[BUG] Synchronization problem between worktrees and main repository.

[AlessandroBorges]

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?

I was working with git worktrees. Claude got confused about which version of the files was in each location. Multiple attempts to apply the same fixes. System-reminders showing different versions of the files. Commits were created but the changes weren't actually applied where expected.

What Should Happen?

Claude should track the changes and copy files FROM worktree/Claude's branch AND copy TO users local repository.

Error Messages/Logs

Steps to Reproduce

1. just use a github project
2. attempt a fix
3. see the mess Claude Code does.

Claude Model

Sonnet (default)

Is this a regression?

No, this never worked

Last Working Version

No response

Claude Code Version

2.0.53

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Other

Additional Information

Running Claude Code from within Claude Desktop.

Claude-logs-2025-12-03T02-02-28-651Z.zip