[Bug] Auto mode bypasses explicit `ask` permissions configured by user

Bug Description

Auto mode is useful, but it's buggy. Auto mode should: automatically decide permissions for most things. Auto mode should not bypass ask permissions rules. Any time permissions are explicitly configured by the user, they should be respected, and no model should be permitted to bypass them.

While there's a lot to like about auto mode, I was dismayed to switch to the tab where Claude Code was running and find out that it had silently run commands (such as git add or git commit) for which I had explicitly configured ask permissions. The fact that I've explicitly configured the permissions means that I want them to be followed. Auto mode should only apply when the user has not explicitly configured permissions.

I realize that some permissions get set inadvertently due to the way permissions prompts work. But the prompts never set ask permissions so in that case the only way for that permission to get set is that the user explicitly set it.

Environment Info

• Platform: win32
• Terminal: windows-terminal
• Version: 2.1.116
• Feedback ID: c1673bcf-dc6d-40c8-b506-4e3cdb2a4cee