## Summary
We've experienced a bit of drift in system prompting for `apply_patch`:
- As pointed out in #2030 , our prettier formatting started altering
prompt.md in a few ways
- We introduced a separate markdown file for apply_patch instructions in
#993, but currently duplicate them in the prompt.md file
- We added a first-class apply_patch tool in #2303, which has yet
another definition
This PR starts to consolidate our logic in a few ways:
- We now only use
`apply_patch_tool_instructions.md](https://github.com/openai/codex/compare/dh--apply-patch-tool-definition?expand=1#diff-d4fffee5f85cb1975d3f66143a379e6c329de40c83ed5bf03ffd3829df985bea)
for system instructions
- We no longer include apply_patch system instructions if the tool is
specified
I'm leaving the definition in openai_tools.rs as duplicated text for now
because we're going to be iterated on the first-class tool soon.
## Testing
- [x] Added integration tests to verify prompt stability
- [x] Tested locally with several different models (gpt-5, gpt-oss,
o4-mini)
As explained in detail in the doc comment for `ParseMode::Lenient`, we
have observed that GPT-4.1 does not always generate a valid invocation
of `apply_patch`. Fortunately, the error is predictable, so we introduce
some new logic to the `codex-apply-patch` crate to recover from this
error.
Because we would like to avoid this becoming a de facto standard (as it
would be incompatible if `apply_patch` were provided as an actual
executable, unless we also introduced the lenient behavior in the
executable, as well), we require passing `ParseMode::Lenient` to
`parse_patch_text()` to make it clear that the caller is opting into
supporting this special case.
Note the analogous change to the TypeScript CLI was
https://github.com/openai/codex/pull/930. In addition to changing the
accepted input to `apply_patch`, it also introduced additional
instructions for the model, which we include in this PR.
Note that `apply-patch` does not depend on either `regex` or
`regex-lite`, so some of the checks are slightly more verbose to avoid
introducing this dependency.
That said, this PR does not leverage the existing
`extract_heredoc_body_from_apply_patch_command()`, which depends on
`tree-sitter` and `tree-sitter-bash`:
5a5aa89914/codex-rs/apply-patch/src/lib.rs (L191-L246)
though perhaps it should.
