diff --git a/lib/codeql.js b/lib/codeql.js
index e58fed8de..44a0d93ff 100644
--- a/lib/codeql.js
+++ b/lib/codeql.js
@@ -31,24 +31,22 @@ const CODEQL_BUNDLE_VERSION = defaults.bundleVersion;
 const CODEQL_BUNDLE_NAME = "codeql-bundle.tar.gz";
 const CODEQL_DEFAULT_ACTION_REPOSITORY = "github/codeql-action";
 function getCodeQLActionRepository(mode) {
-    if (mode === 'actions') {
-        // Actions do not know their own repository name,
-        // so we currently use this hack to find the name based on where our files are.
-        // This can be removed once the change to the runner in https://github.com/actions/runner/pull/585 is deployed.
-        const runnerTemp = util.getRequiredEnvParam("RUNNER_TEMP");
-        const actionsDirectory = path.join(path.dirname(runnerTemp), "_actions");
-        const relativeScriptPath = path.relative(actionsDirectory, __filename);
-        // This handles the case where the Action does not come from an Action repository,
-        // e.g. our integration tests which use the Action code from the current checkout.
-        if (relativeScriptPath.startsWith("..") || path.isAbsolute(relativeScriptPath)) {
-            return CODEQL_DEFAULT_ACTION_REPOSITORY;
-        }
-        const relativeScriptPathParts = relativeScriptPath.split(path.sep);
-        return relativeScriptPathParts[0] + "/" + relativeScriptPathParts[1];
+    if (mode !== 'actions') {
+        return CODEQL_DEFAULT_ACTION_REPOSITORY;
     }
-    else {
+    // Actions do not know their own repository name,
+    // so we currently use this hack to find the name based on where our files are.
+    // This can be removed once the change to the runner in https://github.com/actions/runner/pull/585 is deployed.
+    const runnerTemp = util.getRequiredEnvParam("RUNNER_TEMP");
+    const actionsDirectory = path.join(path.dirname(runnerTemp), "_actions");
+    const relativeScriptPath = path.relative(actionsDirectory, __filename);
+    // This handles the case where the Action does not come from an Action repository,
+    // e.g. our integration tests which use the Action code from the current checkout.
+    if (relativeScriptPath.startsWith("..") || path.isAbsolute(relativeScriptPath)) {
         return CODEQL_DEFAULT_ACTION_REPOSITORY;
     }
+    const relativeScriptPathParts = relativeScriptPath.split(path.sep);
+    return relativeScriptPathParts[0] + "/" + relativeScriptPathParts[1];
 }
 async function getCodeQLBundleDownloadURL(githubUrl, mode, logger) {
     const codeQLActionRepository = getCodeQLActionRepository(mode);
@@ -89,6 +87,8 @@ async function getCodeQLBundleDownloadURL(githubUrl, mode, logger) {
     }
     return `https://github.com/${CODEQL_DEFAULT_ACTION_REPOSITORY}/releases/download/${CODEQL_BUNDLE_VERSION}/${CODEQL_BUNDLE_NAME}`;
 }
+// We have to download CodeQL manually because the toolcache doesn't support Accept headers.
+// This can be removed once https://github.com/actions/toolkit/pull/530 is merged and released.
 async function toolcacheDownloadTool(url, headers, tempDir, logger) {
     const client = new http.HttpClient('CodeQL Action');
     const dest = path.join(tempDir, v4_1.default());
@@ -103,8 +103,8 @@ async function toolcacheDownloadTool(url, headers, tempDir, logger) {
     return dest;
 }
 async function setupCodeQL(codeqlURL, githubAuth, githubUrl, tempDir, toolsDir, mode, logger) {
-    // Setting these two env vars makes the toolcache code safe to use,
-    // but this is obviously not a great thing we're doing and it would
+    // Setting these two env vars makes the toolcache code safe to use outside,
+    // of actions but this is obviously not a great thing we're doing and it would
     // be better to write our own implementation to use outside of actions.
     process.env['RUNNER_TEMP'] = tempDir;
     process.env['RUNNER_TOOL_CACHE'] = toolsDir;
@@ -236,8 +236,7 @@ function getCodeQLForCmd(cmd) {
             ]);
         },
         getTracerEnv: async function (databasePath) {
-            // Write tracer-env.js to a temp location. When running in CLI mode we can't rely
-            // on this file existing so we have to create it ourselves.
+            // Write tracer-env.js to a temp location.
             const tracerEnvJs = path.resolve(databasePath, 'working', 'tracer-env.js');
             fs.mkdirSync(path.dirname(tracerEnvJs), { recursive: true });
             fs.writeFileSync(tracerEnvJs, `
diff --git a/lib/codeql.js.map b/lib/codeql.js.map
index 8f20c74ba..1a2d106a0 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/init.js b/lib/init.js
index 188a28093..4004bde4c 100644
--- a/lib/init.js
+++ b/lib/init.js
@@ -40,24 +40,22 @@ async function runInit(codeql, config) {
         await codeql.databaseInit(util.getCodeQLDatabasePath(config.tempDir, language), language, sourceRoot);
     }
     const tracerConfig = await tracer_config_1.getCombinedTracerConfig(config, codeql);
-    if (tracerConfig !== undefined) {
-        if (process.platform === 'win32') {
-            const injectTracerPath = path.join(config.tempDir, 'inject-tracer.ps1');
-            fs.writeFileSync(injectTracerPath, `
-        Param(
-            [Parameter(Position=0)]
-            [String]
-            $tracer
-        )
-        Get-Process -Name Runner.Worker
-        $process=Get-Process -Name Runner.Worker
-        $id=$process.Id
-        Invoke-Expression "&$tracer --inject=$id"`);
-            await exec.exec('powershell', [
-                injectTracerPath,
-                path.resolve(path.dirname(codeql.getPath()), 'tools', 'win64', 'tracer.exe'),
-            ], { env: { 'ODASA_TRACER_CONFIGURATION': tracerConfig.spec } });
-        }
+    if (tracerConfig !== undefined && process.platform === 'win32') {
+        const injectTracerPath = path.join(config.tempDir, 'inject-tracer.ps1');
+        fs.writeFileSync(injectTracerPath, `
+      Param(
+          [Parameter(Position=0)]
+          [String]
+          $tracer
+      )
+      Get-Process -Name Runner.Worker
+      $process=Get-Process -Name Runner.Worker
+      $id=$process.Id
+      Invoke-Expression "&$tracer --inject=$id"`);
+        await exec.exec('powershell', [
+            injectTracerPath,
+            path.resolve(path.dirname(codeql.getPath()), 'tools', 'win64', 'tracer.exe'),
+        ], { env: { 'ODASA_TRACER_CONFIGURATION': tracerConfig.spec } });
     }
     return tracerConfig;
 }
diff --git a/lib/init.js.map b/lib/init.js.map
index f35c3fd32..0267af6db 100644
--- a/lib/init.js.map
+++ b/lib/init.js.map
@@ -1 +1 @@
-{"version":3,"file":"init.js","sourceRoot":"","sources":["../src/init.ts"],"names":[],"mappings":";;;;;;;;;AAAA,oDAAsC;AACtC,uCAAyB;AACzB,2CAA6B;AAE7B,gEAAkD;AAClD,qCAA+C;AAC/C,4DAA8C;AAG9C,mDAAwE;AACxE,6CAA+B;AAExB,KAAK,UAAU,UAAU,CAC9B,SAA6B,EAC7B,UAAkB,EAClB,SAAiB,EACjB,OAAe,EACf,QAAgB,EAChB,IAAe,EACf,MAAc;IAEd,MAAM,CAAC,UAAU,CAAC,oBAAoB,CAAC,CAAC;IACxC,MAAM,MAAM,GAAG,MAAM,oBAAW,CAC9B,SAAS,EACT,UAAU,EACV,SAAS,EACT,OAAO,EACP,QAAQ,EACR,IAAI,EACJ,MAAM,CAAC,CAAC;IACV,MAAM,MAAM,CAAC,YAAY,EAAE,CAAC;IAC5B,MAAM,CAAC,QAAQ,EAAE,CAAC;IAClB,OAAO,MAAM,CAAC;AAChB,CAAC;AArBD,gCAqBC;AAEM,KAAK,UAAU,UAAU,CAC9B,cAAkC,EAClC,YAAgC,EAChC,UAA8B,EAC9B,UAAyB,EACzB,OAAe,EACf,YAAoB,EACpB,MAAc,EACd,YAAoB,EACpB,UAAkB,EAClB,SAAiB,EACjB,MAAc;IAEd,MAAM,CAAC,UAAU,CAAC,6BAA6B,CAAC,CAAC;IACjD,MAAM,MAAM,GAAG,MAAM,WAAW,CAAC,UAAU,CACzC,cAAc,EACd,YAAY,EACZ,UAAU,EACV,UAAU,EACV,OAAO,EACP,YAAY,EACZ,MAAM,EACN,YAAY,EACZ,UAAU,EACV,SAAS,EACT,MAAM,CAAC,CAAC;IACV,aAAa,CAAC,uBAAuB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACtD,MAAM,CAAC,QAAQ,EAAE,CAAC;IAClB,OAAO,MAAM,CAAC;AAChB,CAAC;AA7BD,gCA6BC;AAEM,KAAK,UAAU,OAAO,CAC3B,MAAc,EACd,MAA0B;IAE1B,MAAM,UAAU,GAAG,IAAI,CAAC,OAAO,EAAE,CAAC;IAElC,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,qBAAqB,CAAC,MAAM,CAAC,OAAO,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAE9E,sEAAsE;IACtE,KAAK,IAAI,QAAQ,IAAI,MAAM,CAAC,SAAS,EAAE;QACrC,yBAAyB;QACzB,MAAM,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,qBAAqB,CAAC,MAAM,CAAC,OAAO,EAAE,QAAQ,CAAC,EAAE,QAAQ,EAAE,UAAU,CAAC,CAAC;KACvG;IAED,MAAM,YAAY,GAAG,MAAM,uCAAuB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACnE,IAAI,YAAY,KAAK,SAAS,EAAE;QAC9B,IAAI,OAAO,CAAC,QAAQ,KAAK,OAAO,EAAE;YAChC,MAAM,gBAAgB,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,mBAAmB,CAAC,CAAC;YACxE,EAAE,CAAC,aAAa,CAAC,gBAAgB,EAAE;;;;;;;;;kDASS,CAAC,CAAC;YAE9C,MAAM,IAAI,CAAC,IAAI,CACb,YAAY,EACZ;gBACE,gBAAgB;gBAChB,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC,EAAE,OAAO,EAAE,OAAO,EAAE,YAAY,CAAC;aAC7E,EACD,EAAE,GAAG,EAAE,EAAE,4BAA4B,EAAE,YAAY,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;SACjE;KACF;IACD,OAAO,YAAY,CAAC;AACtB,CAAC;AAvCD,0BAuCC"}
\ No newline at end of file
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\ No newline at end of file
diff --git a/lib/runner.js b/lib/runner.js
index 387953457..6001a6251 100644
--- a/lib/runner.js
+++ b/lib/runner.js
@@ -64,7 +64,7 @@ function checkEnvironmentSetup(config) {
     if (config.languages.some(languages_1.isTracedLanguage) && !('ODASA_TRACER_CONFIGURATION' in process.env)) {
         throw new Error("Could not detect 'ODASA_TRACER_CONFIGURATION' in environment. " +
             "Make sure that environment variables were correctly exported to future processes. " +
-            "See end out output from 'init' command for instructions.");
+            "See end of output from 'init' command for instructions.");
     }
 }
 program
@@ -77,7 +77,7 @@ program
     .option('--queries <queries>', 'Comma-separated list of additional queries to run. By default, this overrides the same setting in a configuration file.')
     .option('--config-file <file>', 'Path to config file')
     .option('--codeql-path <path>', 'Path to a copy of the CodeQL CLI executable to use. Otherwise downloads a copy.')
-    .option('--temp-dir <dir>', 'Directory to use for temporary files. By default will use current working directory.')
+    .option('--temp-dir <dir>', 'Directory to use for temporary files. By default will use a subdirectory of the current working directory.')
     .option('--tools-dir <dir>', 'Directory to use for CodeQL tools and other files to store between runs. By default will use home directory.')
     .option('--checkout-path <path>', 'Checkout path (default: current working directory)')
     .option('--debug', 'Print more verbose output', false)
@@ -98,35 +98,36 @@ program
         }
         const config = await init_1.initConfig(cmd.languages, cmd.queries, cmd.configFile, repository_1.parseRepositoryNwo(cmd.repository), tempDir, toolsDir, codeql, cmd.checkoutPath || process.cwd(), cmd.githubAuth, parseGithubUrl(cmd.githubUrl), logger);
         const tracerConfig = await init_1.runInit(codeql, config);
-        if (tracerConfig !== undefined) {
-            if (process.platform === 'win32') {
-                const batEnvFile = path.join(config.tempDir, 'codeql-env.bat');
-                const batEnvFileContents = Object.entries(tracerConfig.env)
-                    .map(([key, value]) => `Set ${key}=${value}`)
-                    .join('\n');
-                fs.writeFileSync(batEnvFile, batEnvFileContents);
-                const powershellEnvFile = path.join(config.tempDir, 'codeql-env.sh');
-                const powershellEnvFileContents = Object.entries(tracerConfig.env)
-                    .map(([key, value]) => `$env:${key}="${value}"`)
-                    .join('\n');
-                fs.writeFileSync(powershellEnvFile, powershellEnvFileContents);
-                logger.info(`\nCodeQL environment outputted to "${batEnvFileContents}" and "${powershellEnvFile}". ` +
-                    `Please export these variables to future processes so the build can tbe traced. ` +
-                    `If using cmd/batch run "call ${batEnvFileContents}" ` +
-                    `or if using PowerShell run "cat ${powershellEnvFile} | Invoke-Expression".`);
-            }
-            else {
-                // Assume that anything that's not windows is using a unix-style shell
-                const envFile = path.join(config.tempDir, 'codeql-env.sh');
-                const envFileContents = Object.entries(tracerConfig.env)
-                    // Some vars contain ${LIB} that we do not want to be expanded when executing this script
-                    .map(([key, value]) => `export ${key}="${value.replace('$', '\\$')}"`)
-                    .join('\n');
-                fs.writeFileSync(envFile, envFileContents);
-                logger.info(`\nCodeQL environment outputted to "${envFile}". ` +
-                    `Please export these variables to future processes so the build can tbe traced, ` +
-                    `for example by running "source ${envFile}".`);
-            }
+        if (tracerConfig === undefined) {
+            return;
+        }
+        if (process.platform === 'win32') {
+            const batEnvFile = path.join(config.tempDir, 'codeql-env.bat');
+            const batEnvFileContents = Object.entries(tracerConfig.env)
+                .map(([key, value]) => `Set ${key}=${value}`)
+                .join('\n');
+            fs.writeFileSync(batEnvFile, batEnvFileContents);
+            const powershellEnvFile = path.join(config.tempDir, 'codeql-env.sh');
+            const powershellEnvFileContents = Object.entries(tracerConfig.env)
+                .map(([key, value]) => `$env:${key}="${value}"`)
+                .join('\n');
+            fs.writeFileSync(powershellEnvFile, powershellEnvFileContents);
+            logger.info(`\nCodeQL environment output to "${batEnvFileContents}" and "${powershellEnvFile}". ` +
+                `Please export these variables to future processes so the build can be traced. ` +
+                `If using cmd/batch run "call ${batEnvFileContents}" ` +
+                `or if using PowerShell run "cat ${powershellEnvFile} | Invoke-Expression".`);
+        }
+        else {
+            // Assume that anything that's not windows is using a unix-style shell
+            const envFile = path.join(config.tempDir, 'codeql-env.sh');
+            const envFileContents = Object.entries(tracerConfig.env)
+                // Some vars contain ${LIB} that we do not want to be expanded when executing this script
+                .map(([key, value]) => `export ${key}="${value.replace('$', '\\$')}"`)
+                .join('\n');
+            fs.writeFileSync(envFile, envFileContents);
+            logger.info(`\nCodeQL environment output to "${envFile}". ` +
+                `Please export these variables to future processes so the build can be traced, ` +
+                `for example by running "source ${envFile}".`);
         }
     }
     catch (e) {
@@ -139,7 +140,7 @@ program
     .command('autobuild')
     .description('Attempts to automatically build code')
     .option('--language <language>', 'The language to build. By default will try to detect the dominant language.')
-    .option('--temp-dir <dir>', 'Directory to use for temporary files. By default will use current working directory.')
+    .option('--temp-dir <dir>', 'Directory to use for temporary files. By default will use a subdirectory of the current working directory.')
     .option('--debug', 'Print more verbose output', false)
     .action(async (cmd) => {
     const logger = logging_1.getRunnerLogger(cmd.debug);
@@ -178,7 +179,7 @@ program
     .option('--checkout-path <path>', 'Checkout path (default: current working directory)')
     .option('--no-upload', 'Do not upload results after analysis', false)
     .option('--output-dir <dir>', 'Directory to output SARIF files to. By default will use temp directory.')
-    .option('--temp-dir <dir>', 'Directory to use for temporary files. By default will use current working directory.')
+    .option('--temp-dir <dir>', 'Directory to use for temporary files. By default will use a subdirectory of the current working directory.')
     .option('--debug', 'Print more verbose output', false)
     .action(async (cmd) => {
     const logger = logging_1.getRunnerLogger(cmd.debug);
@@ -190,7 +191,7 @@ program
         await analyze_1.runAnalyze(repository_1.parseRepositoryNwo(cmd.repository), cmd.commit, cmd.ref, undefined, undefined, undefined, cmd.checkoutPath || process.cwd(), undefined, cmd.githubAuth, parseGithubUrl(cmd.githubUrl), cmd.upload, 'runner', outputDir, config, logger);
     }
     catch (e) {
-        logger.error('Upload failed');
+        logger.error('Analyze failed');
         logger.error(e);
         process.exitCode = 1;
     }
diff --git a/lib/runner.js.map b/lib/runner.js.map
index fa0a25b7f..c66138314 100644
--- a/lib/runner.js.map
+++ b/lib/runner.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/src/codeql.ts b/src/codeql.ts
index 49e20b963..96cd04ef0 100644
--- a/src/codeql.ts
+++ b/src/codeql.ts
@@ -102,24 +102,23 @@ const CODEQL_BUNDLE_NAME = "codeql-bundle.tar.gz";
 const CODEQL_DEFAULT_ACTION_REPOSITORY = "github/codeql-action";
 
 function getCodeQLActionRepository(mode: util.Mode): string {
-  if (mode === 'actions') {
-    // Actions do not know their own repository name,
-    // so we currently use this hack to find the name based on where our files are.
-    // This can be removed once the change to the runner in https://github.com/actions/runner/pull/585 is deployed.
-    const runnerTemp = util.getRequiredEnvParam("RUNNER_TEMP");
-    const actionsDirectory = path.join(path.dirname(runnerTemp), "_actions");
-    const relativeScriptPath = path.relative(actionsDirectory, __filename);
-    // This handles the case where the Action does not come from an Action repository,
-    // e.g. our integration tests which use the Action code from the current checkout.
-    if (relativeScriptPath.startsWith("..") || path.isAbsolute(relativeScriptPath)) {
-      return CODEQL_DEFAULT_ACTION_REPOSITORY;
-    }
-    const relativeScriptPathParts = relativeScriptPath.split(path.sep);
-    return relativeScriptPathParts[0] + "/" + relativeScriptPathParts[1];
+  if (mode !== 'actions') {
+    return CODEQL_DEFAULT_ACTION_REPOSITORY;
+  }
 
-  } else {
+  // Actions do not know their own repository name,
+  // so we currently use this hack to find the name based on where our files are.
+  // This can be removed once the change to the runner in https://github.com/actions/runner/pull/585 is deployed.
+  const runnerTemp = util.getRequiredEnvParam("RUNNER_TEMP");
+  const actionsDirectory = path.join(path.dirname(runnerTemp), "_actions");
+  const relativeScriptPath = path.relative(actionsDirectory, __filename);
+  // This handles the case where the Action does not come from an Action repository,
+  // e.g. our integration tests which use the Action code from the current checkout.
+  if (relativeScriptPath.startsWith("..") || path.isAbsolute(relativeScriptPath)) {
     return CODEQL_DEFAULT_ACTION_REPOSITORY;
   }
+  const relativeScriptPathParts = relativeScriptPath.split(path.sep);
+  return relativeScriptPathParts[0] + "/" + relativeScriptPathParts[1];
 }
 
 async function getCodeQLBundleDownloadURL(githubUrl: string, mode: util.Mode, logger: Logger): Promise<string> {
@@ -161,6 +160,8 @@ async function getCodeQLBundleDownloadURL(githubUrl: string, mode: util.Mode, lo
   return `https://github.com/${CODEQL_DEFAULT_ACTION_REPOSITORY}/releases/download/${CODEQL_BUNDLE_VERSION}/${CODEQL_BUNDLE_NAME}`;
 }
 
+// We have to download CodeQL manually because the toolcache doesn't support Accept headers.
+// This can be removed once https://github.com/actions/toolkit/pull/530 is merged and released.
 async function toolcacheDownloadTool(
   url: string,
   headers: IHeaders | undefined,
@@ -189,8 +190,8 @@ export async function setupCodeQL(
   mode: util.Mode,
   logger: Logger): Promise<CodeQL> {
 
-  // Setting these two env vars makes the toolcache code safe to use,
-  // but this is obviously not a great thing we're doing and it would
+  // Setting these two env vars makes the toolcache code safe to use outside,
+  // of actions but this is obviously not a great thing we're doing and it would
   // be better to write our own implementation to use outside of actions.
   process.env['RUNNER_TEMP'] = tempDir;
   process.env['RUNNER_TOOL_CACHE'] = toolsDir;
@@ -334,8 +335,7 @@ function getCodeQLForCmd(cmd: string): CodeQL {
       ]);
     },
     getTracerEnv: async function(databasePath: string) {
-      // Write tracer-env.js to a temp location. When running in CLI mode we can't rely
-      // on this file existing so we have to create it ourselves.
+      // Write tracer-env.js to a temp location.
       const tracerEnvJs = path.resolve(databasePath, 'working', 'tracer-env.js');
       fs.mkdirSync(path.dirname(tracerEnvJs), {recursive: true});
       fs.writeFileSync(tracerEnvJs, `
diff --git a/src/init.ts b/src/init.ts
index 88b301971..a34a00bbe 100644
--- a/src/init.ts
+++ b/src/init.ts
@@ -79,28 +79,26 @@ export async function runInit(
   }
 
   const tracerConfig = await getCombinedTracerConfig(config, codeql);
-  if (tracerConfig !== undefined) {
-    if (process.platform === 'win32') {
-      const injectTracerPath = path.join(config.tempDir, 'inject-tracer.ps1');
-      fs.writeFileSync(injectTracerPath, `
-        Param(
-            [Parameter(Position=0)]
-            [String]
-            $tracer
-        )
-        Get-Process -Name Runner.Worker
-        $process=Get-Process -Name Runner.Worker
-        $id=$process.Id
-        Invoke-Expression "&$tracer --inject=$id"`);
+  if (tracerConfig !== undefined && process.platform === 'win32') {
+    const injectTracerPath = path.join(config.tempDir, 'inject-tracer.ps1');
+    fs.writeFileSync(injectTracerPath, `
+      Param(
+          [Parameter(Position=0)]
+          [String]
+          $tracer
+      )
+      Get-Process -Name Runner.Worker
+      $process=Get-Process -Name Runner.Worker
+      $id=$process.Id
+      Invoke-Expression "&$tracer --inject=$id"`);
 
-      await exec.exec(
-        'powershell',
-        [
-          injectTracerPath,
-          path.resolve(path.dirname(codeql.getPath()), 'tools', 'win64', 'tracer.exe'),
-        ],
-        { env: { 'ODASA_TRACER_CONFIGURATION': tracerConfig.spec } });
-    }
+    await exec.exec(
+      'powershell',
+      [
+        injectTracerPath,
+        path.resolve(path.dirname(codeql.getPath()), 'tools', 'win64', 'tracer.exe'),
+      ],
+      { env: { 'ODASA_TRACER_CONFIGURATION': tracerConfig.spec } });
   }
   return tracerConfig;
 }
diff --git a/src/runner.ts b/src/runner.ts
index a1f6c2912..3eee39219 100644
--- a/src/runner.ts
+++ b/src/runner.ts
@@ -61,7 +61,7 @@ function checkEnvironmentSetup(config: Config) {
   if (config.languages.some(isTracedLanguage) && !('ODASA_TRACER_CONFIGURATION' in process.env)) {
     throw new Error("Could not detect 'ODASA_TRACER_CONFIGURATION' in environment. " +
       "Make sure that environment variables were correctly exported to future processes. " +
-      "See end out output from 'init' command for instructions.");
+      "See end of output from 'init' command for instructions.");
   }
 }
 
@@ -89,7 +89,7 @@ program
   .option('--queries <queries>', 'Comma-separated list of additional queries to run. By default, this overrides the same setting in a configuration file.')
   .option('--config-file <file>', 'Path to config file')
   .option('--codeql-path <path>', 'Path to a copy of the CodeQL CLI executable to use. Otherwise downloads a copy.')
-  .option('--temp-dir <dir>', 'Directory to use for temporary files. By default will use current working directory.')
+  .option('--temp-dir <dir>', 'Directory to use for temporary files. By default will use a subdirectory of the current working directory.')
   .option('--tools-dir <dir>', 'Directory to use for CodeQL tools and other files to store between runs. By default will use home directory.')
   .option('--checkout-path <path>', 'Checkout path (default: current working directory)')
   .option('--debug', 'Print more verbose output', false)
@@ -131,38 +131,40 @@ program
         logger);
 
       const tracerConfig = await runInit(codeql, config);
-      if (tracerConfig !== undefined) {
-        if (process.platform === 'win32') {
-          const batEnvFile = path.join(config.tempDir, 'codeql-env.bat');
-          const batEnvFileContents = Object.entries(tracerConfig.env)
-            .map(([key, value]) => `Set ${key}=${value}`)
-            .join('\n');
-          fs.writeFileSync(batEnvFile, batEnvFileContents);
+      if (tracerConfig === undefined) {
+        return;
+      }
 
-          const powershellEnvFile = path.join(config.tempDir, 'codeql-env.sh');
-          const powershellEnvFileContents = Object.entries(tracerConfig.env)
-            .map(([key, value]) => `$env:${key}="${value}"`)
-            .join('\n');
-          fs.writeFileSync(powershellEnvFile, powershellEnvFileContents);
+      if (process.platform === 'win32') {
+        const batEnvFile = path.join(config.tempDir, 'codeql-env.bat');
+        const batEnvFileContents = Object.entries(tracerConfig.env)
+          .map(([key, value]) => `Set ${key}=${value}`)
+          .join('\n');
+        fs.writeFileSync(batEnvFile, batEnvFileContents);
 
-          logger.info(`\nCodeQL environment outputted to "${batEnvFileContents}" and "${powershellEnvFile}". ` +
-            `Please export these variables to future processes so the build can tbe traced. ` +
-            `If using cmd/batch run "call ${batEnvFileContents}" ` +
-            `or if using PowerShell run "cat ${powershellEnvFile} | Invoke-Expression".`);
+        const powershellEnvFile = path.join(config.tempDir, 'codeql-env.sh');
+        const powershellEnvFileContents = Object.entries(tracerConfig.env)
+          .map(([key, value]) => `$env:${key}="${value}"`)
+          .join('\n');
+        fs.writeFileSync(powershellEnvFile, powershellEnvFileContents);
 
-        } else {
-          // Assume that anything that's not windows is using a unix-style shell
-          const envFile = path.join(config.tempDir, 'codeql-env.sh');
-          const envFileContents = Object.entries(tracerConfig.env)
-            // Some vars contain ${LIB} that we do not want to be expanded when executing this script
-            .map(([key, value]) => `export ${key}="${value.replace('$', '\\$')}"`)
-            .join('\n');
-          fs.writeFileSync(envFile, envFileContents);
+        logger.info(`\nCodeQL environment output to "${batEnvFileContents}" and "${powershellEnvFile}". ` +
+          `Please export these variables to future processes so the build can be traced. ` +
+          `If using cmd/batch run "call ${batEnvFileContents}" ` +
+          `or if using PowerShell run "cat ${powershellEnvFile} | Invoke-Expression".`);
 
-          logger.info(`\nCodeQL environment outputted to "${envFile}". ` +
-            `Please export these variables to future processes so the build can tbe traced, ` +
-            `for example by running "source ${envFile}".`);
-        }
+      } else {
+        // Assume that anything that's not windows is using a unix-style shell
+        const envFile = path.join(config.tempDir, 'codeql-env.sh');
+        const envFileContents = Object.entries(tracerConfig.env)
+          // Some vars contain ${LIB} that we do not want to be expanded when executing this script
+          .map(([key, value]) => `export ${key}="${value.replace('$', '\\$')}"`)
+          .join('\n');
+        fs.writeFileSync(envFile, envFileContents);
+
+        logger.info(`\nCodeQL environment output to "${envFile}". ` +
+          `Please export these variables to future processes so the build can be traced, ` +
+          `for example by running "source ${envFile}".`);
       }
 
     } catch (e) {
@@ -182,7 +184,7 @@ program
   .command('autobuild')
   .description('Attempts to automatically build code')
   .option('--language <language>', 'The language to build. By default will try to detect the dominant language.')
-  .option('--temp-dir <dir>', 'Directory to use for temporary files. By default will use current working directory.')
+  .option('--temp-dir <dir>', 'Directory to use for temporary files. By default will use a subdirectory of the current working directory.')
   .option('--debug', 'Print more verbose output', false)
   .action(async (cmd: AutobuildArgs) => {
     const logger = getRunnerLogger(cmd.debug);
@@ -233,7 +235,7 @@ program
   .option('--checkout-path <path>', 'Checkout path (default: current working directory)')
   .option('--no-upload', 'Do not upload results after analysis', false)
   .option('--output-dir <dir>', 'Directory to output SARIF files to. By default will use temp directory.')
-  .option('--temp-dir <dir>', 'Directory to use for temporary files. By default will use current working directory.')
+  .option('--temp-dir <dir>', 'Directory to use for temporary files. By default will use a subdirectory of the current working directory.')
   .option('--debug', 'Print more verbose output', false)
   .action(async (cmd: AnalyzeArgs) => {
     const logger = getRunnerLogger(cmd.debug);
@@ -259,7 +261,7 @@ program
         config,
         logger);
     } catch (e) {
-      logger.error('Upload failed');
+      logger.error('Analyze failed');
       logger.error(e);
       process.exitCode = 1;
     }