Configured file permissions not being respected for ~/.claude/** paths

Describe the bug

Claude Code is prompting for permission when reading files under ~/.claude/ despite having explicit permission configured in settings.json.

Configuration

In .claude/settings.json:

{
  "permissions": {
    "Read:~/.claude/**": true
  }
}

Additionally, my ~/.claude/CLAUDE.md (global instructions) explicitly states:

- **Notes Files:** `~/.claude/NOTES.md` and `~/.claude/COMPLETED_NOTES.md` - Full read/write access, modify automatically without asking

Expected behavior

Claude should be able to read ~/.claude/NOTES.md without prompting for permission, as it matches the configured Read:~/.claude/** permission pattern.

Actual behavior

When Claude attempts to read ~/.claude/NOTES.md, the system still prompts the user for permission and returns this error when rejected:

The user doesn't want to proceed with this tool use. The tool use was rejected

Steps to reproduce

1. Configure "Read:~/.claude/**": true in .claude/settings.json
2. Ask Claude to read a file under ~/.claude/ (e.g., ~/.claude/NOTES.md)
3. Observe that permission is still requested despite the configuration

Environment

• Platform: macOS (Darwin 25.2.0)
• Claude Code version: v2.1.27

Impact

This breaks workflows that rely on Claude automatically managing notes/state files in ~/.claude/ without user intervention.