[BUG] File reverts to previous content after pre-commit hook modifies it in-place

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

After Claude Code edits a file and commits it (where a pre-commit hook modifies the file in-place during the commit), Claude Code's internal view of the file reverts to the pre-edit content in subsequent turns. This causes Claude to repeatedly re-apply the same edits, believing they were never saved — even though the actual on-disk file and git history are correct.

What Should Happen?

After a successful commit, Claude Code's internal file state should reflect the committed on-disk content. If a pre-commit hook modifies a file during commit, the post-hook version should be what Claude sees in the next turn.

Error Messages/Logs

No explicit error is shown. The symptom appears as a system reminder in Claude's context:


Note: /path/to/aerospike.conf was modified, either by the user or by a linter.


This fires repeatedly with the old content, overriding what Claude just wrote. From Claude's perspective the file looks like the pre-edit version, while `git show HEAD -- aerospike.conf` and `md5` of the on-disk file both confirm the correct post-edit content was committed and is on disk.

Steps to Reproduce

1. Set up a repo with a pre-commit hook that modifies files in-place (e.g. trailing-whitespace from pre-commit-hooks v5.0.0)
2. Ask Claude Code to edit a non-Python config file (e.g. .conf)
3. Claude edits the file correctly
4. Claude attempts to commit — pre-commit hook fails on first try, modifies the file in-place, Claude re-stages and commits successfully
5. In the next turn, ask Claude to check the file contents
6. Claude reports the pre-edit content, not the committed version
7. Verify with git show HEAD -- <file> — committed content is correct
8. Verify with md5 <file> — on-disk file is correct
9. Only Claude Code's internal state is stale

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.85 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Environment

• OS: macOS 14 (Darwin 24.4.0)
• Pre-commit hooks: pre-commit-hooks v5.0.0 (trailing-whitespace, end-of-file-fixer)
• File type: .conf (non-Python, no ruff/mypy involvement)
• Claude Code model: claude-sonnet-4-6

Workaround

Have the user commit manually — Claude Code's stale state does not affect the actual on-disk file or git history.