[FEATURE] Allow opt-out of .claude/ protected directory prompts via settings.json

Preflight Checklist

• [x] I have searched existing requests and this feature hasn't been requested yet
• [x] This is a single feature request (not multiple features)

Problem Statement

Problem

Since v2.1.78, all Edit/Write operations to files under .claude/ trigger a permission prompt,
even with bypassPermissions mode, --dangerously-skip-permissions, or explicit allow rules like
Edit(.claude/**) in settings.json. The protected directory gate is evaluated before the
permission allow rules, making it impossible to opt out via configuration.

Impact

Workflows that heavily edit .claude/ files (skills, hooks, MCP servers, scripts) are constantly
interrupted by prompts. In my project, ~35% of all edits target .claude/ — every single one
prompts.

Tested on v2.1.81 (Windows 11, CLI):

• Edit on Software/*.py → no prompt ✓
• Edit on .claude/server.py → prompt ✗
• Adding Edit(.claude/**) to user settings.json allow rules → still prompts ✗
• --dangerously-skip-permissions → still prompts (confirmed by #35718) ✗

This also appears to cause issues with worktree operations that need to read/write .claude/ state.

Proposed Solution

Add a protectedDirectories override in settings.json (user-level):

{
  "protectedDirectories": {
    "exempt": [".claude/"]
  }
}


### Alternative Solutions

_No response_

### Priority

High - Significant impact on productivity

### Feature Category

File operations

### Use Case Example

 I maintain custom MCP servers, hooks, and skills under `.claude/` that I edit frequently (~35% of all edits in my project). Since v2.1.78, every Edit/Write to any `.claude/` file triggers a permission prompt — even with `--dangerously-skip-permissions`, `bypassPermissions` mode, or explicit `Edit(.claude/**)` allow rules in settings.json. I need a way to opt out of protected directory prompts via configuration, e.g. a `protectedDirectories` override in settings.json.

### Additional Context

Context
v2.1.78 changelog: "Fixed .git, .claude protected directories being writable without prompt
in bypassPermissions mode" — this is the change that introduced the current behavior
.claude/skills/ is documented as exempt but isn't (#37157)
The protection makes sense as a default, but power users who manage their own .claude/ files
(custom MCP servers, hooks, skills) need an escape hatch
Related Issues
#35718 — --dangerously-skip-permissions does not bypass .claude/ prompts
#37157 — .claude/skills/ not exempt despite documentation
#36168 — Bypass permissions broken in versions > v2.1.77
#36219 — VS Code Edit prompts despite bypassPermissions
Environment
Claude Code v2.1.81
Windows 11, CLI
User settings.json with "Edit" and "Write" in allow list