[Bug] Auto-update creates duplicate npm installation in ~/.claude/ with native installation

Bug Description
"Auto-update creates ~/.claude/local npm installation even when using native
installation, causing 'multiple installations found' warning after every update."

Environment Info

• Platform: linux
• Terminal: vte-based
• Version: 2.1.19
• Feedback ID: beec233a-c9a8-40cd-a08f-43e50eab3206

Errors

[{"error":"Error: ENOENT: no such file or directory, scandir '/etc/claude-code/.claude/skills'\n    at readdirSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:1903)\n    at pJ (/$bunfs/root/claude:11:35427)\n    at readdirSync (/$bunfs/root/claude:12:1864)\n    at XY$ (/$bunfs/root/claude:2213:380)\n    at XY$ (/$bunfs/root/claude:2213:1350)\n    at <anonymous> (/$bunfs/root/claude:2213:4440)\n    at <anonymous> (/$bunfs/root/claude:2213:5171)\n    at A (/$bunfs/root/claude:11:7251)\n    at Z71 (/$bunfs/root/claude:4860:4342)","timestamp":"2026-01-26T15:57:37.627Z"},{"error":"Error: ENOENT: no such file or directory, scandir '/home/itay-sadovnik/.claude/skills'\n    at readdirSync (unknown)\n    at <anonymous> (/$bunfs/root/claude:12:1903)\n    at pJ (/$bunfs/root/claude:11:35427)\n    at readdirSync (/$bunfs/root/claude:12:1864)\n    at XY$ (/$bunfs/root/claude:2213:380)\n    at XY$ (/$bunfs/root/claude:2213:1350)\n    at <anonymous> (/$bunfs/root/claude:2213:4483)\n    at <anonymous> (/$bunfs/root/claude:2213:5171)\n    at A (/$bunfs/root/claude:11:7251)\n    at Z71 (/$bunfs/root/claude:4860:4342)","timestamp":"2026-01-26T15:57:37.627Z"},{"error":"Error: NON-FATAL: Lock acquisition failed for /home/itay-sadovnik/.local/share/claude/versions/2.1.19 (expected in multi-process scenarios)\n    at $N$ (/$bunfs/root/claude:4001:2091)\n    at VjA (/$bunfs/root/claude:4001:1202)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-01-26T15:57:37.666Z"}]