P0+P1 fixes: RCE sandbox, SQL injection, RLS tenant isolation, DB roles, test syntax, attachment, permission registry, membership check

app/core/permission_registry.py

@@ -128,17 +128,31 @@ class PermissionRegistry:
         self._core_field_definitions: list[dict[str, str]] = list(CORE_FIELD_DEFINITIONS)
 
     def initialize(self, active_plugin_names: set[str] | None = None) -> None:
-        """Build the registry from core permissions and active plugin manifests."""
+        """Build the registry from core permissions and active plugin manifests.
+
+        Preserves already-registered plugin permissions (fixes P1.3 bug where
+        initialize() would wipe plugin permissions registered before startup).
+        """
+        # Preserve existing plugin permissions
+        existing_plugin_perms = self._plugin_permissions.copy()
+
+        # Reset only core permissions, keep plugin permissions
         self._permissions = {}
-        self._plugin_permissions = {}
         self._active_plugins = active_plugin_names or set()
 
         # Register core permissions
         for perm in CORE_PERMISSIONS:
             self._permissions[perm["key"]] = perm
 
+        # Re-apply plugin permissions that were registered before initialize()
+        for plugin_name, perms in existing_plugin_perms.items():
+            self._plugin_permissions[plugin_name] = perms
+            for entry in perms:
+                self._permissions[entry["key"]] = entry
+
         self._initialized = True
-        logger.info("Permission registry initialized with %d core permissions", len(CORE_PERMISSIONS))
+        logger.info("Permission registry initialized with %d core permissions, %d plugin permissions",
+                    len(CORE_PERMISSIONS), len(existing_plugin_perms))
 
     def register_plugin_permissions(self, plugin_name: str, permissions: list[str]) -> None:
         """Register permissions from a plugin manifest."""