bypassPermissions mode still prompts for edits to ~/.claude/ files

Description

With claudeCode.initialPermissionMode set to "bypassPermissions" in VS Code User settings, edits to files under ~/.claude/ (e.g. ~/.claude/commands/*.md, ~/.claude/rules/*.md) still trigger the "Make this edit to [file]?" confirmation dialog.

Edits to files outside ~/.claude/ (e.g. project files under ~/Documents/) are correctly auto-approved — no prompt.

Expected behavior

bypassPermissions should bypass all permission checks, including edits to ~/.claude/ files. If this directory is intentionally protected, this should be documented, and ideally there should be a way to opt out.

Steps to reproduce

1. Set "claudeCode.initialPermissionMode": "bypassPermissions" in VS Code User settings.json
2. Open a Claude Code session in VS Code
3. Ask Claude to edit any file under ~/.claude/ (e.g. a custom command/skill file in ~/.claude/commands/)
4. Observe the "Make this edit?" confirmation dialog appears
5. Ask Claude to edit a file outside ~/.claude/ — no dialog appears

Environment

• Claude Code v2.1.81 (VS Code extension)
• macOS 15 (Darwin 25.3.0)
• VS Code (latest stable)