fix(cli): Prevent stdout/stderr patching for extension commands (#13600)

Co-authored-by: jacob314 <jacob314@gmail.com>

packages/cli/src/config/config.ts

@@ -312,19 +312,6 @@ export async function parseArguments(settings: Settings): Promise<CliArgs> {
     process.exit(0);
   }
 
-  // If yargs handled --help/--version it will have exited; nothing to do here.
-
-  // Handle case where MCP subcommands are executed - they should exit the process
-  // and not return to main CLI logic
-  if (
-    result._.length > 0 &&
-    (result._[0] === 'mcp' || result._[0] === 'extensions')
-  ) {
-    // MCP commands handle their own execution and process exit
-    await runExitCleanup();
-    process.exit(0);
-  }
-
   // Normalize query args: handle both quoted "@path file" and unquoted @path file
   const queryArg = (result as { query?: string | string[] | undefined }).query;
   const q: string | undefined = Array.isArray(queryArg)