[Bug]: install-hooks rewrites Codex config.toml, destroying comments, formatting, and custom notify wrappers

[yoshi47]

What broke?

git-ai install-hooks (also called automatically by the installer) rewrites ~/.codex/config.toml entirely, which:

1. Strips all comments (inline and standalone)
2. Reformats the entire file (reorders keys, collapses multi-line arrays)
3. Overwrites custom notify configurations that wrap git-ai in a shell command (e.g. bash -lc)

Steps to reproduce

1. Create ~/.codex/config.toml with comments and a shell-wrapped notify:
   notify = ["bash", "-lc", "git-ai checkpoint codex --hook-input & afplay ~/Documents/celebration.wav"]
   model = "gpt-5.4"

[features]
multi_agent = true # enable multi-agent collaboration tools
collaboration_modes = true # enable collaboration mode selection

[mcp_servers.mcp]
...

2. Run git-ai install-hooks --dry-run=false
3. Check ~/.codex/config.toml

Expected vs actual behavior

Expected: Only the notify field is added/updated; comments, formatting, and key order are preserved.

Actual:

• All comments are removed
• Key ordering changes (notify moves to bottom of root table)
• Multi-line arrays collapsed to single line
• Custom notify = ["bash", "-lc", "git-ai checkpoint codex --hook-input & afplay ..."] is completely replaced with notify =
  ["/path/to/git-ai", "checkpoint", "codex", "--hook-input"] because is_git_ai_codex_notify_args() only checks args[0] for a git-ai
  binary path

Diagnostics (git-ai debug)

N/A

Extra context (optional)