Update Gemini-CLI instruction

Recently Gemini-CLI has updated the [settings structure](https://github.com/google-gemini/gemini-cli/blob/1eaf21f6a288cd96bf648eb93d73634fd9b2c6df/docs/cli/configuration.md?plain=1#L161-L163) and the instruction on how to enable AGENTS.md has become outdated.
