[BUG] Worktree agents edit files in worktree path instead of main repo — changes silently lost

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?

When Claude Code operates in a git worktree (e.g. .claude/worktrees/optimistic-bhabha), file edits target the worktree copy rather than the main repository. If the user runs dotnet run (or any build/serve command) from the main repo, edits are silently ignored — no error, no warning.

Steps to reproduce:

Start a Claude Code session that creates a worktree (e.g. via EnterWorktree)
Edit a file — e.g. src/MyProject/Services/MyService.cs
The edit lands at .claude/worktrees/<name>/src/MyProject/Services/MyService.cs
User runs dotnet run from the main repo at C:\myproject\src\MyApp
Changes are not picked up — no error surfaced
Expected behavior: Either (a) edits should target the main repo when the user's dev server runs there, or (b) Claude Code should warn when it detects the user is running commands from a different path than where edits are being applied.

Impact: High — causes silent failures that are very difficult to diagnose. The user sees no errors but changes simply don't take effect, leading to wasted debugging cycles.

What Should Happen?

Expected behavior: Either (a) edits should target the main repo when the user's dev server runs there, or (b) Claude Code should warn when it detects the user is running commands from a different path than where edits are being applied.

Error Messages/Logs

Steps to Reproduce

Start a Claude Code session that creates a worktree (e.g. via EnterWorktree)
Edit a file — e.g. src/MyProject/Services/MyService.cs
The edit lands at .claude/worktrees/<name>/src/MyProject/Services/MyService.cs
User runs dotnet run from the main repo at C:\myproject\src\MyApp
Changes are not picked up — no error surfaced
Expected behavior: Either (a) edits should target the main repo when the user's dev server runs there, or (b) Claude Code should warn when it detects the user is running commands from a different path than where edits are being applied.

Claude Model

Not sure / Multiple models

Is this a regression?

Yes, this worked in a previous version

Last Working Version

Claude 1.1.6679 (f8f4ff) 2026-03-13T18:26:03.000Z

Claude Code Version

Claude 1.1.6679 (f8f4ff) 2026-03-13T18:26:03.000Z

Platform

Other

Operating System

Windows

Terminal/Shell

Other

Additional Information

Using Claude Code for Windows.