[BUG] Claude Code Desktop version forcing worktree usage with latest version

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 I was asked to relaunch Claude Code this morning to update to the latest version my repo had several issues. Apparantly the new version forces the user into worktrees instead of being able to work in main repo. The app couldn't find my database in the code except for an empty one and then told me the only thing it could do is restore from a commit from 2 days ago. I would have had to redo 2 days of work if I didn't realize what was going on. Now that Claude knows what's going on it was able to find my latest repo copy but is saying I have no choice but to use worktrees unless I want to use CLI. I'm the only user of this repo and I'm building a small app. You need to let me work from the Desktop app in main repo like the app used to do. I'm not a power user who knows how to consistently use CLI. The whole reason I moved from Codex to Claude Code is because the Desktop app works better. Can this be changed so I can opt out of this in my settings?

What Should Happen?

Let me work from the Desktop Claude Code app in my main repo and not forced into a worktree.

Error Messages/Logs

Steps to Reproduce

Login and try accessing your main repo and you can't.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.80

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

_No response_