[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.

tests/Inspector/Http/snapshots/HttpCombinedRegistrationTest-resources_list.json

@@ -1,9 +1,9 @@
 {
   "resources": [
     {
-      "name": "priority_config_discovered",
+      "name": "priority_config_manual",
       "uri": "config://priority",
-      "description": "A resource discovered via attributes.\n\nThis will be overridden by a manual registration with the same URI."
+      "description": "Manually registered resource that overrides a discovered one."
     }
   ]
 }

tests/Inspector/Http/snapshots/HttpCombinedRegistrationTest-resources_read-config_priority.json

@@ -3,7 +3,7 @@
     {
       "uri": "config://priority",
       "mimeType": "text/plain",
-      "text": "Discovered Priority Config: Low"
+      "text": "Manual Priority Config: HIGH (overrides discovered)"
     }
   ]
 }