Fix Yargs Command Shadowing and API Key Requirement for Subcommands

[mattKorwel]

What happened?

The Gemini CLI uses yargs for argument parsing. A greedy default command ($0 [query..]) was registered at the top of the command chain, causing it to shadow explicit subcommands like mcp, extensions, skills, and hooks.

When a user runs a subcommand (e.g., gemini extensions install ...), yargs incorrectly matches it against the default command, treating the subcommand and its arguments as a conversational query. This triggers the main application logic in gemini.tsx, which attempts to initialize the Gemini API client. This initialization requires a GEMINI_API_KEY, which is not needed for administrative subcommands, leading to a fatal error if the key is missing.

What did you expect to happen?

• Subcommands should be matched first and executed without requiring a Gemini API key (unless the subcommand itself requires it).
• The default conversational query should only be matched if no explicit subcommand is provided.
• The application should not attempt to initialize the LLM client or enter interactive mode when a management subcommand is being executed.

Anything else we need to know?

Implementation Plan

1. Reorder Command Registration in packages/cli/src/config/config.ts

   • Register all explicit subcommands (mcp, extensions, skills, hooks) before the default $0 command.
   • Ensure mcpCommand is actually registered using yargsInstance.command(mcpCommand).

2. Add High-Priority Middleware to Set isCommand

   • Add a yargs middleware at the top level of parseArguments to explicitly flag when a subcommand is matched.

   yargsInstance.middleware((argv) => {
     const subcommands = ['mcp', 'extensions', 'extension', 'skills', 'skill', 'hooks', 'hook'];
     if (subcommands.includes(argv._[0] as string)) {
       argv.isCommand = true;
     }
   }, true);

3. Update gemini.tsx to Respect isCommand

   • Skip authentication (partialConfig.refreshAuth and validateNonInteractiveAuth) if argv.isCommand is true.
   • Skip sandbox/child process relaunching logic if argv.isCommand is true.

Verification & Testing

• Manual Verification: Run gemini extensions install ... without a GEMINI_API_KEY set and verify it proceeds to installation.
• Unit Tests: Ensure that argv.isCommand is correctly set in parseArguments for various subcommands.