Codex CLI tends to add and remove blank lines when patching files

[pmetzger]

What version of Codex CLI is running?

codex-cli 0.128.0

What subscription do you have?

Pro

Which model were you using?

GPT 5.5

What platform is your computer?

No response

What terminal emulator and version are you using (if applicable)?

Terminal.app

What issue are you seeing?

Whatever patch tool is being used by Codex when rewriting files has a habit of adding or removing blank lines at the ends of files, seemingly at random. I've gotten to the point where my prompts and AGENTS files repeatedly say things like "double check that you don't modify blank lines at the ends of files". I suspect this is a bug in the tool the agent is using and not in the main part of the agent itself, but that's a guess.

What steps can reproduce the bug?

Modify a lot of files, look at the diffs, notice that blank lines get removed or sometimes added to the ends of files without much rhyme or reason.

What is the expected behavior?

No response

Additional information

No response

[etraut-openai]

If you have a repro, please use /feedback to upload the logs and session details and then post the session ID here.

[pmetzger]

FYI: This is a comment the agent makes over and over again to me in various forms:

apply_patch is not preserving trailing empty lines at EOF, so I’m using a
narrow mechanical Perl rewrite to restore the exact trailing-newline counts
from HEAD for the affected files. This is only for EOF whitespace restoration.

I presume apply_patch is a tool. I'd see what it does to empty lines at EOF; maybe it simply is a mechanical problem. Removal is far more frequent in my experience than addition.

[pmetzger]

@etraut-openai It's session ID 019df459-19b3-7c41-8ecc-13dd9b9fb48b

[pmetzger]

FWIW, it may be that I'm mistaken and that it's only removing blank lines at the end as a result of apply_patch and that problems with adding them back are caused by it fighting apply_patch; the underlying problem may very well just be an issue with apply_patch.