If you run a codex instance outside of the current working directory
from where you launched the codex binary it won't be able to apply
patches correctly, even if the sandbox policy allows it. This manifests
weird behaviours, such as
* Reading the same filename in the binary working directory, and
overwriting it in the session working directory. e.g. if you have a
`readme` in both folders it will overwrite the readme in the session
working directory with the readme in the binary working directory
*applied with the suggested patch*.
* The LLM ends up in weird loops trying to verify and debug why the
apply_patch won't work, and it can result in it applying patches by
manually writing python or javascript if it figures out that either is
supported by the system instead.
I added a test-case to ensure that the patch contents are based on the
cwd.
## Issue: mixing relative & absolute paths in apply_patch
1. The apply_patch tool use relative paths based on the session working
directory.
2. `unified_diff_from_chunks` eventually ends up [reading the source
file](https://github.com/reflectionai/codex/blob/main/codex-rs/apply-patch/src/lib.rs#L410)
to figure out what the diff is, by using the relative path.
3. The changes are targeted using an absolute path derived from the
current working directory.
The end-result in case session working directory differs from the binary
working directory: we get the diff for a file relative to the binary
working directory, and apply it on a file in the session working
directory.
84e01f4b62