[Bug] Bypass all permissions setting not respected during operations

**Bug Description**
I am on bypass all permissions and still on every single step or edit, Claude is asking me for permissions. Please fix this bug zI am bypassing all permissions, yet Claude still asks for permissions at every step or edit. Please fix this bug.

**Environment Info**
- Platform: darwin
- Terminal: ghostty
- Version: 2.1.263
- Feedback ID: bdc8fd7e-69e5-4fb6-9147-ffc6238765f1

**Errors**
```json
[]
```

No files, tests, or entry points are identified. First reproduce on darwin in Ghostty with Claude Code 2.1.263 and the bypass-all-permissions setting, then trace the permission checks reached during an operation or edit. Done means that setting consistently prevents permission prompts while the reported workflow is exercised.

索引モデルが issue の本文から書いたものです。