[Bug] File operations write to repo root instead of worktree directory

Bug Description
I have claude running in a worktree (~/projects/bild/estimator/.conductor/minsk) but it just wrote files to the repo root (~/projects/bild/estimator/supabase/migrations/20260203000003_add_project_uploads_rls.sql)

Environment Info

• Platform: darwin
• Terminal: cursor
• Version: 2.1.30
• Feedback ID: babe9770-e558-447a-a423-17f8d1086e4e

<img width="779" height="131" alt="Image" src="https://github.com/user-attachments/assets/31946854-c658-418a-a143-7d3b48265ab7" />

<img width="764" height="146" alt="Image" src="https://github.com/user-attachments/assets/a670c63e-d068-4a66-bd71-9935d4a126c2" />

Errors

[{"error":"Error: ENOENT: no such file or directory, open '/Users/owenboyd/.claude/remote-settings.json'\n    at openSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:947)\n    at i5 (/$bunfs/root/claude:11:40709)\n    at readSync (/$bunfs/root/claude:12:875)\n    at a5 (/$bunfs/root/claude:6083:113)\n    at oG (/$bunfs/root/claude:6085:226)\n    at BdR (/$bunfs/root/claude:121:25774)\n    at DdR (/$bunfs/root/claude:121:25937)\n    at N_ (/$bunfs/root/claude:121:27674)\n    at Ms0 (/$bunfs/root/claude:122:1170)","timestamp":"2026-02-03T20:12:32.461Z"},{"error":"Error: Request was aborted.\n    at makeRequest (/$bunfs/root/claude:361:3940)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-03T21:10:14.911Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at readFileSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:742)\n    at i5 (/$bunfs/root/claude:11:40709)\n    at readFileSync (/$bunfs/root/claude:12:701)\n    at swB (/$bunfs/root/claude:6080:17689)\n    at call (/$bunfs/root/claude:3545:2360)\n    at call (/$bunfs/root/claude:3541:8808)\n    at <anonymous> (/$bunfs/root/claude:3557:1608)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-03T23:34:37.335Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at readFileSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:742)\n    at i5 (/$bunfs/root/claude:11:40709)\n    at readFileSync (/$bunfs/root/claude:12:701)\n    at swB (/$bunfs/root/claude:6080:17689)\n    at call (/$bunfs/root/claude:3545:2360)\n    at call (/$bunfs/root/claude:3541:8808)\n    at <anonymous> (/$bunfs/root/claude:3557:1608)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-02-03T23:34:59.000Z"}]