diff --git a/lib/analysis-paths.js b/lib/analysis-paths.js
index 87e625ceb3..6099f9895a 100644
--- a/lib/analysis-paths.js
+++ b/lib/analysis-paths.js
@@ -1,5 +1,13 @@
 "use strict";
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (Object.hasOwnProperty.call(mod, k)) result[k] = mod[k];
+    result["default"] = mod;
+    return result;
+};
 Object.defineProperty(exports, "__esModule", { value: true });
+const path = __importStar(require("path"));
 function isInterpretedLanguage(language) {
     return language === "javascript" || language === "python";
 }
@@ -24,7 +32,7 @@ function printPathFiltersWarning(config, logger) {
     }
 }
 exports.printPathFiltersWarning = printPathFiltersWarning;
-function includeAndExcludeAnalysisPaths(config) {
+function includeAndExcludeAnalysisPaths(config, logger) {
     // The 'LGTM_INDEX_INCLUDE' and 'LGTM_INDEX_EXCLUDE' environment variables
     // control which files/directories are traversed when scanning.
     // This allows including files that otherwise would not be scanned, or
@@ -35,8 +43,15 @@ function includeAndExcludeAnalysisPaths(config) {
     if (config.paths.length !== 0) {
         process.env["LGTM_INDEX_INCLUDE"] = buildIncludeExcludeEnvVar(config.paths);
     }
-    if (config.pathsIgnore.length !== 0) {
-        process.env["LGTM_INDEX_EXCLUDE"] = buildIncludeExcludeEnvVar(config.pathsIgnore);
+    // Always ignore the temporary directory. This is required if the runner has been downloaded to the checkout directory of the repository being analyzed.
+    const tempRelativeToWorking = path.relative(process.cwd(), config.tempDir);
+    let pathsIgnore = config.pathsIgnore;
+    if (!tempRelativeToWorking.startsWith("..")) {
+        logger.warning("Storing the CodeQL Runner in the directory being analyzed is not recommended.");
+        pathsIgnore = pathsIgnore.concat(config.tempDir);
+    }
+    if (pathsIgnore.length !== 0) {
+        process.env["LGTM_INDEX_EXCLUDE"] = buildIncludeExcludeEnvVar(pathsIgnore);
     }
     // The 'LGTM_INDEX_FILTERS' environment variable controls which files are
     // extracted or ignored. It does not control which directories are traversed.
diff --git a/lib/analysis-paths.js.map b/lib/analysis-paths.js.map
index f846d4c2e2..d934bf5ba1 100644
--- a/lib/analysis-paths.js.map
+++ b/lib/analysis-paths.js.map
@@ -1 +1 @@
-{"version":3,"file":"analysis-paths.js","sourceRoot":"","sources":["../src/analysis-paths.ts"],"names":[],"mappings":";;AAGA,SAAS,qBAAqB,CAAC,QAAQ;IACrC,OAAO,QAAQ,KAAK,YAAY,IAAI,QAAQ,KAAK,QAAQ,CAAC;AAC5D,CAAC;AAED,6FAA6F;AAChF,QAAA,+BAA+B,GAAG,cAAc,CAAC;AAE9D,uFAAuF;AACvF,SAAS,yBAAyB,CAAC,KAAe;IAChD,iCAAiC;IACjC,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IAEnD,uDAAuD;IACvD,IAAI,OAAO,CAAC,QAAQ,KAAK,OAAO,EAAE;QAChC,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,uCAA+B,CAAC,CAAC,CAAC;KACvE;IAED,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC1B,CAAC;AAED,SAAgB,uBAAuB,CACrC,MAA0B,EAC1B,MAAc;IAEd,oEAAoE;IACpE,sEAAsE;IACtE,IACE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,MAAM,CAAC,WAAW,CAAC,MAAM,KAAK,CAAC,CAAC;QAC9D,CAAC,MAAM,CAAC,SAAS,CAAC,KAAK,CAAC,qBAAqB,CAAC,EAC9C;QACA,MAAM,CAAC,OAAO,CACZ,4FAA4F,CAC7F,CAAC;KACH;AACH,CAAC;AAdD,0DAcC;AAED,SAAgB,8BAA8B,CAAC,MAA0B;IACvE,0EAA0E;IAC1E,+DAA+D;IAC/D,sEAAsE;IACtE,qDAAqD;IACrD,gFAAgF;IAChF,sEAAsE;IACtE,sDAAsD;IACtD,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE;QAC7B,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,GAAG,yBAAyB,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;KAC7E;IACD,IAAI,MAAM,CAAC,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE;QACnC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,GAAG,yBAAyB,CAC3D,MAAM,CAAC,WAAW,CACnB,CAAC;KACH;IAED,yEAAyE;IACzE,6EAA6E;IAC7E,wDAAwD;IACxD,MAAM,OAAO,GAAa,EAAE,CAAC;IAC7B,OAAO,CAAC,IAAI,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC;IACzD,OAAO,CAAC,IAAI,CAAC,GAAG,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC;IAC/D,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE;QACxB,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;KACxD;AACH,CAAC;AA1BD,wEA0BC"}
\ No newline at end of file
+{"version":3,"file":"analysis-paths.js","sourceRoot":"","sources":["../src/analysis-paths.ts"],"names":[],"mappings":";;;;;;;;;AAAA,2CAA6B;AAI7B,SAAS,qBAAqB,CAAC,QAAQ;IACrC,OAAO,QAAQ,KAAK,YAAY,IAAI,QAAQ,KAAK,QAAQ,CAAC;AAC5D,CAAC;AAED,6FAA6F;AAChF,QAAA,+BAA+B,GAAG,cAAc,CAAC;AAE9D,uFAAuF;AACvF,SAAS,yBAAyB,CAAC,KAAe;IAChD,iCAAiC;IACjC,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IAEnD,uDAAuD;IACvD,IAAI,OAAO,CAAC,QAAQ,KAAK,OAAO,EAAE;QAChC,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,uCAA+B,CAAC,CAAC,CAAC;KACvE;IAED,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC1B,CAAC;AAED,SAAgB,uBAAuB,CACrC,MAA0B,EAC1B,MAAc;IAEd,oEAAoE;IACpE,sEAAsE;IACtE,IACE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,MAAM,CAAC,WAAW,CAAC,MAAM,KAAK,CAAC,CAAC;QAC9D,CAAC,MAAM,CAAC,SAAS,CAAC,KAAK,CAAC,qBAAqB,CAAC,EAC9C;QACA,MAAM,CAAC,OAAO,CACZ,4FAA4F,CAC7F,CAAC;KACH;AACH,CAAC;AAdD,0DAcC;AAED,SAAgB,8BAA8B,CAAC,MAA0B,EAAE,MAAc;IACvF,0EAA0E;IAC1E,+DAA+D;IAC/D,sEAAsE;IACtE,qDAAqD;IACrD,gFAAgF;IAChF,sEAAsE;IACtE,sDAAsD;IACtD,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE;QAC7B,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,GAAG,yBAAyB,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;KAC7E;IACD,wJAAwJ;IACxJ,MAAM,qBAAqB,GAAG,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC;IAC3E,IAAI,WAAW,GAAG,MAAM,CAAC,WAAW,CAAC;IACrC,IAAI,CAAC,qBAAqB,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE;QAC3C,MAAM,CAAC,OAAO,CAAC,+EAA+E,CAAC,CAAC;QAChG,WAAW,GAAG,WAAW,CAAC,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;KAClD;IACD,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE;QAC5B,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,GAAG,yBAAyB,CAAC,WAAW,CAAC,CAAC;KAC5E;IAED,yEAAyE;IACzE,6EAA6E;IAC7E,wDAAwD;IACxD,MAAM,OAAO,GAAa,EAAE,CAAC;IAC7B,OAAO,CAAC,IAAI,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC;IACzD,OAAO,CAAC,IAAI,CAAC,GAAG,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC;IAC/D,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE;QACxB,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,GAAG,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;KACxD;AACH,CAAC;AA/BD,wEA+BC"}
\ No newline at end of file
diff --git a/lib/analysis-paths.test.js b/lib/analysis-paths.test.js
index 1c52637380..3009d3fa01 100644
--- a/lib/analysis-paths.test.js
+++ b/lib/analysis-paths.test.js
@@ -11,7 +11,9 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const ava_1 = __importDefault(require("ava"));
+const path = __importStar(require("path"));
 const analysisPaths = __importStar(require("./analysis-paths"));
+const logging_1 = require("./logging");
 const testing_utils_1 = require("./testing-utils");
 const util = __importStar(require("./util"));
 testing_utils_1.setupTests(ava_1.default);
@@ -27,7 +29,7 @@ ava_1.default("emptyPaths", async (t) => {
             toolCacheDir: tmpDir,
             codeQLCmd: "",
         };
-        analysisPaths.includeAndExcludeAnalysisPaths(config);
+        analysisPaths.includeAndExcludeAnalysisPaths(config, logging_1.getRunnerLogger(true));
         t.is(process.env["LGTM_INDEX_INCLUDE"], undefined);
         t.is(process.env["LGTM_INDEX_EXCLUDE"], undefined);
         t.is(process.env["LGTM_INDEX_FILTERS"], undefined);
@@ -45,10 +47,29 @@ ava_1.default("nonEmptyPaths", async (t) => {
             toolCacheDir: tmpDir,
             codeQLCmd: "",
         };
-        analysisPaths.includeAndExcludeAnalysisPaths(config);
+        analysisPaths.includeAndExcludeAnalysisPaths(config, logging_1.getRunnerLogger(true));
         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/**");
     });
 });
+ava_1.default("exclude temp dir", async (t) => {
+    return await util.withTmpDir(async (toolCacheDir) => {
+        const tempDir = path.join(process.cwd(), "codeql-runner-temp");
+        const config = {
+            languages: [],
+            queries: {},
+            pathsIgnore: [],
+            paths: [],
+            originalUserInput: {},
+            tempDir: tempDir,
+            toolCacheDir: toolCacheDir,
+            codeQLCmd: "",
+        };
+        analysisPaths.includeAndExcludeAnalysisPaths(config, logging_1.getRunnerLogger(true));
+        t.is(process.env["LGTM_INDEX_INCLUDE"], undefined);
+        t.is(process.env["LGTM_INDEX_EXCLUDE"], tempDir);
+        t.is(process.env["LGTM_INDEX_FILTERS"], undefined);
+    });
+});
 //# 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 5feb620b95..6fca4ca08e 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,mDAA6C;AAC7C,6CAA+B;AAE/B,0BAAU,CAAC,aAAI,CAAC,CAAC;AAEjB,aAAI,CAAC,YAAY,EAAE,KAAK,EAAE,CAAC,EAAE,EAAE;IAC7B,OAAO,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;QAC5C,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,EAAE,CAAC,EAAE,EAAE;IAChC,OAAO,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;QAC5C,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,CACF,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EACjC,gGAAgG,CACjG,CAAC;IACJ,CAAC,CAAC,CAAC;AACL,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;AACvB,2CAA6B;AAE7B,gEAAkD;AAClD,uCAA4C;AAC5C,mDAA6C;AAC7C,6CAA+B;AAE/B,0BAAU,CAAC,aAAI,CAAC,CAAC;AAEjB,aAAI,CAAC,YAAY,EAAE,KAAK,EAAE,CAAC,EAAE,EAAE;IAC7B,OAAO,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;QAC5C,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,EAAE,yBAAe,CAAC,IAAI,CAAC,CAAC,CAAC;QAC5E,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,EAAE,CAAC,EAAE,EAAE;IAChC,OAAO,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;QAC5C,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,EAAE,yBAAe,CAAC,IAAI,CAAC,CAAC,CAAC;QAC5E,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,CACF,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EACjC,gGAAgG,CACjG,CAAC;IACJ,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC;AAEH,aAAI,CAAC,kBAAkB,EAAE,KAAK,EAAE,CAAC,EAAE,EAAE;IACnC,OAAO,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAE,YAAY,EAAE,EAAE;QAClD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,oBAAoB,CAAC,CAAC;QAC/D,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,OAAO;YAChB,YAAY,EAAE,YAAY;YAC1B,SAAS,EAAE,EAAE;SACd,CAAC;QACF,aAAa,CAAC,8BAA8B,CAAC,MAAM,EAAE,yBAAe,CAAC,IAAI,CAAC,CAAC,CAAC;QAC5E,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,OAAO,CAAC,CAAC;QACjD,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,EAAE,SAAS,CAAC,CAAC;IACrD,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}
\ No newline at end of file
diff --git a/lib/analyze.js b/lib/analyze.js
index a8b186514e..1f4d3cd5e5 100644
--- a/lib/analyze.js
+++ b/lib/analyze.js
@@ -18,7 +18,7 @@ const util = __importStar(require("./util"));
 async function createdDBForScannedLanguages(config, logger) {
     // Insert the LGTM_INDEX_X env vars at this point so they are set when
     // we extract any scanned languages.
-    analysisPaths.includeAndExcludeAnalysisPaths(config);
+    analysisPaths.includeAndExcludeAnalysisPaths(config, logger);
     const codeql = codeql_1.getCodeQL(config.codeQLCmd);
     for (const language of config.languages) {
         if (languages_1.isScannedLanguage(language)) {
diff --git a/lib/analyze.js.map b/lib/analyze.js.map
index 6dbfba9ce4..28c17462d6 100644
--- a/lib/analyze.js.map
+++ b/lib/analyze.js.map
@@ -1 +1 @@
-{"version":3,"file":"analyze.js","sourceRoot":"","sources":["../src/analyze.ts"],"names":[],"mappings":";;;;;;;;;AAAA,uCAAyB;AACzB,2CAA6B;AAE7B,gEAAkD;AAClD,qCAAqC;AAErC,2CAAgD;AAGhD,gEAAkD;AAClD,yDAA2C;AAC3C,6CAA+B;AAmC/B,KAAK,UAAU,4BAA4B,CACzC,MAA0B,EAC1B,MAAc;IAEd,sEAAsE;IACtE,oCAAoC;IACpC,aAAa,CAAC,8BAA8B,CAAC,MAAM,CAAC,CAAC;IAErD,MAAM,MAAM,GAAG,kBAAS,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;IAC3C,KAAK,MAAM,QAAQ,IAAI,MAAM,CAAC,SAAS,EAAE;QACvC,IAAI,6BAAiB,CAAC,QAAQ,CAAC,EAAE;YAC/B,MAAM,CAAC,UAAU,CAAC,cAAc,QAAQ,EAAE,CAAC,CAAC;YAC5C,MAAM,MAAM,CAAC,sBAAsB,CACjC,IAAI,CAAC,qBAAqB,CAAC,MAAM,CAAC,OAAO,EAAE,QAAQ,CAAC,EACpD,QAAQ,CACT,CAAC;YACF,MAAM,CAAC,QAAQ,EAAE,CAAC;SACnB;KACF;AACH,CAAC;AAED,KAAK,UAAU,wBAAwB,CACrC,MAA0B,EAC1B,MAAc;IAEd,MAAM,4BAA4B,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAEnD,MAAM,MAAM,GAAG,kBAAS,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;IAC3C,KAAK,MAAM,QAAQ,IAAI,MAAM,CAAC,SAAS,EAAE;QACvC,MAAM,CAAC,UAAU,CAAC,cAAc,QAAQ,EAAE,CAAC,CAAC;QAC5C,MAAM,MAAM,CAAC,gBAAgB,CAC3B,IAAI,CAAC,qBAAqB,CAAC,MAAM,CAAC,OAAO,EAAE,QAAQ,CAAC,CACrD,CAAC;QACF,MAAM,CAAC,QAAQ,EAAE,CAAC;KACnB;AACH,CAAC;AAED,2DAA2D;AACpD,KAAK,UAAU,UAAU,CAC9B,WAAmB,EACnB,UAAkB,EAClB,eAAuB,EACvB,WAAmB,EACnB,MAA0B,EAC1B,MAAc;IAEd,MAAM,YAAY,GAAwB,EAAE,CAAC;IAE7C,KAAK,MAAM,QAAQ,IAAI,MAAM,CAAC,SAAS,EAAE;QACvC,MAAM,CAAC,UAAU,CAAC,aAAa,QAAQ,EAAE,CAAC,CAAC;QAE3C,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;QACzC,IAAI,OAAO,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,IAAI,OAAO,CAAC,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;YAC/D,MAAM,IAAI,KAAK,CACb,qBAAqB,QAAQ,gDAAgD,CAC9E,CAAC;SACH;QAED,IAAI;YACF,KAAK,MAAM,IAAI,IAAI,CAAC,SAAS,EAAE,QAAQ,CAAC,EAAE;gBACxC,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE;oBAC5B,MAAM,SAAS,GAAG,IAAI,IAAI,EAAE,CAAC,OAAO,EAAE,CAAC;oBAEvC,MAAM,YAAY,GAAG,IAAI,CAAC,qBAAqB,CAC7C,MAAM,CAAC,OAAO,EACd,QAAQ,CACT,CAAC;oBACF,uEAAuE;oBACvE,2EAA2E;oBAC3E,MAAM,cAAc,GAAG,GAAG,YAAY,YAAY,IAAI,MAAM,CAAC;oBAC7D,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC;yBACrC,GAAG,CAAC,CAAC,CAAS,EAAE,EAAE,CAAC,YAAY,CAAC,EAAE,CAAC;yBACnC,IAAI,CAAC,IAAI,CAAC,CAAC;oBACd,EAAE,CAAC,aAAa,CAAC,cAAc,EAAE,kBAAkB,CAAC,CAAC;oBACrD,MAAM,CAAC,KAAK,CACV,wBAAwB,QAAQ,QAAQ,kBAAkB,EAAE,CAC7D,CAAC;oBAEF,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,GAAG,QAAQ,IAAI,IAAI,QAAQ,CAAC,CAAC;oBAEtE,MAAM,MAAM,GAAG,kBAAS,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;oBAC3C,MAAM,MAAM,CAAC,eAAe,CAC1B,YAAY,EACZ,SAAS,EACT,cAAc,EACd,UAAU,EACV,eAAe,EACf,WAAW,CACZ,CAAC;oBAEF,MAAM,CAAC,KAAK,CACV,8BAA8B,QAAQ,gBAAgB,SAAS,GAAG,CACnE,CAAC;oBACF,MAAM,CAAC,QAAQ,EAAE,CAAC;oBAElB,yBAAyB;oBACzB,MAAM,OAAO,GAAG,IAAI,IAAI,EAAE,CAAC,OAAO,EAAE,CAAC;oBACrC,YAAY,CAAC,WAAW,IAAI,YAAY,QAAQ,cAAc,CAAC;wBAC7D,OAAO,GAAG,SAAS,CAAC;iBACvB;aACF;SACF;QAAC,OAAO,CAAC,EAAE;YACV,MAAM,CAAC,KAAK,CAAC,8BAA8B,QAAQ,KAAK,CAAC,EAAE,CAAC,CAAC;YAC7D,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YACf,YAAY,CAAC,wBAAwB,GAAG,QAAQ,CAAC;YACjD,OAAO,YAAY,CAAC;SACrB;KACF;IAED,OAAO,YAAY,CAAC;AACtB,CAAC;AAxED,gCAwEC;AAEM,KAAK,UAAU,UAAU,CAC9B,aAA4B,EAC5B,SAAiB,EACjB,GAAW,EACX,WAA+B,EAC/B,YAAgC,EAChC,aAAiC,EACjC,YAAoB,EACpB,WAA+B,EAC/B,UAAkB,EAClB,SAAiB,EACjB,QAAiB,EACjB,IAAe,EACf,SAAiB,EACjB,UAAkB,EAClB,eAAuB,EACvB,WAAmB,EACnB,MAA0B,EAC1B,MAAc;IAEd,8DAA8D;IAC9D,OAAO,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,0BAA0B,CAAC,CAAC;IAEzD,EAAE,CAAC,SAAS,CAAC,SAAS,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAE7C,MAAM,CAAC,IAAI,CAAC,8BAA8B,CAAC,CAAC;IAC5C,MAAM,wBAAwB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAE/C,MAAM,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC;IAClC,MAAM,YAAY,GAAG,MAAM,UAAU,CACnC,SAAS,EACT,UAAU,EACV,eAAe,EACf,WAAW,EACX,MAAM,EACN,MAAM,CACP,CAAC;IAEF,IAAI,CAAC,QAAQ,EAAE;QACb,MAAM,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC;QACrC,OAAO,EAAE,GAAG,YAAY,EAAE,CAAC;KAC5B;IAED,MAAM,WAAW,GAAG,MAAM,UAAU,CAAC,MAAM,CACzC,SAAS,EACT,aAAa,EACb,SAAS,EACT,GAAG,EACH,WAAW,EACX,YAAY,EACZ,aAAa,EACb,YAAY,EACZ,WAAW,EACX,UAAU,EACV,SAAS,EACT,IAAI,EACJ,MAAM,CACP,CAAC;IAEF,OAAO,EAAE,GAAG,YAAY,EAAE,GAAG,WAAW,EAAE,CAAC;AAC7C,CAAC;AA5DD,gCA4DC"}
\ No newline at end of file
+{"version":3,"file":"analyze.js","sourceRoot":"","sources":["../src/analyze.ts"],"names":[],"mappings":";;;;;;;;;AAAA,uCAAyB;AACzB,2CAA6B;AAE7B,gEAAkD;AAClD,qCAAqC;AAErC,2CAAgD;AAGhD,gEAAkD;AAClD,yDAA2C;AAC3C,6CAA+B;AAmC/B,KAAK,UAAU,4BAA4B,CACzC,MAA0B,EAC1B,MAAc;IAEd,sEAAsE;IACtE,oCAAoC;IACpC,aAAa,CAAC,8BAA8B,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAE7D,MAAM,MAAM,GAAG,kBAAS,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;IAC3C,KAAK,MAAM,QAAQ,IAAI,MAAM,CAAC,SAAS,EAAE;QACvC,IAAI,6BAAiB,CAAC,QAAQ,CAAC,EAAE;YAC/B,MAAM,CAAC,UAAU,CAAC,cAAc,QAAQ,EAAE,CAAC,CAAC;YAC5C,MAAM,MAAM,CAAC,sBAAsB,CACjC,IAAI,CAAC,qBAAqB,CAAC,MAAM,CAAC,OAAO,EAAE,QAAQ,CAAC,EACpD,QAAQ,CACT,CAAC;YACF,MAAM,CAAC,QAAQ,EAAE,CAAC;SACnB;KACF;AACH,CAAC;AAED,KAAK,UAAU,wBAAwB,CACrC,MAA0B,EAC1B,MAAc;IAEd,MAAM,4BAA4B,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAEnD,MAAM,MAAM,GAAG,kBAAS,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;IAC3C,KAAK,MAAM,QAAQ,IAAI,MAAM,CAAC,SAAS,EAAE;QACvC,MAAM,CAAC,UAAU,CAAC,cAAc,QAAQ,EAAE,CAAC,CAAC;QAC5C,MAAM,MAAM,CAAC,gBAAgB,CAC3B,IAAI,CAAC,qBAAqB,CAAC,MAAM,CAAC,OAAO,EAAE,QAAQ,CAAC,CACrD,CAAC;QACF,MAAM,CAAC,QAAQ,EAAE,CAAC;KACnB;AACH,CAAC;AAED,2DAA2D;AACpD,KAAK,UAAU,UAAU,CAC9B,WAAmB,EACnB,UAAkB,EAClB,eAAuB,EACvB,WAAmB,EACnB,MAA0B,EAC1B,MAAc;IAEd,MAAM,YAAY,GAAwB,EAAE,CAAC;IAE7C,KAAK,MAAM,QAAQ,IAAI,MAAM,CAAC,SAAS,EAAE;QACvC,MAAM,CAAC,UAAU,CAAC,aAAa,QAAQ,EAAE,CAAC,CAAC;QAE3C,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;QACzC,IAAI,OAAO,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,IAAI,OAAO,CAAC,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;YAC/D,MAAM,IAAI,KAAK,CACb,qBAAqB,QAAQ,gDAAgD,CAC9E,CAAC;SACH;QAED,IAAI;YACF,KAAK,MAAM,IAAI,IAAI,CAAC,SAAS,EAAE,QAAQ,CAAC,EAAE;gBACxC,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE;oBAC5B,MAAM,SAAS,GAAG,IAAI,IAAI,EAAE,CAAC,OAAO,EAAE,CAAC;oBAEvC,MAAM,YAAY,GAAG,IAAI,CAAC,qBAAqB,CAC7C,MAAM,CAAC,OAAO,EACd,QAAQ,CACT,CAAC;oBACF,uEAAuE;oBACvE,2EAA2E;oBAC3E,MAAM,cAAc,GAAG,GAAG,YAAY,YAAY,IAAI,MAAM,CAAC;oBAC7D,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CAAC;yBACrC,GAAG,CAAC,CAAC,CAAS,EAAE,EAAE,CAAC,YAAY,CAAC,EAAE,CAAC;yBACnC,IAAI,CAAC,IAAI,CAAC,CAAC;oBACd,EAAE,CAAC,aAAa,CAAC,cAAc,EAAE,kBAAkB,CAAC,CAAC;oBACrD,MAAM,CAAC,KAAK,CACV,wBAAwB,QAAQ,QAAQ,kBAAkB,EAAE,CAC7D,CAAC;oBAEF,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,GAAG,QAAQ,IAAI,IAAI,QAAQ,CAAC,CAAC;oBAEtE,MAAM,MAAM,GAAG,kBAAS,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;oBAC3C,MAAM,MAAM,CAAC,eAAe,CAC1B,YAAY,EACZ,SAAS,EACT,cAAc,EACd,UAAU,EACV,eAAe,EACf,WAAW,CACZ,CAAC;oBAEF,MAAM,CAAC,KAAK,CACV,8BAA8B,QAAQ,gBAAgB,SAAS,GAAG,CACnE,CAAC;oBACF,MAAM,CAAC,QAAQ,EAAE,CAAC;oBAElB,yBAAyB;oBACzB,MAAM,OAAO,GAAG,IAAI,IAAI,EAAE,CAAC,OAAO,EAAE,CAAC;oBACrC,YAAY,CAAC,WAAW,IAAI,YAAY,QAAQ,cAAc,CAAC;wBAC7D,OAAO,GAAG,SAAS,CAAC;iBACvB;aACF;SACF;QAAC,OAAO,CAAC,EAAE;YACV,MAAM,CAAC,KAAK,CAAC,8BAA8B,QAAQ,KAAK,CAAC,EAAE,CAAC,CAAC;YAC7D,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YACf,YAAY,CAAC,wBAAwB,GAAG,QAAQ,CAAC;YACjD,OAAO,YAAY,CAAC;SACrB;KACF;IAED,OAAO,YAAY,CAAC;AACtB,CAAC;AAxED,gCAwEC;AAEM,KAAK,UAAU,UAAU,CAC9B,aAA4B,EAC5B,SAAiB,EACjB,GAAW,EACX,WAA+B,EAC/B,YAAgC,EAChC,aAAiC,EACjC,YAAoB,EACpB,WAA+B,EAC/B,UAAkB,EAClB,SAAiB,EACjB,QAAiB,EACjB,IAAe,EACf,SAAiB,EACjB,UAAkB,EAClB,eAAuB,EACvB,WAAmB,EACnB,MAA0B,EAC1B,MAAc;IAEd,8DAA8D;IAC9D,OAAO,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,0BAA0B,CAAC,CAAC;IAEzD,EAAE,CAAC,SAAS,CAAC,SAAS,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAE7C,MAAM,CAAC,IAAI,CAAC,8BAA8B,CAAC,CAAC;IAC5C,MAAM,wBAAwB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAE/C,MAAM,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC;IAClC,MAAM,YAAY,GAAG,MAAM,UAAU,CACnC,SAAS,EACT,UAAU,EACV,eAAe,EACf,WAAW,EACX,MAAM,EACN,MAAM,CACP,CAAC;IAEF,IAAI,CAAC,QAAQ,EAAE;QACb,MAAM,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC;QACrC,OAAO,EAAE,GAAG,YAAY,EAAE,CAAC;KAC5B;IAED,MAAM,WAAW,GAAG,MAAM,UAAU,CAAC,MAAM,CACzC,SAAS,EACT,aAAa,EACb,SAAS,EACT,GAAG,EACH,WAAW,EACX,YAAY,EACZ,aAAa,EACb,YAAY,EACZ,WAAW,EACX,UAAU,EACV,SAAS,EACT,IAAI,EACJ,MAAM,CACP,CAAC;IAEF,OAAO,EAAE,GAAG,YAAY,EAAE,GAAG,WAAW,EAAE,CAAC;AAC7C,CAAC;AA5DD,gCA4DC"}
\ No newline at end of file
diff --git a/src/analysis-paths.test.ts b/src/analysis-paths.test.ts
index c84c343d86..2b015852d5 100644
--- a/src/analysis-paths.test.ts
+++ b/src/analysis-paths.test.ts
@@ -1,6 +1,8 @@
 import test from "ava";
+import * as path from "path";
 
 import * as analysisPaths from "./analysis-paths";
+import { getRunnerLogger } from "./logging";
 import { setupTests } from "./testing-utils";
 import * as util from "./util";
 
@@ -18,7 +20,7 @@ test("emptyPaths", async (t) => {
       toolCacheDir: tmpDir,
       codeQLCmd: "",
     };
-    analysisPaths.includeAndExcludeAnalysisPaths(config);
+    analysisPaths.includeAndExcludeAnalysisPaths(config, getRunnerLogger(true));
     t.is(process.env["LGTM_INDEX_INCLUDE"], undefined);
     t.is(process.env["LGTM_INDEX_EXCLUDE"], undefined);
     t.is(process.env["LGTM_INDEX_FILTERS"], undefined);
@@ -37,7 +39,7 @@ test("nonEmptyPaths", async (t) => {
       toolCacheDir: tmpDir,
       codeQLCmd: "",
     };
-    analysisPaths.includeAndExcludeAnalysisPaths(config);
+    analysisPaths.includeAndExcludeAnalysisPaths(config, getRunnerLogger(true));
     t.is(process.env["LGTM_INDEX_INCLUDE"], "path1\npath2");
     t.is(process.env["LGTM_INDEX_EXCLUDE"], "path4\npath5");
     t.is(
@@ -46,3 +48,23 @@ test("nonEmptyPaths", async (t) => {
     );
   });
 });
+
+test("exclude temp dir", async (t) => {
+  return await util.withTmpDir(async (toolCacheDir) => {
+    const tempDir = path.join(process.cwd(), "codeql-runner-temp");
+    const config = {
+      languages: [],
+      queries: {},
+      pathsIgnore: [],
+      paths: [],
+      originalUserInput: {},
+      tempDir: tempDir,
+      toolCacheDir: toolCacheDir,
+      codeQLCmd: "",
+    };
+    analysisPaths.includeAndExcludeAnalysisPaths(config, getRunnerLogger(true));
+    t.is(process.env["LGTM_INDEX_INCLUDE"], undefined);
+    t.is(process.env["LGTM_INDEX_EXCLUDE"], tempDir);
+    t.is(process.env["LGTM_INDEX_FILTERS"], undefined);
+  });
+});
diff --git a/src/analysis-paths.ts b/src/analysis-paths.ts
index 084719b191..c9e9b9c157 100644
--- a/src/analysis-paths.ts
+++ b/src/analysis-paths.ts
@@ -1,3 +1,4 @@
+import * as path from "path";
 import * as configUtils from "./config-utils";
 import { Logger } from "./logging";
 
@@ -37,7 +38,7 @@ export function printPathFiltersWarning(
   }
 }
 
-export function includeAndExcludeAnalysisPaths(config: configUtils.Config) {
+export function includeAndExcludeAnalysisPaths(config: configUtils.Config, logger: Logger) {
   // The 'LGTM_INDEX_INCLUDE' and 'LGTM_INDEX_EXCLUDE' environment variables
   // control which files/directories are traversed when scanning.
   // This allows including files that otherwise would not be scanned, or
@@ -48,10 +49,15 @@ export function includeAndExcludeAnalysisPaths(config: configUtils.Config) {
   if (config.paths.length !== 0) {
     process.env["LGTM_INDEX_INCLUDE"] = buildIncludeExcludeEnvVar(config.paths);
   }
-  if (config.pathsIgnore.length !== 0) {
-    process.env["LGTM_INDEX_EXCLUDE"] = buildIncludeExcludeEnvVar(
-      config.pathsIgnore
-    );
+  // Always ignore the temporary directory. This is required if the runner has been downloaded to the checkout directory of the repository being analyzed.
+  const tempRelativeToWorking = path.relative(process.cwd(), config.tempDir);
+  let pathsIgnore = config.pathsIgnore;
+  if (!tempRelativeToWorking.startsWith("..")) {
+    logger.warning("Storing the CodeQL Runner in the directory being analyzed is not recommended.");
+    pathsIgnore = pathsIgnore.concat(config.tempDir);
+  }
+  if (pathsIgnore.length !== 0) {
+    process.env["LGTM_INDEX_EXCLUDE"] = buildIncludeExcludeEnvVar(pathsIgnore);
   }
 
   // The 'LGTM_INDEX_FILTERS' environment variable controls which files are
diff --git a/src/analyze.ts b/src/analyze.ts
index 8b9e80ab6b..07238caf73 100644
--- a/src/analyze.ts
+++ b/src/analyze.ts
@@ -50,7 +50,7 @@ async function createdDBForScannedLanguages(
 ) {
   // Insert the LGTM_INDEX_X env vars at this point so they are set when
   // we extract any scanned languages.
-  analysisPaths.includeAndExcludeAnalysisPaths(config);
+  analysisPaths.includeAndExcludeAnalysisPaths(config, logger);
 
   const codeql = getCodeQL(config.codeQLCmd);
   for (const language of config.languages) {