[BUG] Claude Opus 4.8 makes changes outside the current worktree for the current session

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 using worktree mode with Claude Opus 4.8 in Claude Code MacOS desktop app (latest version - Claude 1.9659.2 (390d6c) 2026-05-28T21:50:01.000Z) it starts making changes outside the current worktree e.g. it tries to make changes in default worktree where default/primary branch is checked-out.

What Should Happen?

Claude should make changes in current worktree only

Error Messages/Logs

Reply from Claude: You're right — my edits were landing in the main repo (/myApp/app/...), not this worktree (.../.claude/worktrees/silly-austin-4ced74/app/...). The Explore agents reported main-repo paths and I followed them blindly. Let me undo the stray file in main and redo everything in the worktree.

Steps to Reproduce

1. Start a session with worktree option checked/selected.
2. Use plan mode to create a plan.
3. Accept plan. <-- its very likely that the plan mode is confusing claude with paths that refer to main repo not current worktree
4. Claude starts making changes in main repo outside current worktree.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

Claude 1.9659.2 (390d6c) 2026-05-28T21:50:01.000Z

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

N/A