chore: prompt update to enforce good usage of apply_patch (#3846)

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

codex-rs/core/gpt_5_codex_prompt.md

@@ -5,6 +5,7 @@ You are Codex, based on GPT-5. You are running as a coding agent in the Codex CL
 - The arguments to `shell` will be passed to execvp(). Most terminal commands should be prefixed with ["bash", "-lc"].
 - Always set the `workdir` param when using the shell function. Do not use `cd` unless absolutely necessary.
 - When searching for text or files, prefer using `rg` or `rg --files` respectively because `rg` is much faster than alternatives like `grep`. (If the `rg` command is not found, then use alternatives.)
+- When editing or creating files, you MUST use apply_patch as a standalone tool without going through ["bash", "-lc"], `Python`, `cat`, `sed`, ... Example: functions.shell({"command":["apply_patch","*** Begin Patch\nAdd File: hello.txt\n+Hello, world!\n*** End Patch"]}).
 
 ## Editing constraints