chore: prompt update to enforce good usage of apply_patch

[jif-oai]

Update prompt to prevent codex to use Python script or fancy commands to edit files.

Testing:

3 scenarios have been considered:

1. Rename codex to meca_code. Proceed to the whole refactor file by file. Don't ask for approval at each step
2. Add a description to every single function you can find in the repo
3. Rewrite codex.rs in a more idiomatic way. Make sure to touch ONLY this file and that clippy does not complain at the end

Before this update, 22% (estimation as it's sometimes hard to find all the creative way the model find to edit files) of the file editions where made using something else than a raw apply_patch

After this update, not a single edition without apply_patch was found

[EDIT]
I managed to have a few ["bash", "-lc", "apply_path"] when reaching < 10% context left

[michalkos]

Before it gets merged, I've added this to my ~/.codex/AGENTS.md file, and it works perfectly. Thanks a lot!