[BUG] Default worktree location inside repo causes major problems for react-native and other projects

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?

The core issue: EnterWorktree defaults to .claude/worktrees/<name> inside the repo, which creates a full duplicate of the project tree nested within itself. For any project with native tooling (React Native, iOS/Android builds, CocoaPods, Gradle), this causes silent, hard-to-diagnose build failures because:

Xcode can pick up duplicate source files or podspec references from the nested copy
CocoaPods resolves paths relative to the project root and may find the wrong Podfile
Watchman/Metro scans the entire tree and can serve files from the wrong location
Yoga/shadow view measurement (in your case) returned zero height for a native picker, likely because the build referenced the wrong copy of native module sources
The fact that it took hours of investigation to trace a "picker shows no content" bug back to the worktree nesting — and the fix was simply building from the main repo — shows how insidious this is.

The default .claude/worktrees/ location inside the repo is unsafe for projects with native build tooling.

My specific symptom: UIDatePicker countdown spinner invisible due to native module build confusion from nested duplicate project tree

What Should Happen?

A better default would be a sibling directory (e.g., ../<repo>-worktrees/<name>) or ~/.claude/worktrees/<repo>/<name>

Error Messages/Logs

Steps to Reproduce

1. This would be almost impossible to reproduce IMO without my specific setup, as it is a very edge situation.

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.49 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

iTerm2

Additional Information

Using Claude Code desktop app.
I'm pretty sure previous versions of Claude Code created worktrees in ~/.claude by default. Not sure exactly which versions. That is a better default for this type of project.