[BUG] Permission Bypass Functionality Breaks When Adding ignorePatterns to Global Settings

Environment

• Platform (select one):
• [x] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 1.0.55 (Claude Code)
• Operating System: Darwin 24.5.0 (macOS)
• Terminal: Claude Code

Bug Description

The permission bypass functionality ("defaultMode": "bypassPermissions") completely stops working when ignorePatterns is added to the global settings file (~/.claude/settings.json). This affects both the visual indicator and the actual permission bypass functionality.

Steps to Reproduce

1. Start with a clean global settings file (~/.claude/settings.json) containing only:

``json
{
"permissions": {
"allow": ["*"],
"deny": [],
"defaultMode": "bypassPermissions"
},
"includeCoAuthoredBy": false,
"enableAllProjectMcpServers": true
}
``

1. Verify that:

• "Bypassing Permissions" appears in the bottom-right status bar
• Claude can access files outside the project directory without permission prompts

1. Add ignorePatterns to the global settings:

``json
{
"permissions": {
"allow": ["*"],
"deny": [],
"defaultMode": "bypassPermissions"
},
"includeCoAuthoredBy": false,
"enableAllProjectMcpServers": true,
"ignorePatterns": [
"*.bak",
"*.tmp",
"cscope.out"
]
}
``

1. Restart Claude Code or wait for configuration reload

Expected Behavior

• The permission bypass functionality should continue to work regardless of other configuration options
• The "Bypassing Permissions" status indicator should remain visible
• Claude should be able to access files outside the project directory without permission prompts

Actual Behavior

• The "Bypassing Permissions" status indicator disappears from the status bar
• The permission bypass functionality stops working entirely
• Claude can no longer access files outside the project directory without explicit permissions
• File operations that previously worked are now blocked

Additional Context

• Severity: HIGH - Core functionality is broken
• This is not just a visual bug - the actual permission bypass functionality is disabled
• The issue is reproducible and reversible - removing ignorePatterns from the global settings restores both the status display and functionality
• This forces users to choose between using global ignore patterns and having permission bypass functionality
• Workaround: The only current workaround is to avoid using ignorePatterns in the global settings file, which severely limits the ability to configure Claude Code for optimal performance
• Impact:
• High: Core permission bypass functionality is broken
• Forces users to choose between essential features
• Significantly impacts user workflow and Claude Code's usability