[BUG] Global settings seem to be getting ignored when doing simple commands like running ls in bash

Environment

• Platform (select one):
• [ ] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: <!-- output of claude --version --> 1.0.17
• Operating System: <!-- e.g. macOS 14.3, Windows 11, Ubuntu 22.04 --> macOS
• Terminal: <!-- e.g. iTerm2, Terminal App --> iTerm2 through vs code

Bug Description

<!-- A clear and concise description of the bug -->

Steps to Reproduce

1. <!-- First step --> create settings.json in ~/.claude/settings.json
2. <!-- Second step --> try running a claude terminal (using vs code for me) and running ls
3. <!-- And so on... -->

Expected Behavior

<!-- What you expected to happen --> it shouldnt ask for permissions

Actual Behavior

<!-- What actually happened --> it asks for permissions, and also acknowledges that it has a bug

Additional Context

<!-- Add any other context about the problem here, such as screenshots, logs, etc. -->