Ignore the tools directory as well and remove the warning.

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);

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);
   }

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) {