deactivateOrphaned() treated ALL is_system=1 permissions as module-owned.
Core seed permissions (users.view, tenants.view, etc.) are also is_system=1,
so they were incorrectly deactivated — breaking admin panel access.
Fix: scan all module manifests on disk (enabled or not) to build the set of
module-owned permission keys. Only deactivate permissions whose key appears
in that set. Core seed permissions are never touched.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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