[Server] Untangle origin tracking from Registry (#302)

Drop the isManual flag from ElementReference and the discovery-state methods
from RegistryInterface. The Registry becomes a flat last-write-wins map;
DiscoveryLoader owns its own owned-set bookkeeping so re-running discovery
only removes elements it itself contributed. Adds ChainLoader for explicit
composition. Manual-over-discovered precedence is preserved via loader
ordering, not a flag on the reference.

src/Capability/Registry/ResourceReference.php

@@ -28,9 +28,8 @@ class ResourceReference extends ElementReference
     public function __construct(
         public readonly Resource $resource,
         callable|array|string $handler,
-        bool $isManual = false,
     ) {
-        parent::__construct($handler, $isManual);
+        parent::__construct($handler);
     }
 
     /**