Permissions reset on every Copilot CLI startup

[titan-ron]

Describe the bug

The permissions.allow configuration in ~/.copilot/config.json is being reset/cleared every time Copilot CLI starts.

Affected version

0.0.384 Commit: 0b21260

Steps to reproduce the behavior

1. Edit ~/.copilot/config.json and add permissions:

{
  "permissions": {
    "allow": ["shell(git:*)", "shell(nx build:*)"]
  }
}

2. Verify the file contains the permissions
3. Start Copilot CLI with copilot
4. Exit Copilot CLI
5. Check ~/.copilot/config.json - permissions are gone

Expected behavior

The permissions.allow array should persist across Copilot CLI sessions.

Additional context

No response