From 62f25fda9bde54b33a0833831357a4721160ea65 Mon Sep 17 00:00:00 2001
From: Chris Gavin <chris@chrisgavin.me>
Date: Thu, 1 Oct 2020 09:29:13 +0100
Subject: [PATCH] Ignore the tools directory as well and remove the warning.

---
 lib/analysis-paths.js          |  9 ++++++---
 lib/analysis-paths.js.map      |  2 +-
 lib/analysis-paths.test.js     |  7 +++----
 lib/analysis-paths.test.js.map |  2 +-
 lib/analyze.js                 |  2 +-
 lib/analyze.js.map             |  2 +-
 src/analysis-paths.test.ts     |  7 +++----
 src/analysis-paths.ts          | 17 +++++++++--------
 src/analyze.ts                 |  2 +-
 9 files changed, 26 insertions(+), 24 deletions(-)

diff --git a/lib/analysis-paths.js b/lib/analysis-paths.js
index b9c2ce3bf..c892849c3 100644
--- a/lib/analysis-paths.js
+++ b/lib/analysis-paths.js
@@ -32,7 +32,7 @@ function printPathFiltersWarning(config, logger) {
     }
 }
 exports.printPathFiltersWarning = printPathFiltersWarning;
-function includeAndExcludeAnalysisPaths(config, logger) {
+function includeAndExcludeAnalysisPaths(config) {
     // 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
@@ -43,13 +43,16 @@ function includeAndExcludeAnalysisPaths(config, logger) {
     if (config.paths.length !== 0) {
         process.env["LGTM_INDEX_INCLUDE"] = buildIncludeExcludeEnvVar(config.paths);
     }
-    // If the temporary directory is in the working directory ignore that too.
+    // If the temporary or tools directory is in the working directory ignore that too.
     const tempRelativeToWorking = path.relative(process.cwd(), config.tempDir);
+    const toolsRelativeToWorking = path.relative(process.cwd(), config.toolCacheDir);
     let pathsIgnore = config.pathsIgnore;
     if (!tempRelativeToWorking.startsWith("..")) {
-        logger.warning("Storing the CodeQL Runner in the directory being analyzed is not recommended.");
         pathsIgnore = pathsIgnore.concat(tempRelativeToWorking);
     }
+    if (!toolsRelativeToWorking.startsWith("..")) {
+        pathsIgnore = pathsIgnore.concat(toolsRelativeToWorking);
+    }
     if (pathsIgnore.length !== 0) {
         process.env["LGTM_INDEX_EXCLUDE"] = buildIncludeExcludeEnvVar(pathsIgnore);
     }
diff --git a/lib/analysis-paths.js.map b/lib/analysis-paths.js.map
index 5d8ebbd19..c0786490a 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":";;;;;;;;;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,CAC5C,MAA0B,EAC1B,MAAc;IAEd,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,0EAA0E;IAC1E,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,CACZ,+EAA+E,CAChF,CAAC;QACF,WAAW,GAAG,WAAW,CAAC,MAAM,CAAC,qBAAqB,CAAC,CAAC;KACzD;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;AApCD,wEAoCC"}
\ 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;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,mFAAmF;IACnF,MAAM,qBAAqB,GAAG,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC;IAC3E,MAAM,sBAAsB,GAAG,IAAI,CAAC,QAAQ,CAC1C,OAAO,CAAC,GAAG,EAAE,EACb,MAAM,CAAC,YAAY,CACpB,CAAC;IACF,IAAI,WAAW,GAAG,MAAM,CAAC,WAAW,CAAC;IACrC,IAAI,CAAC,qBAAqB,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE;QAC3C,WAAW,GAAG,WAAW,CAAC,MAAM,CAAC,qBAAqB,CAAC,CAAC;KACzD;IACD,IAAI,CAAC,sBAAsB,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE;QAC5C,WAAW,GAAG,WAAW,CAAC,MAAM,CAAC,sBAAsB,CAAC,CAAC;KAC1D;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;AArCD,wEAqCC"}
\ No newline at end of file
diff --git a/lib/analysis-paths.test.js b/lib/analysis-paths.test.js
index 060d7b142..a0e0d639b 100644
--- a/lib/analysis-paths.test.js
+++ b/lib/analysis-paths.test.js
@@ -13,7 +13,6 @@ 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);
@@ -29,7 +28,7 @@ ava_1.default("emptyPaths", async (t) => {
             toolCacheDir: tmpDir,
             codeQLCmd: "",
         };
-        analysisPaths.includeAndExcludeAnalysisPaths(config, logging_1.getRunnerLogger(true));
+        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);
@@ -47,7 +46,7 @@ ava_1.default("nonEmptyPaths", async (t) => {
             toolCacheDir: tmpDir,
             codeQLCmd: "",
         };
-        analysisPaths.includeAndExcludeAnalysisPaths(config, logging_1.getRunnerLogger(true));
+        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/**");
@@ -66,7 +65,7 @@ ava_1.default("exclude temp dir", async (t) => {
             toolCacheDir,
             codeQLCmd: "",
         };
-        analysisPaths.includeAndExcludeAnalysisPaths(config, logging_1.getRunnerLogger(true));
+        analysisPaths.includeAndExcludeAnalysisPaths(config);
         t.is(process.env["LGTM_INDEX_INCLUDE"], undefined);
         t.is(process.env["LGTM_INDEX_EXCLUDE"], "codeql-runner-temp");
         t.is(process.env["LGTM_INDEX_FILTERS"], undefined);
diff --git a/lib/analysis-paths.test.js.map b/lib/analysis-paths.test.js.map
index 8f6a96fe0..22b8e5d9a 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;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;YACP,YAAY;YACZ,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,oBAAoB,CAAC,CAAC;QAC9D,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
+{"version":3,"file":"analysis-paths.test.js","sourceRoot":"","sources":["../src/analysis-paths.test.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,8CAAuB;AACvB,2CAA6B;AAE7B,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;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;YACP,YAAY;YACZ,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,oBAAoB,CAAC,CAAC;QAC9D,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 1f4d3cd5e..a8b186514 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, logger);
+    analysisPaths.includeAndExcludeAnalysisPaths(config);
     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 28c17462d..6dbfba9ce 100644
--- a/lib/analyze.js.map
+++ b/lib/analyze.js.map
@@ -1 +1 @@
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\ 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,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
diff --git a/src/analysis-paths.test.ts b/src/analysis-paths.test.ts
index 160d053fa..925ecffe8 100644
--- a/src/analysis-paths.test.ts
+++ b/src/analysis-paths.test.ts
@@ -2,7 +2,6 @@ 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";
 
@@ -20,7 +19,7 @@ test("emptyPaths", async (t) => {
       toolCacheDir: tmpDir,
       codeQLCmd: "",
     };
-    analysisPaths.includeAndExcludeAnalysisPaths(config, getRunnerLogger(true));
+    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);
@@ -39,7 +38,7 @@ test("nonEmptyPaths", async (t) => {
       toolCacheDir: tmpDir,
       codeQLCmd: "",
     };
-    analysisPaths.includeAndExcludeAnalysisPaths(config, getRunnerLogger(true));
+    analysisPaths.includeAndExcludeAnalysisPaths(config);
     t.is(process.env["LGTM_INDEX_INCLUDE"], "path1\npath2");
     t.is(process.env["LGTM_INDEX_EXCLUDE"], "path4\npath5");
     t.is(
@@ -62,7 +61,7 @@ test("exclude temp dir", async (t) => {
       toolCacheDir,
       codeQLCmd: "",
     };
-    analysisPaths.includeAndExcludeAnalysisPaths(config, getRunnerLogger(true));
+    analysisPaths.includeAndExcludeAnalysisPaths(config);
     t.is(process.env["LGTM_INDEX_INCLUDE"], undefined);
     t.is(process.env["LGTM_INDEX_EXCLUDE"], "codeql-runner-temp");
     t.is(process.env["LGTM_INDEX_FILTERS"], undefined);
diff --git a/src/analysis-paths.ts b/src/analysis-paths.ts
index 66f2a772d..1b80d3907 100644
--- a/src/analysis-paths.ts
+++ b/src/analysis-paths.ts
@@ -38,10 +38,7 @@ export function printPathFiltersWarning(
   }
 }
 
-export function includeAndExcludeAnalysisPaths(
-  config: configUtils.Config,
-  logger: Logger
-) {
+export function includeAndExcludeAnalysisPaths(config: configUtils.Config) {
   // 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
@@ -52,15 +49,19 @@ export function includeAndExcludeAnalysisPaths(
   if (config.paths.length !== 0) {
     process.env["LGTM_INDEX_INCLUDE"] = buildIncludeExcludeEnvVar(config.paths);
   }
-  // If the temporary directory is in the working directory ignore that too.
+  // If the temporary or tools directory is in the working directory ignore that too.
   const tempRelativeToWorking = path.relative(process.cwd(), config.tempDir);
+  const toolsRelativeToWorking = path.relative(
+    process.cwd(),
+    config.toolCacheDir
+  );
   let pathsIgnore = config.pathsIgnore;
   if (!tempRelativeToWorking.startsWith("..")) {
-    logger.warning(
-      "Storing the CodeQL Runner in the directory being analyzed is not recommended."
-    );
     pathsIgnore = pathsIgnore.concat(tempRelativeToWorking);
   }
+  if (!toolsRelativeToWorking.startsWith("..")) {
+    pathsIgnore = pathsIgnore.concat(toolsRelativeToWorking);
+  }
   if (pathsIgnore.length !== 0) {
     process.env["LGTM_INDEX_EXCLUDE"] = buildIncludeExcludeEnvVar(pathsIgnore);
   }
diff --git a/src/analyze.ts b/src/analyze.ts
index 07238caf7..8b9e80ab6 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, logger);
+  analysisPaths.includeAndExcludeAnalysisPaths(config);
 
   const codeql = getCodeQL(config.codeQLCmd);
   for (const language of config.languages) {