFile: string, resultMap: { [language: stri
   const nwo = tok[0] + '/' + tok[1];
 
   // Checkout the external repository
-  const rootOfRepo = await externalQueries.checkoutExternalRepository(nwo, ref);
+  const rootOfRepo = await externalQueries.checkoutExternalRepository(nwo, ref, tempDir);
 
   const queryPath = tok.length > 2
     ? path.join(rootOfRepo, tok.slice(2).join('/'))
     : rootOfRepo;
 
-  await runResolveQueries(resultMap, [queryPath], rootOfRepo, true);
+  await runResolveQueries(codeQL, resultMap, [queryPath], rootOfRepo, true);
 }
 
 /**
@@ -246,8 +259,10 @@ async function addRemoteQueries(configFile: string, resultMap: { [language: stri
 async function parseQueryUses(
   configFile: string,
   languages: string[],
+  codeQL: CodeQL,
   resultMap: { [language: string]: string[] },
-  queryUses: string) {
+  queryUses: string,
+  tempDir: string) {
 
   queryUses = queryUses.trim();
   if (queryUses === "") {
@@ -256,18 +271,18 @@ async function parseQueryUses(
 
   // Check for the local path case before we start trying to parse the repository name
   if (queryUses.startsWith("./")) {
-    await addLocalQueries(configFile, resultMap, queryUses.slice(2));
+    await addLocalQueries(configFile, codeQL, resultMap, queryUses.slice(2));
     return;
   }
 
   // Check for one of the builtin suites
   if (queryUses.indexOf('/') === -1 && queryUses.indexOf('@') === -1) {
-    await addBuiltinSuiteQueries(configFile, languages, resultMap, queryUses);
+    await addBuiltinSuiteQueries(configFile, languages, codeQL, resultMap, queryUses);
     return;
   }
 
   // Otherwise, must be a reference to another repo
-  await addRemoteQueries(configFile, resultMap, queryUses);
+  await addRemoteQueries(configFile, codeQL, resultMap, queryUses, tempDir);
 }
 
 // Regex validating stars in paths or paths-ignore entries.
@@ -424,17 +439,6 @@ export function getUnknownLanguagesError(languages: string[]): string {
  * Gets the set of languages in the current repository
  */
 async function getLanguagesInRepo(): Promise<Language[]> {
-  // Translate between GitHub's API names for languages and ours
-  const codeqlLanguages: {[lang: string]: Language} = {
-    'C': 'cpp',
-    'C++': 'cpp',
-    'C#': 'csharp',
-    'Go': 'go',
-    'Java': 'java',
-    'JavaScript': 'javascript',
-    'TypeScript': 'javascript',
-    'Python': 'python',
-  };
   let repo_nwo = process.env['GITHUB_REPOSITORY']?.split("/");
   if (repo_nwo) {
     let owner = repo_nwo[0];
@@ -453,9 +457,10 @@ async function getLanguagesInRepo(): Promise<Language[]> {
     // Since sets in javascript maintain insertion order, using a set here and then splatting it
     // into an array gives us an array of languages ordered by popularity
     let languages: Set<Language> = new Set();
-    for (let lang in response.data) {
-      if (lang in codeqlLanguages) {
-        languages.add(codeqlLanguages[lang]);
+    for (let lang of Object.keys(response.data)) {
+      let parsedLang = parseLanguage(lang);
+      if (parsedLang !== undefined) {
+        languages.add(parsedLang);
       }
     }
     return [...languages];
@@ -496,50 +501,46 @@ async function getLanguages(): Promise<Language[]> {
   }
 
   // Make sure they are supported
-  const checkedLanguages: Language[] = [];
+  const parsedLanguages: Language[] = [];
   const unknownLanguages: string[] = [];
   for (let language of languages) {
-    // Normalise to lower case
-    language = language.toLowerCase();
-    // Resolve any known aliases
-    if (language in LANGUAGE_ALIASES) {
-      language = LANGUAGE_ALIASES[language];
-    }
-
-    const checkedLanguage = ALL_LANGUAGES.find(l => l === language);
-    if (checkedLanguage === undefined) {
+    const parsedLanguage = parseLanguage(language);
+    if (parsedLanguage === undefined) {
       unknownLanguages.push(language);
-    } else if (checkedLanguages.indexOf(checkedLanguage) === -1) {
-      checkedLanguages.push(checkedLanguage);
+    } else if (parsedLanguages.indexOf(parsedLanguage) === -1) {
+      parsedLanguages.push(parsedLanguage);
     }
   }
   if (unknownLanguages.length > 0) {
     throw new Error(getUnknownLanguagesError(unknownLanguages));
   }
 
-  return checkedLanguages;
+  return parsedLanguages;
 }
 
 /**
  * Get the default config for when the user has not supplied one.
  */
-export async function getDefaultConfig(): Promise<Config> {
+export async function getDefaultConfig(tempDir: string, toolCacheDir: string, codeQL: CodeQL): Promise<Config> {
   const languages = await getLanguages();
   const queries = {};
-  await addDefaultQueries(languages, queries);
+  await addDefaultQueries(codeQL, languages, queries);
   return {
     languages: languages,
     queries: queries,
     pathsIgnore: [],
     paths: [],
     originalUserInput: {},
+    tempDir,
+    toolCacheDir,
+    codeQLCmd: codeQL.getPath(),
   };
 }
 
 /**
  * Load the config from the given file.
  */
-async function loadConfig(configFile: string): Promise<Config> {
+async function loadConfig(configFile: string, tempDir: string, toolCacheDir: string, codeQL: CodeQL): Promise<Config> {
   let parsedYAML: UserConfig;
 
   if (isLocal(configFile)) {
@@ -577,7 +578,7 @@ async function loadConfig(configFile: string): Promise<Config> {
     disableDefaultQueries = parsedYAML[DISABLE_DEFAULT_QUERIES_PROPERTY]!;
   }
   if (!disableDefaultQueries) {
-    await addDefaultQueries(languages, queries);
+    await addDefaultQueries(codeQL, languages, queries);
   }
 
   if (QUERIES_PROPERTY in parsedYAML) {
@@ -588,7 +589,7 @@ async function loadConfig(configFile: string): Promise<Config> {
       if (!(QUERIES_USES_PROPERTY in query) || typeof query[QUERIES_USES_PROPERTY] !== "string") {
         throw new Error(getQueryUsesInvalid(configFile));
       }
-      await parseQueryUses(configFile, languages, queries, query[QUERIES_USES_PROPERTY]);
+      await parseQueryUses(configFile, languages, codeQL, queries, query[QUERIES_USES_PROPERTY], tempDir);
     }
   }
 
@@ -630,7 +631,10 @@ async function loadConfig(configFile: string): Promise<Config> {
     queries,
     pathsIgnore,
     paths,
-    originalUserInput: parsedYAML
+    originalUserInput: parsedYAML,
+    tempDir,
+    toolCacheDir,
+    codeQLCmd: codeQL.getPath(),
   };
 }
 
@@ -640,16 +644,16 @@ async function loadConfig(configFile: string): Promise<Config> {
  * This will parse the config from the user input if present, or generate
  * a default config. The parsed config is then stored to a known location.
  */
-export async function initConfig(): Promise<Config> {
+export async function initConfig(tempDir: string, toolCacheDir: string, codeQL: CodeQL): Promise<Config> {
   const configFile = core.getInput('config-file');
   let config: Config;
 
   // If no config file was provided create an empty one
   if (configFile === '') {
     core.debug('No configuration file was provided');
-    config = await getDefaultConfig();
+    config = await getDefaultConfig(tempDir, toolCacheDir, codeQL);
   } else {
-    config = await loadConfig(configFile);
+    config = await loadConfig(configFile, tempDir, toolCacheDir, codeQL);
   }
 
   // Save the config so we can easily access it again in the future
@@ -711,8 +715,8 @@ async function getRemoteConfig(configFile: string): Promise<UserConfig> {
 /**
  * Get the file path where the parsed config will be stored.
  */
-export function getPathToParsedConfigFile(): string {
-  return path.join(util.getRequiredEnvParam('RUNNER_TEMP'), 'config');
+export function getPathToParsedConfigFile(tempDir: string): string {
+  return path.join(tempDir, 'config');
 }
 
 /**
@@ -720,7 +724,7 @@ export function getPathToParsedConfigFile(): string {
  */
 async function saveConfig(config: Config) {
   const configString = JSON.stringify(config);
-  const configFile = getPathToParsedConfigFile();
+  const configFile = getPathToParsedConfigFile(config.tempDir);
   fs.mkdirSync(path.dirname(configFile), { recursive: true });
   fs.writeFileSync(configFile, configString, 'utf8');
   core.debug('Saved config:');
@@ -735,8 +739,8 @@ async function saveConfig(config: Config) {
  * stored to a known location. On the second and further calls, this will
  * return the contents of the parsed config from the known location.
  */
-export async function getConfig(): Promise<Config> {
-  const configFile = getPathToParsedConfigFile();
+export async function getConfig(tempDir: string): Promise<Config> {
+  const configFile = getPathToParsedConfigFile(tempDir);
   if (!fs.existsSync(configFile)) {
     throw new Error("Config file could not be found at expected location. Has the 'init' action been called?");
   }
diff --git a/src/external-queries.test.ts b/src/external-queries.test.ts
index 9bec00064..87ed7d796 100644
--- a/src/external-queries.test.ts
+++ b/src/external-queries.test.ts
@@ -10,8 +10,10 @@ setupTests(test);
 
 test("checkoutExternalQueries", async t => {
   await util.withTmpDir(async tmpDir => {
-    process.env["RUNNER_TEMP"] = tmpDir;
-    await externalQueries.checkoutExternalRepository("github/codeql-go", "df4c6869212341b601005567381944ed90906b6b");
+    await externalQueries.checkoutExternalRepository(
+      "github/codeql-go",
+      "df4c6869212341b601005567381944ed90906b6b",
+      tmpDir);
 
     // COPYRIGHT file existed in df4c6869212341b601005567381944ed90906b6b but not in the default branch
     t.true(fs.existsSync(path.join(tmpDir, "github", "codeql-go", "COPYRIGHT")));
diff --git a/src/external-queries.ts b/src/external-queries.ts
index f8b7d84fd..2fdcf61e9 100644
--- a/src/external-queries.ts
+++ b/src/external-queries.ts
@@ -3,17 +3,13 @@ import * as exec from '@actions/exec';
 import * as fs from 'fs';
 import * as path from 'path';
 
-import * as util from './util';
-
 /**
  * Check out repository at the given ref, and return the directory of the checkout.
  */
-export async function checkoutExternalRepository(repository: string, ref: string): Promise<string> {
-  const folder = util.getRequiredEnvParam('RUNNER_TEMP');
-
+export async function checkoutExternalRepository(repository: string, ref: string, tempDir: string): Promise<string> {
   core.info('Checking out ' + repository);
 
-  const checkoutLocation = path.join(folder, repository);
+  const checkoutLocation = path.join(tempDir, repository);
   if (!fs.existsSync(checkoutLocation)) {
     const repoURL = 'https://github.com/' + repository + '.git';
     await exec.exec('git', ['clone', repoURL, checkoutLocation]);
diff --git a/src/finalize-db.ts b/src/finalize-db.ts
index ce2b037fe..3b3798855 100644
--- a/src/finalize-db.ts
+++ b/src/finalize-db.ts
@@ -2,8 +2,9 @@ import * as core from '@actions/core';
 import * as fs from 'fs';
 import * as path from 'path';
 
-import { getCodeQL, isScannedLanguage } from './codeql';
+import { getCodeQL } from './codeql';
 import * as configUtils from './config-utils';
+import { isScannedLanguage } from './languages';
 import { getActionsLogger } from './logging';
 import { parseRepositoryNwo } from './repository';
 import * as sharedEnv from './shared-environment';
@@ -58,7 +59,7 @@ async function sendStatusReport(
 }
 
 async function createdDBForScannedLanguages(databaseFolder: string, config: configUtils.Config) {
-  const codeql = getCodeQL();
+  const codeql = getCodeQL(config.codeQLCmd);
   for (const language of config.languages) {
     if (isScannedLanguage(language)) {
       core.startGroup('Extracting ' + language);
@@ -71,7 +72,7 @@ async function createdDBForScannedLanguages(databaseFolder: string, config: conf
 async function finalizeDatabaseCreation(databaseFolder: string, config: configUtils.Config) {
   await createdDBForScannedLanguages(databaseFolder, config);
 
-  const codeql = getCodeQL();
+  const codeql = getCodeQL(config.codeQLCmd);
   for (const language of config.languages) {
     core.startGroup('Finalizing ' + language);
     await codeql.finalizeDatabase(path.join(databaseFolder, language));
@@ -85,7 +86,7 @@ async function runQueries(
   sarifFolder: string,
   config: configUtils.Config): Promise<QueriesStatusReport> {
 
-  const codeql = getCodeQL();
+  const codeql = getCodeQL(config.codeQLCmd);
   for (let language of fs.readdirSync(databaseFolder)) {
     core.startGroup('Analyzing ' + language);
 
@@ -129,12 +130,12 @@ async function run() {
     if (!await util.sendStatusReport(await util.createStatusReportBase('finish', 'starting', startedAt), true)) {
       return;
     }
-    const config = await configUtils.getConfig();
+    const config = await configUtils.getConfig(util.getRequiredEnvParam('RUNNER_TEMP'));
 
     core.exportVariable(sharedEnv.ODASA_TRACER_CONFIGURATION, '');
     delete process.env[sharedEnv.ODASA_TRACER_CONFIGURATION];
 
-    const databaseFolder = util.getCodeQLDatabasesDir();
+    const databaseFolder = util.getCodeQLDatabasesDir(config.tempDir);
 
     const sarifFolder = core.getInput('output');
     fs.mkdirSync(sarifFolder, { recursive: true });
diff --git a/src/fingerprints.test.ts b/src/fingerprints.test.ts
index bd73e2218..9ffd94cc5 100644
--- a/src/fingerprints.test.ts
+++ b/src/fingerprints.test.ts
@@ -4,6 +4,7 @@ import * as fs from 'fs';
 import * as path from 'path';
 
 import * as fingerprints from './fingerprints';
+import { getCLILogger } from './logging';
 import {setupTests} from './testing-utils';
 
 setupTests(test);
@@ -115,7 +116,7 @@ test('hash', (t: ava.Assertions) => {
 function testResolveUriToFile(uri: any, index: any, artifactsURIs: any[]) {
   const location = { "uri": uri, "index": index };
   const artifacts = artifactsURIs.map(uri => ({ "location": { "uri": uri } }));
-  return fingerprints.resolveUriToFile(location, artifacts);
+  return fingerprints.resolveUriToFile(location, artifacts, getCLILogger());
 }
 
 test('resolveUriToFile', t => {
@@ -174,7 +175,7 @@ test('addFingerprints', t => {
   // The URIs in the SARIF files resolve to files in the testdata directory
   process.env['GITHUB_WORKSPACE'] = path.normalize(__dirname + '/../src/testdata');
 
-  t.deepEqual(fingerprints.addFingerprints(input), expected);
+  t.deepEqual(fingerprints.addFingerprints(input, getCLILogger()), expected);
 });
 
 test('missingRegions', t => {
@@ -189,5 +190,5 @@ test('missingRegions', t => {
   // The URIs in the SARIF files resolve to files in the testdata directory
   process.env['GITHUB_WORKSPACE'] = path.normalize(__dirname + '/../src/testdata');
 
-  t.deepEqual(fingerprints.addFingerprints(input), expected);
+  t.deepEqual(fingerprints.addFingerprints(input, getCLILogger()), expected);
 });
diff --git a/src/fingerprints.ts b/src/fingerprints.ts
index 83ab602e1..c296c5464 100644
--- a/src/fingerprints.ts
+++ b/src/fingerprints.ts
@@ -1,7 +1,8 @@
-import * as core from '@actions/core';
 import * as fs from 'fs';
 import Long from 'long';
 
+import { Logger } from './logging';
+
 const tab = '\t'.charCodeAt(0);
 const space = ' '.charCodeAt(0);
 const lf = '\n'.charCodeAt(0);
@@ -124,7 +125,7 @@ export function hash(callback: hashCallback, input: string) {
 
 // Generate a hash callback function that updates the given result in-place
 // when it recieves a hash for the correct line number. Ignores hashes for other lines.
-function locationUpdateCallback(result: any, location: any): hashCallback {
+function locationUpdateCallback(result: any, location: any, logger: Logger): hashCallback {
   let locationStartLine = location.physicalLocation?.region?.startLine;
   if (locationStartLine === undefined) {
     // We expect the region section to be present, but it can be absent if the
@@ -148,7 +149,7 @@ function locationUpdateCallback(result: any, location: any): hashCallback {
     if (!existingFingerprint) {
       result.partialFingerprints.primaryLocationLineHash = hash;
     } else if (existingFingerprint !== hash) {
-      core.warning('Calculated fingerprint of ' + hash +
+      logger.warning('Calculated fingerprint of ' + hash +
         ' for file ' + location.physicalLocation.artifactLocation.uri +
         ' line ' + lineNumber +
         ', but found existing inconsistent fingerprint value ' + existingFingerprint);
@@ -160,14 +161,14 @@ function locationUpdateCallback(result: any, location: any): hashCallback {
 // the source file so we can hash it.
 // If possible returns a absolute file path for the source file,
 // or if not possible then returns undefined.
-export function resolveUriToFile(location: any, artifacts: any[]): string | undefined {
+export function resolveUriToFile(location: any, artifacts: any[], logger: Logger): string | undefined {
   // This may be referencing an artifact
   if (!location.uri && location.index !== undefined) {
     if (typeof location.index !== 'number' ||
       location.index < 0 ||
       location.index >= artifacts.length ||
       typeof artifacts[location.index].location !== 'object') {
-      core.debug(`Ignoring location as URI "${location.index}" is invalid`);
+      logger.debug(`Ignoring location as URI "${location.index}" is invalid`);
       return undefined;
     }
     location = artifacts[location.index].location;
@@ -175,7 +176,7 @@ export function resolveUriToFile(location: any, artifacts: any[]): string | unde
 
   // Get the URI and decode
   if (typeof location.uri !== 'string') {
-    core.debug(`Ignoring location as index "${location.uri}" is invalid`);
+    logger.debug(`Ignoring location as index "${location.uri}" is invalid`);
     return undefined;
   }
   let uri = decodeURIComponent(location.uri);
@@ -186,14 +187,14 @@ export function resolveUriToFile(location: any, artifacts: any[]): string | unde
     uri = uri.substring(fileUriPrefix.length);
   }
   if (uri.indexOf('://') !== -1) {
-    core.debug(`Ignoring location URI "${uri}" as the scheme is not recognised`);
+    logger.debug(`Ignoring location URI "${uri}" as the scheme is not recognised`);
     return undefined;
   }
 
   // Discard any absolute paths that aren't in the src root
   const srcRootPrefix = process.env['GITHUB_WORKSPACE'] + '/';
   if (uri.startsWith('/') && !uri.startsWith(srcRootPrefix)) {
-    core.debug(`Ignoring location URI "${uri}" as it is outside of the src root`);
+    logger.debug(`Ignoring location URI "${uri}" as it is outside of the src root`);
     return undefined;
   }
 
@@ -206,7 +207,7 @@ export function resolveUriToFile(location: any, artifacts: any[]): string | unde
 
   // Check the file exists
   if (!fs.existsSync(uri)) {
-    core.debug(`Unable to compute fingerprint for non-existent file: ${uri}`);
+    logger.debug(`Unable to compute fingerprint for non-existent file: ${uri}`);
     return undefined;
   }
 
@@ -215,7 +216,7 @@ export function resolveUriToFile(location: any, artifacts: any[]): string | unde
 
 // Compute fingerprints for results in the given sarif file
 // and return an updated sarif file contents.
-export function addFingerprints(sarifContents: string): string {
+export function addFingerprints(sarifContents: string, logger: Logger): string {
   let sarif = JSON.parse(sarifContents);
 
   // Gather together results for the same file and construct
@@ -229,18 +230,18 @@ export function addFingerprints(sarifContents: string): string {
       // Check the primary location is defined correctly and is in the src root
       const primaryLocation = (result.locations || [])[0];
       if (!primaryLocation?.physicalLocation?.artifactLocation) {
-        core.debug(`Unable to compute fingerprint for invalid location: ${JSON.stringify(primaryLocation)}`);
+        logger.debug(`Unable to compute fingerprint for invalid location: ${JSON.stringify(primaryLocation)}`);
         continue;
       }
 
-      const filepath = resolveUriToFile(primaryLocation.physicalLocation.artifactLocation, artifacts);
+      const filepath = resolveUriToFile(primaryLocation.physicalLocation.artifactLocation, artifacts, logger);
       if (!filepath) {
         continue;
       }
       if (!callbacksByFile[filepath]) {
         callbacksByFile[filepath] = [];
       }
-      callbacksByFile[filepath].push(locationUpdateCallback(result, primaryLocation));
+      callbacksByFile[filepath].push(locationUpdateCallback(result, primaryLocation, logger));
     }
   }
 
diff --git a/src/languages.test.ts b/src/languages.test.ts
new file mode 100644
index 000000000..93881a907
--- /dev/null
+++ b/src/languages.test.ts
@@ -0,0 +1,47 @@
+import test from 'ava';
+
+import {isScannedLanguage, isTracedLanguage, Language, parseLanguage} from './languages';
+import {setupTests} from './testing-utils';
+
+setupTests(test);
+
+test('parseLangauge', async t => {
+  // Exact matches
+  t.deepEqual(parseLanguage('csharp'), Language.csharp);
+  t.deepEqual(parseLanguage('cpp'), Language.cpp);
+  t.deepEqual(parseLanguage('go'), Language.go);
+  t.deepEqual(parseLanguage('java'), Language.java);
+  t.deepEqual(parseLanguage('javascript'), Language.javascript);
+  t.deepEqual(parseLanguage('python'), Language.python);
+
+  // Aliases
+  t.deepEqual(parseLanguage('c'), Language.cpp);
+  t.deepEqual(parseLanguage('c++'), Language.cpp);
+  t.deepEqual(parseLanguage('c#'), Language.csharp);
+  t.deepEqual(parseLanguage('typescript'), Language.javascript);
+
+  // Not matches
+  t.deepEqual(parseLanguage('foo'), undefined);
+  t.deepEqual(parseLanguage(' '), undefined);
+  t.deepEqual(parseLanguage(''), undefined);
+});
+
+test('isTracedLanguage', async t => {
+  t.true(isTracedLanguage(Language.cpp));
+  t.true(isTracedLanguage(Language.java));
+  t.true(isTracedLanguage(Language.csharp));
+
+  t.false(isTracedLanguage(Language.go));
+  t.false(isTracedLanguage(Language.javascript));
+  t.false(isTracedLanguage(Language.python));
+});
+
+test('isScannedLanguage', async t => {
+  t.false(isScannedLanguage(Language.cpp));
+  t.false(isScannedLanguage(Language.java));
+  t.false(isScannedLanguage(Language.csharp));
+
+  t.true(isScannedLanguage(Language.go));
+  t.true(isScannedLanguage(Language.javascript));
+  t.true(isScannedLanguage(Language.python));
+});
diff --git a/src/languages.ts b/src/languages.ts
new file mode 100644
index 000000000..40c1de7ab
--- /dev/null
+++ b/src/languages.ts
@@ -0,0 +1,44 @@
+// All the languages supported by CodeQL
+export enum Language {
+  csharp = 'csharp',
+  cpp = 'cpp',
+  go = 'go',
+  java = 'java',
+  javascript = 'javascript',
+  python = 'python',
+}
+
+// Additional names for languages
+const LANGUAGE_ALIASES: {[lang: string]: Language} = {
+  'c': Language.cpp,
+  'c++': Language.cpp,
+  'c#': Language.csharp,
+  'typescript': Language.javascript,
+};
+
+// Translate from user input or GitHub's API names for languages to CodeQL's names for languages
+export function parseLanguage(language: string): Language | undefined {
+  // Normalise to lower case
+  language = language.toLowerCase();
+
+  // See if it's an exact match
+  if (language in Language) {
+    return language as Language;
+  }
+
+  // Check language aliases
+  if (language in LANGUAGE_ALIASES) {
+    return LANGUAGE_ALIASES[language];
+  }
+
+  return undefined;
+}
+
+
+export function isTracedLanguage(language: Language): boolean {
+  return ['cpp', 'java', 'csharp'].includes(language);
+}
+
+export function isScannedLanguage(language: Language): boolean {
+  return !isTracedLanguage(language);
+}
diff --git a/src/setup-tracer.ts b/src/setup-tracer.ts
index 1f672b9c2..9e25439da 100644
--- a/src/setup-tracer.ts
+++ b/src/setup-tracer.ts
@@ -4,8 +4,9 @@ import * as fs from 'fs';
 import * as path from 'path';
 
 import * as analysisPaths from './analysis-paths';
-import { CodeQL, isTracedLanguage, setupCodeQL } from './codeql';
+import { CodeQL, setupCodeQL } from './codeql';
 import * as configUtils from './config-utils';
+import { isTracedLanguage } from './languages';
 import * as util from './util';
 
 type TracerConfig = {
@@ -52,7 +53,7 @@ async function tracerConfig(
   return info;
 }
 
-function concatTracerConfigs(configs: TracerConfig[]): TracerConfig {
+function concatTracerConfigs(tracerConfigs: TracerConfig[], config: configUtils.Config): TracerConfig {
   // A tracer config is a map containing additional environment variables and a tracer 'spec' file.
   // A tracer 'spec' file has the following format [log_file, number_of_blocks, blocks_text]
 
@@ -60,7 +61,7 @@ function concatTracerConfigs(configs: TracerConfig[]): TracerConfig {
   const env: { [key: string]: string; } = {};
   let copyExecutables = false;
   let envSize = 0;
-  for (const v of configs) {
+  for (const v of tracerConfigs) {
     for (let e of Object.entries(v.env)) {
       const name = e[0];
       const value = e[1];
@@ -80,7 +81,7 @@ function concatTracerConfigs(configs: TracerConfig[]): TracerConfig {
   }
 
   // Concatenate spec files into a new spec file
-  let languages = Object.keys(configs);
+  let languages = Object.keys(tracerConfigs);
   const cppIndex = languages.indexOf('cpp');
   // Make sure cpp is the last language, if it's present since it must be concatenated last
   if (cppIndex !== -1) {
@@ -92,16 +93,15 @@ function concatTracerConfigs(configs: TracerConfig[]): TracerConfig {
   let totalLines: string[] = [];
   let totalCount = 0;
   for (let lang of languages) {
-    const lines = fs.readFileSync(configs[lang].spec, 'utf8').split(/\r?\n/);
+    const lines = fs.readFileSync(tracerConfigs[lang].spec, 'utf8').split(/\r?\n/);
     const count = parseInt(lines[1], 10);
     totalCount += count;
     totalLines.push(...lines.slice(2));
   }
 
-  const tempFolder = util.getRequiredEnvParam('RUNNER_TEMP');
-  const newLogFilePath = path.resolve(tempFolder, 'compound-build-tracer.log');
-  const spec = path.resolve(tempFolder, 'compound-spec');
-  const compoundTempFolder = path.resolve(tempFolder, 'compound-temp');
+  const newLogFilePath = path.resolve(config.tempDir, 'compound-build-tracer.log');
+  const spec = path.resolve(config.tempDir, 'compound-spec');
+  const compoundTempFolder = path.resolve(config.tempDir, 'compound-temp');
   const newSpecContent = [newLogFilePath, totalCount.toString(10), ...totalLines];
 
   if (copyExecutables) {
@@ -186,7 +186,10 @@ async function run() {
     core.endGroup();
 
     core.startGroup('Load language configuration');
-    config = await configUtils.initConfig();
+    config = await configUtils.initConfig(
+      util.getRequiredEnvParam('RUNNER_TEMP'),
+      util.getRequiredEnvParam('RUNNER_TOOL_CACHE'),
+      codeql);
     analysisPaths.includeAndExcludeAnalysisPaths(config);
     core.endGroup();
 
@@ -212,7 +215,7 @@ async function run() {
     const codeqlRam = process.env['CODEQL_RAM'] || '6500';
     core.exportVariable('CODEQL_RAM', codeqlRam);
 
-    const databaseFolder = util.getCodeQLDatabasesDir();
+    const databaseFolder = util.getCodeQLDatabasesDir(config.tempDir);
     fs.mkdirSync(databaseFolder, { recursive: true });
 
     let tracedLanguageConfigs: TracerConfig[] = [];
@@ -229,27 +232,28 @@ async function run() {
       }
     }
     if (tracedLanguageConfigs.length > 0) {
-      const mainTracerConfig = concatTracerConfigs(tracedLanguageConfigs);
+      const mainTracerConfig = concatTracerConfigs(tracedLanguageConfigs, config);
       if (mainTracerConfig.spec) {
         for (let entry of Object.entries(mainTracerConfig.env)) {
           core.exportVariable(entry[0], entry[1]);
         }
 
         core.exportVariable('ODASA_TRACER_CONFIGURATION', mainTracerConfig.spec);
+        const codeQLDir = path.dirname(codeql.getPath());
         if (process.platform === 'darwin') {
           core.exportVariable(
             'DYLD_INSERT_LIBRARIES',
-            path.join(codeql.getDir(), 'tools', 'osx64', 'libtrace.dylib'));
+            path.join(codeQLDir, 'tools', 'osx64', 'libtrace.dylib'));
         } else if (process.platform === 'win32') {
           await exec.exec(
             'powershell',
             [
               path.resolve(__dirname, '..', 'src', 'inject-tracer.ps1'),
-              path.resolve(codeql.getDir(), 'tools', 'win64', 'tracer.exe'),
+              path.resolve(codeQLDir, 'tools', 'win64', 'tracer.exe'),
             ],
             { env: { 'ODASA_TRACER_CONFIGURATION': mainTracerConfig.spec } });
         } else {
-          core.exportVariable('LD_PRELOAD', path.join(codeql.getDir(), 'tools', 'linux64', '${LIB}trace.so'));
+          core.exportVariable('LD_PRELOAD', path.join(codeQLDir, 'tools', 'linux64', '${LIB}trace.so'));
         }
       }
     }
diff --git a/src/upload-lib.ts b/src/upload-lib.ts
index 94a762fad..2455b934d 100644
--- a/src/upload-lib.ts
+++ b/src/upload-lib.ts
@@ -235,7 +235,7 @@ async function uploadFiles(
   }
 
   let sarifPayload = combineSarifFiles(sarifFiles);
-  sarifPayload = fingerprints.addFingerprints(sarifPayload);
+  sarifPayload = fingerprints.addFingerprints(sarifPayload, logger);
 
   const zipped_sarif = zlib.gzipSync(sarifPayload).toString('base64');
   let checkoutURI = fileUrl(checkoutPath);
diff --git a/src/util.test.ts b/src/util.test.ts
index 844c749a4..e31c96557 100644
--- a/src/util.test.ts
+++ b/src/util.test.ts
@@ -116,3 +116,37 @@ test('prepareEnvironment() when a local run', t => {
 
   process.env.CODEQL_LOCAL_RUN = origLocalRun;
 });
+
+test('getExtraOptionsEnvParam() succeeds on valid JSON with invalid options (for now)', t => {
+  const origExtraOptions = process.env.CODEQL_ACTION_EXTRA_OPTIONS;
+
+  const options = {foo: 42};
+
+  process.env.CODEQL_ACTION_EXTRA_OPTIONS = JSON.stringify(options);
+
+  t.deepEqual(util.getExtraOptionsEnvParam(), <any>options);
+
+  process.env.CODEQL_ACTION_EXTRA_OPTIONS = origExtraOptions;
+});
+
+
+test('getExtraOptionsEnvParam() succeeds on valid options', t => {
+  const origExtraOptions = process.env.CODEQL_ACTION_EXTRA_OPTIONS;
+
+  const options = { database: { init: ["--debug"] } };
+  process.env.CODEQL_ACTION_EXTRA_OPTIONS =
+    JSON.stringify(options);
+
+  t.deepEqual(util.getExtraOptionsEnvParam(), options);
+
+  process.env.CODEQL_ACTION_EXTRA_OPTIONS = origExtraOptions;
+});
+
+test('getExtraOptionsEnvParam() fails on invalid JSON', t => {
+  const origExtraOptions = process.env.CODEQL_ACTION_EXTRA_OPTIONS;
+
+  process.env.CODEQL_ACTION_EXTRA_OPTIONS = "{{invalid-json}}";
+  t.throws(util.getExtraOptionsEnvParam);
+
+  process.env.CODEQL_ACTION_EXTRA_OPTIONS = origExtraOptions;
+});
diff --git a/src/util.ts b/src/util.ts
index e3ab9d831..c4bf9c93e 100644
--- a/src/util.ts
+++ b/src/util.ts
@@ -39,6 +39,26 @@ export function getRequiredEnvParam(paramName: string): string {
   return value;
 }
 
+/**
+ * Get the extra options for the codeql commands.
+ */
+export function getExtraOptionsEnvParam(): object {
+  const varName = 'CODEQL_ACTION_EXTRA_OPTIONS';
+  const raw = process.env[varName];
+  if (raw === undefined || raw.length === 0) {
+    return {};
+  }
+  try {
+    return JSON.parse(raw);
+  } catch (e) {
+    throw new Error(
+      varName +
+        ' environment variable is set, but does not contain valid JSON: ' +
+        e.message
+    );
+  }
+}
+
 export function isLocalRun(): boolean {
   return !!process.env.CODEQL_LOCAL_RUN
     && process.env.CODEQL_LOCAL_RUN !== 'false'
@@ -375,27 +395,34 @@ export function getMemoryFlag(): string {
 }
 
 /**
- * Get the codeql `--threads` value specified for the `threads` input. The value
- * defaults to 1. The value will be capped to the number of available CPUs.
+ * Get the codeql `--threads` value specified for the `threads` input.
+ * If not value was specified, all available threads will be used.
+ *
+ * The value will be capped to the number of available CPUs.
  *
  * @returns string
  */
 export function getThreadsFlag(): string {
-  let numThreads = 1;
+  let numThreads: number;
   const numThreadsString = core.getInput("threads");
+  const maxThreads = os.cpus().length;
   if (numThreadsString) {
     numThreads = Number(numThreadsString);
     if (Number.isNaN(numThreads)) {
       throw new Error(`Invalid threads setting "${numThreadsString}", specified.`);
     }
-    const maxThreads = os.cpus().length;
     if (numThreads > maxThreads) {
+      core.info(`Clamping desired number of threads (${numThreads}) to max available (${maxThreads}).`);
       numThreads = maxThreads;
     }
     const minThreads = -maxThreads;
     if (numThreads < minThreads) {
+      core.info(`Clamping desired number of free threads (${numThreads}) to max available (${minThreads}).`);
       numThreads = minThreads;
     }
+  } else {
+    // Default to using all threads
+    numThreads = maxThreads;
   }
   return `--threads=${numThreads}`;
 }
@@ -403,6 +430,6 @@ export function getThreadsFlag(): string {
 /**
  * Get the directory where CodeQL databases should be placed.
  */
-export function getCodeQLDatabasesDir() {
-  return path.resolve(getRequiredEnvParam('RUNNER_TEMP'), 'codeql_databases');
+export function getCodeQLDatabasesDir(tempDir: string) {
+  return path.resolve(tempDir, 'codeql_databases');
 }