[BUG] settings.local.json permissions.allow overwrites existing manual settings

Question

**Description:**
When Claude Code programmatically updates `permissions.allow` in `settings.local.json`, it completely overwrites any manually added paths instead of merging them.

**Steps to Reproduce:**
1. Manually add custom paths to `.claude/settings.local.json`:
   ```json
   {
     "permissions": {
       "allow": ["/my/custom/path1", "/my/custom/path2"]
     }
   }