[BUG] permissions from user settings.json is NOT applied at project level

[siraj-samsudeen]

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

[github-actions]

Found 3 possible duplicate issues:

1. [BUG] Config file (~/.claude/settings.json) ignored - Global Deny Commands #4365
2. [BUG] Global settings seem to be getting ignored when doing simple commands like running ls in bash #1820
3. gh api permission not working despite being in settings.json #5112

If your issue is a duplicate, please close it and 👍 the existing issue instead.

🤖 Generated with Claude Code

[wangkanai]

This permissions issue may be related to #5314 - PostToolUse hooks not triggering for Edit operations on .cs files.

The problem in #5314 involves hooks configured in .claude/settings.json not being executed despite proper syntax and verbose mode being enabled. If permissions from user settings.json are not being applied at the project level as described in this issue, it could explain why PostToolUse hooks fail to execute.

Our hook configuration includes:

{
  "enableAllProjectMcpServers": true,
  "verbose": true,
  "hooks": {
    "PostToolUse": [...]
  }
}

If the settings.json configuration isn't being properly applied at the project level, the hook system might not be receiving the configuration needed to execute hooks after Edit/MultiEdit/Write operations.

[Sergiodelahoz]

I'm having the same issue! in MacOS, using claude code, user/.claude/settings.json allow list and deny list commands are completely ignored. It is a bit annoying to deal with this.

[tonydehnke]

Same here on MacOS. Would love a real fix.