[Bug] Permanent folder deletion without user confirmation

Bug Description
Claude Code dangerously deleted a folder permanently without me asking to. thankfully i had a backup folder, but it is really risky. it shouldn't delete permanently without asking first.

Environment Info

• Platform: win32
• Terminal: null
• Version: 2.0.60
• Feedback ID: b1d368d7-097f-4761-b453-610818c31149

Errors

[{"error":"Error: EISDIR: illegal operation on a directory, read\n    at readFileSync (unknown)\n    at readFileSync (B:/~BUN/root/claude.exe:12:370)\n    at OiI (B:/~BUN/root/claude.exe:4487:17669)\n    at call (B:/~BUN/root/claude.exe:1401:912)\n    at call (B:/~BUN/root/claude.exe:1397:5711)\n    at <anonymous> (B:/~BUN/root/claude.exe:1613:1513)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-12-09T14:59:39.226Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at readFileSync (unknown)\n    at readFileSync (B:/~BUN/root/claude.exe:12:370)\n    at OiI (B:/~BUN/root/claude.exe:4487:17669)\n    at call (B:/~BUN/root/claude.exe:1401:912)\n    at call (B:/~BUN/root/claude.exe:1397:5711)\n    at <anonymous> (B:/~BUN/root/claude.exe:1613:1513)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-12-09T14:59:59.428Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at readFileSync (unknown)\n    at readFileSync (B:/~BUN/root/claude.exe:12:370)\n    at OiI (B:/~BUN/root/claude.exe:4487:17669)\n    at call (B:/~BUN/root/claude.exe:1401:912)\n    at call (B:/~BUN/root/claude.exe:1397:5711)\n    at <anonymous> (B:/~BUN/root/claude.exe:1613:1513)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-12-09T15:00:15.589Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at readFileSync (unknown)\n    at readFileSync (B:/~BUN/root/claude.exe:12:370)\n    at OiI (B:/~BUN/root/claude.exe:4487:17669)\n    at call (B:/~BUN/root/claude.exe:1401:912)\n    at call (B:/~BUN/root/claude.exe:1397:5711)\n    at <anonymous> (B:/~BUN/root/claude.exe:1613:1513)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-12-09T15:00:49.369Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at readFileSync (unknown)\n    at readFileSync (B:/~BUN/root/claude.exe:12:370)\n    at OiI (B:/~BUN/root/claude.exe:4487:17669)\n    at call (B:/~BUN/root/claude.exe:1401:912)\n    at call (B:/~BUN/root/claude.exe:1397:5711)\n    at <anonymous> (B:/~BUN/root/claude.exe:1613:1513)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-12-09T15:01:28.451Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at readFileSync (unknown)\n    at readFileSync (B:/~BUN/root/claude.exe:12:370)\n    at OiI (B:/~BUN/root/claude.exe:4487:17669)\n    at call (B:/~BUN/root/claude.exe:1401:912)\n    at call (B:/~BUN/root/claude.exe:1397:5711)\n    at <anonymous> (B:/~BUN/root/claude.exe:1613:1513)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-12-09T15:01:31.077Z"}]