[Bug] Auto-mode config tool corrupts permission settings

Bug Description
my permissions were all working fine in auto mode. After running the auto-mode config tool the settings are a mess, and half the permissions I need aren't available any more.
A couple of days ago Claude asked if it could run the auto-mode config tool to better optimize auto-mode to work on my environment. I allowed it to do this, but since then my agents have continuously been hitting a variety of permissions issues, which keeps stopping them from being able to achieve their objectives. I've run 'claude auto-mode critique' and updated my settings with much of its feedback, but I'm still getting issues that didn't exist before running the optimizer.

Environment Info

• Platform: win32
• Terminal: windows-terminal
• Version: 2.1.292
• Feedback ID: 674445b0-6b5c-4d6b-9f2e-4105ff0c666f