[BUG] Edit tool breaks hardlinks

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?

Already reported but closed due to inactivity https://github.com/anthropics/claude-code/issues/28376

This is a serious bug. I can't let claude-code modify anything that is a hardlink. There is no workaround.

What Should Happen?

Do not replace hardlinks, edit them in place.

Steps to Reproduce

1. Create a test file and hard link:

``bash
echo "line 1" > /tmp/source.md
echo "line 2" >> /tmp/source.md
cp -l /tmp/source.md /tmp/deployed.md
# Verify same inode:
stat /tmp/source.md /tmp/deployed.md
``

1. Open Claude Code in the directory containing source.md

1. Ask Claude: "Edit /tmp/source.md — replace 'line 1' with 'modified line 1'"

1. Claude uses the Edit tool. The edit succeeds.

1. Check the hard link:

```bash
stat /tmp/source.md /tmp/deployed.md
# source.md has a NEW inode number
# deployed.md has the OLD inode number
# They are no longer linked

cat /tmp/deployed.md
# Still shows "line 1" — old content
```

Claude Model

Opus

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.92 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

iTerm2

Additional Information

_No response_