Desktop app always starts sessions in "Accept Edits" mode instead of "Bypass Permissions", even though defaultMode: "bypassPermissions" is set in ~/.claude/settings.json

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Desktop app always starts sessions in "Accept Edits" mode instead of "Bypass Permissions", even though defaultMode: "bypassPermissions" is configured in ~/.claude/settings.json

What Should Happen?

Sessions should start in Bypass Permissions mode as configured in settings.json

Error Messages/Logs

Warning: "Bypass Permissions mode isn't enabled. The session started in Accept Edits"
"Permission mode couldn't be changed. You can try again."

Steps to Reproduce

1. Set ~/.claude/settings.json with "permissions": { "defaultMode": "bypassPermissions" }
2. Enable "Allow bypass permissions mode" in Desktop Settings
3. Run CLI with --dangerously-skip-permissions and accept
4. Open desktop app → start new session
5. Send any message

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.146

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

CLI works correctly — shows "bypass permissions on".
Desktop GUI ignores the same settings.json.
Mode reverts to "Accept Edits" after sending first message even if manually switched.
skipDangerousModePermissionPrompt: true is also set.