UI Permission settings ignored: opencode.json overrides Settings silently

Summary

Setting all permissions to "Allow" in Settings > Permissions UI has no effect. Backend still generates permission prompts according to the project opencode.json. 3270 prompts were generated while UI showed everything as allowed.

Evidence

• User set all permissions to "allow" in GUI (Settings > Permissions)
• Over 27 days: 3270 prompts generated (2743 bash, 1360 external_directory, 103 task, 57 todowrite)
• All prompts were invisible — dialog never rendered
• Backend sat idle for up to 12.5 minutes waiting for answers that could never arrive
• App appeared frozen but was just blocked on unanswered prompts
• 48.9% of prompts were repeats of previously allowed values

Root Cause

Project-level opencode.json takes precedence over UI settings. When opencode.json has "*": "ask", the permission toggle in Settings is silently ignored. Settings UI should either:

1. Override opencode.json (reflect actual effective permissions)
2. Or show a warning when project config overrides UI settings

Impact

• User trusts the UI, expects no prompts — gets thousands
• Prompts are invisible (dialog does not render)
• App appears frozen — user force-restarts, losing work
• Each restart resets all "allow always" decisions

Version: 1.18.16, Electron 42.3.3, Windows 10