Environment

• Platform (select one):
  • Other: Claude Code on macOS with VS Code
• Claude CLI version: 1.0.68 (Claude Code)
• Operating System: macOS Darwin 23.6.0
• Terminal: Terminal App

Bug Description

User-level permissions in ~/.claude/settings.json are not being enforced
during command execution, even though they appear as loaded in the
/permissions command. The same permissions work correctly when placed in
project-level .settings.local.json but fail when moved to user-level
settings.

Steps to Reproduce

1. Copy working permissions from a project's .settings.local.json to
   user-level ~/.claude/settings.json:
   {
   "permissions": {
   "allow": [
   "mix:",
   "mcp__serena__",
   "mcp__context7__",
   "Bash(ls:)",
   "Bash(find:)",
   "Bash(grep:)",
   "Bash(sqlite3:)",
   "Bash(mkdir:)",
   "Bash(cp:)",
   "Bash(mv:)",
   "Bash(git add:)",
   "Bash(git push:)",
   "Bash(git checkout:)",
   "Bash(git stash show:)",
   "Bash(git stash pop:)",
   "Bash(git fetch:)",
   "Bash(git stash push:)",
   "Bash(git merge:)",
   "Bash(git cherry-pick:)",
   "Bash(python:)",
   "Bash(python3 -m pip install:)",
   "Bash(npm install:)",
   "Bash(npx playwright test:*)"
   ]
   }
   }
2. Open a project in VS Code with Claude Code
3. Run /permissions - it correctly shows all permissions as loaded
4. Try to run any allowed command (e.g., mix --version)
5. Claude Code still asks for permission despite the command being in the
   allow list

Expected Behavior

• I want a way to allow the mcp of serena to execute all its commands without asking for explicit permission each time.
• Commands in the user-level allow list should execute without requiring
  approval
• User-level permissions should work identically to project-level
  permissions
• If /permissions shows a command as allowed, it should not require
  approval

Actual Behavior

• All commands require manual approval even when listed in user-level
  permissions
• /permissions command shows the permissions as loaded but they are not
  enforced
• The exact same permissions work when placed in project
  .settings.local.json but not in ~/.claude/settings.json
• MCP wildcard permissions (e.g., mcp__serena__*) also don't work at the
  user level

Additional Context

• These permissions were originally auto-generated by Claude Code (not
  manually written) - I just copied them from .settings.local.json to the user-level settings.json
• This significantly impacts workflow as every command requires manual
  approval across all projects