Fix a bug in cli config parsing

When the config specifies queries in external repositories and no other
queries and cli config parsing is enabled, the analyze job is not able
to find any queries to run and it fails. This PR fixes the problem.

Also add some logging statements when writing a copy of the user config
file.

src/codeql.ts

@@ -855,7 +855,8 @@ async function getCodeQLForCmd(
       config: Config,
       sourceRoot: string,
       processName: string | undefined,
-      featureEnablement: FeatureEnablement
+      featureEnablement: FeatureEnablement,
+      logger: Logger
     ) {
       const extraArgs = config.languages.map(
         (language) => `--language=${language}`
@@ -888,7 +889,8 @@ async function getCodeQLForCmd(
       const configLocation = await generateCodeScanningConfig(
         codeql,
         config,
-        featureEnablement
+        featureEnablement,
+        logger
       );
       // Only pass external repository token if a config file is going to be parsed by the CLI.
       let externalRepositoryToken: string | undefined;
@@ -1386,7 +1388,8 @@ async function runTool(
 async function generateCodeScanningConfig(
   codeql: CodeQL,
   config: Config,
-  featureEnablement: FeatureEnablement
+  featureEnablement: FeatureEnablement,
+  logger: Logger
 ): Promise<string | undefined> {
   if (!(await util.useCodeScanningConfigInCli(codeql, featureEnablement))) {
     return;
@@ -1448,6 +1451,10 @@ async function generateCodeScanningConfig(
       augmentedConfig.packs["javascript"].push(packString);
     }
   }
+  logger.info(`Writing augmented user configuration file to ${configLocation}`);
+  logger.startGroup("Augmented user configuration file contents");
+  logger.info(yaml.dump(augmentedConfig));
+  logger.endGroup();
 
   fs.writeFileSync(configLocation, yaml.dump(augmentedConfig));
   return configLocation;