Thanks for the info! This is a known bug with file handling that is already being tracked.
Even in “Run Everything (Unsandboxed)” mode, Cursor asks for confirmation for every file - this is due to incorrect file path handling, especially in worktrees.
Quick checks:
- Are you using git worktrees?
- Open Help → Toggle Developer Tools → Console and share any errors
- Try disabling all protections: Cursor Settings > Agents > Auto-Run > turn off External-File Protection and Dotfile Protection
Related bug here: Cursor 2.0 Agent in Git Worktree asks to write to every file inside the worktree - same issue.
The team is already working on a fix. Please share your test results and console logs.