Fix LayerClassifier to update networkx data in-place via classify_store

The original classify() mutated temporary GraphNode copies that weren't
persisted back to the graph. New classify_store() method updates the
networkx node data dict directly. Moved to run after linkers so all
nodes (including linker-created MODULE nodes) get classified.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: aksOps

src/code_intelligence/analyzer.py

@@ -378,18 +378,18 @@ def _report(msg: str) -> None:
                         exc_info=True,
                     )
 
-        # ----------------------------------------------------------
-        # 5b. Classify layers
-        # ----------------------------------------------------------
-        from code_intelligence.classifiers.layer_classifier import LayerClassifier
-        LayerClassifier().classify(list(builder._store.all_nodes()))
-
         # ----------------------------------------------------------
         # 6. Run cross-file linkers
         # ----------------------------------------------------------
         _report("🔗 Linking cross-file relationships…")
         builder.run_linkers()
 
+        # ----------------------------------------------------------
+        # 6b. Classify layers (after linkers so all nodes are covered)
+        # ----------------------------------------------------------
+        from code_intelligence.classifiers.layer_classifier import LayerClassifier
+        LayerClassifier().classify_store(builder._store)
+
         # ----------------------------------------------------------
         # 7. Record run and return result
         # ----------------------------------------------------------

src/code_intelligence/classifiers/layer_classifier.py

@@ -3,9 +3,9 @@
 from __future__ import annotations
 
 import re
-from typing import Sequence
+from typing import Any, Sequence
 
-from code_intelligence.models.graph import GraphNode, NodeKind
+from code_intelligence.models.graph import GraphNode, NodeKind, SourceLocation
 
 _FRONTEND_NODE_KINDS = {NodeKind.COMPONENT, NodeKind.HOOK}
 _BACKEND_NODE_KINDS = {NodeKind.GUARD, NodeKind.MIDDLEWARE, NodeKind.ENDPOINT, NodeKind.REPOSITORY, NodeKind.DATABASE_CONNECTION, NodeKind.QUERY}
@@ -34,6 +34,27 @@ def classify(self, nodes: Sequence[GraphNode]) -> None:
         for node in nodes:
             node.properties["layer"] = self._classify_one(node)
 
+    def classify_store(self, store: Any) -> None:
+        """Classify nodes directly in a GraphStore, updating networkx data in-place."""
+        for node_id, data in store.graph.nodes(data=True):
+            if "kind" not in data:
+                continue
+            # Build a lightweight GraphNode for classification
+            loc = data.get("location")
+            if isinstance(loc, dict):
+                loc = SourceLocation(**loc)
+            node = GraphNode(
+                id=data.get("id", node_id),
+                kind=NodeKind(data["kind"]),
+                label=data.get("label", ""),
+                location=loc,
+                properties=data.get("properties", {}),
+            )
+            layer = self._classify_one(node)
+            # Update the networkx data dict directly
+            props = data.setdefault("properties", {})
+            props["layer"] = layer
+
     def _classify_one(self, node: GraphNode) -> str:
         if node.kind in _FRONTEND_NODE_KINDS:
             return "frontend"