Bypass permissions mode still prompts for edits to ~/.claude/settings.json

Bug Description

When running Claude Code with --dangerously-skip-permissions, editing Claude's own config files (e.g. ~/.claude/settings.json) still triggers a permission prompt ("Do you want to make this edit to settings.json?").

This defeats the purpose of the flag — all file operations should be auto-approved in this mode.

Steps to Reproduce

1. Launch Claude Code with claude --dangerously-skip-permissions
2. Ask Claude to modify a setting (e.g. "set effortLevel to high in settings.json")
3. Claude reads ~/.claude/settings.json, then attempts to edit it
4. A permission prompt appears asking to confirm the edit

Expected Behavior

The edit should proceed automatically without prompting, since --dangerously-skip-permissions is active.

Actual Behavior

Claude shows the diff and asks "Do you want to make this edit to settings.json?" — same as normal permission mode.

Environment

• Claude Code v2.1.81
• Model: Opus 4.6 (1M context), Claude Max
• Platform: macOS (Darwin, ARM64)
• ~/.claude/settings.json already contains "skipDangerousModePermissionPrompt": true

Screenshot

<img width="1079" height="891" alt="Image" src="https://github.com/user-attachments/assets/4d454928-5b74-4717-827f-c39f90ec016e" />

(Screenshot shows the permission prompt appearing in bypass mode when editing settings.json)