bypassPermissions mode not working in Claude Code Desktop (Windows), works in CLI

Bug Description

When setting permissions.defaultMode to "bypassPermissions" in ~/.claude/settings.json, the setting takes effect in the CLI but does NOT take effect in the Claude Code Desktop app.

Environment

• OS: Windows
• Claude Code Version: 2.1.150
• App: Claude Code Desktop

Steps to Reproduce

1. Open ~/.claude/settings.json and add:

``json
{
"permissions": {
"defaultMode": "bypassPermissions"
}
}
``

1. Also add the same setting to ~/.claude/settings.local.json
2. Fully quit Claude Code Desktop (including system tray)
3. Restart Claude Code Desktop and open a new conversation
4. Try to execute a Bash command or write to .claude/ directory

Expected Behavior

All permission prompts should be skipped (bypassPermissions mode).

Actual Behavior

The session still starts in "Accept Edits" mode. Error message appears:

"Bypass Permissions mode isn't enabled. The session started in Accept Edits — enable Bypass Permissions in Settings to use it."

Verification

• CLI with claude --dangerously-skip-permissions: Works correctly ✅
• Desktop app with defaultMode: "bypassPermissions": Does not work ❌

Troubleshooting Already Done

• Verified no managed settings (registry HKLM\SOFTWARE\Policies\ClaudeCode — does not exist)
• Verified no managed-settings.json in C:\Program Files\ClaudeCode\
• Verified tengu_disable_bypass_permissions_mode is false in .claude.json
• Tried both settings.json and settings.local.json
• Full restart including system tray / computer reboot
• No project-level settings overriding the user-level config

Suspected Cause

Claude Code Desktop may not properly read or apply the defaultMode: "bypassPermissions" setting at session start, while the CLI handles it correctly.