[Bug] Claude Code deletes files without proper conflict resolution confirmation

Bug Description
it's so awful at git

it asked me if I wanted to do a git stash bc of a conflict in cwd, I told him he could delete it since we're workign on a copy elsewhwere and he goes ahead and deletes the file elsewhere instead of cwd

this is like the 5th git disaster today

Environment Info

• Platform: darwin
• Terminal: ghostty
• Version: 2.1.19
• Feedback ID: 224cb8a6-d566-4820-8b79-aa98d711e1af

Errors

[{"error":"Error: ENOENT: no such file or directory, scandir '/Library/Application Support/ClaudeCode/.claude/skills'\n    at readdirSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:1903)\n    at mW (/$bunfs/root/claude:11:35435)\n    at readdirSync (/$bunfs/root/claude:12:1864)\n    at ILR (/$bunfs/root/claude:2215:380)\n    at ILR (/$bunfs/root/claude:2215:1350)\n    at <anonymous> (/$bunfs/root/claude:2215:4440)\n    at <anonymous> (/$bunfs/root/claude:2215:5171)\n    at A (/$bunfs/root/claude:11:7259)\n    at FZ8 (/$bunfs/root/claude:4862:4342)","timestamp":"2026-01-24T06:34:35.060Z"},{"error":"Error: ENOENT: no such file or directory, scandir '/Users/jaamesd/.claude/skills'\n    at readdirSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:1903)\n    at mW (/$bunfs/root/claude:11:35435)\n    at readdirSync (/$bunfs/root/claude:12:1864)\n    at ILR (/$bunfs/root/claude:2215:380)\n    at ILR (/$bunfs/root/claude:2215:1350)\n    at <anonymous> (/$bunfs/root/claude:2215:4483)\n    at <anonymous> (/$bunfs/root/claude:2215:5171)\n    at A (/$bunfs/root/claude:11:7259)\n    at FZ8 (/$bunfs/root/claude:4862:4342)","timestamp":"2026-01-24T06:34:35.060Z"},{"error":"Error: ENOENT: no such file or directory, scandir '/Library/Application Support/ClaudeCode/.claude/skills'\n    at readdirSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:1903)\n    at mW (/$bunfs/root/claude:11:35435)\n    at readdirSync (/$bunfs/root/claude:12:1864)\n    at ILR (/$bunfs/root/claude:2215:380)\n    at ILR (/$bunfs/root/claude:2215:1350)\n    at <anonymous> (/$bunfs/root/claude:2215:4440)\n    at <anonymous> (/$bunfs/root/claude:2215:5171)\n    at A (/$bunfs/root/claude:11:7259)\n    at FZ8 (/$bunfs/root/claude:4862:4342)","timestamp":"2026-01-24T06:34:36.690Z"},{"error":"Error: ENOENT: no such file or directory, scandir '/Users/jaamesd/.claude/skills'\n    at readdirSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:1903)\n    at mW (/$bunfs/root/claude:11:35435)\n    at readdirSync (/$bunfs/root/claude:12:1864)\n    at ILR (/$bunfs/root/claude:2215:380)\n    at ILR (/$bunfs/root/claude:2215:1350)\n    at <anonymous> (/$bunfs/root/claude:2215:4483)\n    at <anonymous> (/$bunfs/root/claude:2215:5171)\n    at A (/$bunfs/root/claude:11:7259)\n    at FZ8 (/$bunfs/root/claude:4862:4342)","timestamp":"2026-01-24T06:34:36.690Z"},{"error":"Error: ENOENT: no such file or directory, scandir '/Library/Application Support/ClaudeCode/.claude/skills'\n    at readdirSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:1903)\n    at mW (/$bunfs/root/claude:11:35435)\n    at readdirSync (/$bunfs/root/claude:12:1864)\n    at ILR (/$bunfs/root/claude:2215:380)\n    at ILR (/$bunfs/root/claude:2215:1350)\n    at <anonymous> (/$bunfs/root/claude:2215:4440)\n    at <anonymous> (/$bunfs/root/claude:2215:5171)\n    at A (/$bunfs/root/claude:11:7259)\n    at FZ8 (/$bunfs/root/claude:4862:4342)","timestamp":"2026-01-24T09:21:27.814Z"},{"error":"Error: ENOENT: no such file or directory, scandir '/Users/jaamesd/.claude/skills'\n    at readdirSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:1903)\n    at mW (/$bunfs/root/claude:11:35435)\n    at readdirSync (/$bunfs/root/claude:12:1864)\n    at ILR (/$bunfs/root/claude:2215:380)\n    at ILR (/$bunfs/root/claude:2215:1350)\n    at <anonymous> (/$bunfs/root/claude:2215:4483)\n    at <anonymous> (/$bunfs/root/claude:2215:5171)\n    at A (/$bunfs/root/claude:11:7259)\n    at FZ8 (/$bunfs/root/claude:4862:4342)","timestamp":"2026-01-24T09:21:27.814Z"},{"error":"Error: Request was aborted.\n    at makeRequest (/$bunfs/root/claude:161:3940)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-01-24T10:12:56.424Z"},{"error":"Error: Request was aborted.\n    at makeRequest (/$bunfs/root/claude:161:3940)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-01-24T10:15:48.995Z"},{"error":"Error: Request was aborted.\n    at xs (/$bunfs/root/claude:5156:3626)\n    at async <anonymous> (/$bunfs/root/claude:5158:10656)\n    at async RWA (/$bunfs/root/claude:961:17573)\n    at async h2 (/$bunfs/root/claude:5158:…

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