fix: resolve OpenAI Codex CLI integration conflicts

- Create .codex directory and config.toml file for MCP integration
- Ensure AGENTS.md is properly included for Codex CLI custom rules
- Update hardlinks script to support AGENTS.md for Codex
- Verify documentation has correct installation method and commands

Co-authored-by: Booker Zhao <binggg@users.noreply.github.com>

Author: claude[bot]