fix: phantom route writes, duplicate members, and minor issues from review round 2

- Write phantom Route nodes in _write_clients_producers_and_calls using MERGE
  (pass5 creates phantom routes for cross-service calls that were never
  persisted to Kuzu, silently dropping HTTP_CALLS/ASYNC_CALLS edges)
- Remove redundant _load_existing_members before full pass1_parse in global
  pass 5-6 step (was creating duplicate stub members alongside full entries)
- Use conn.close() + del instead of bare del for Kuzu handle cleanup on
  fallback (avoids relying on CPython ref-counting for file lock release)
- Add FileNotFoundError handling in FileHashTracker.detect_changes for files
  that vanish between listing and hashing
- Remove redundant inline import json in cli.py _cmd_increment
- Update stale _delete_file_scope docstring to match implementation

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Author: HumanBean17

build_ast_graph.py

@@ -462,7 +462,10 @@ def detect_changes(self, source_root: Path, ignore: LayeredIgnore) -> tuple[set[
         # Detect added and changed files.
         for rel_path in current_files:
             abs_path = source_root / rel_path
-            file_hash = _hash_file(abs_path)
+            try:
+                file_hash = _hash_file(abs_path)
+            except FileNotFoundError:
+                continue
             stored_hash = self._hashes.get(rel_path)
             if stored_hash is None:
                 added.add(rel_path)
@@ -612,9 +615,9 @@ def _find_dependents(conn: kuzu.Connection, changed_node_ids: set[str]) -> set[s
 def _delete_file_scope(conn: kuzu.Connection, filenames: set[str]) -> None:
     """Delete all nodes and edges originating from the given files.
 
-    Skip phantom nodes (filename=""). For Symbol-to-Symbol and UNRESOLVED_AT
-    edge tables only. Client/Producer/Route edges are handled separately in
-    pass 5-6 global rebuild.
+    Skip phantom nodes (filename=""). Deletes ALL edge types in Phase 1,
+    then nodes in subsequent phases. Route/Client/Producer nodes use
+    DETACH DELETE as a safety net for any edges missed in Phase 1.
 
     Edges are deleted in batch across all filenames first to avoid Kuzu
     "has connected edges" errors when edges from one file point to nodes
@@ -3442,11 +3445,16 @@ def incremental_rebuild(
             if version < 17:
                 if verbose:
                     _verbose_stderr_line(f"[increment] ontology version {version} < 17; falling back to full rebuild")
+                conn.close()
                 del conn, db
                 return _fallback_to_full(source_root, kuzu_path, verbose, t_start)
     except Exception as e:
         if verbose:
             _verbose_stderr_line(f"[increment] failed to read ontology version: {e}; falling back to full rebuild")
+        try:
+            conn.close()
+        except Exception:
+            pass
         del conn, db
         return _fallback_to_full(source_root, kuzu_path, verbose, t_start)
 
@@ -3550,11 +3558,8 @@ def incremental_rebuild(
         if verbose:
             _verbose_stderr_line("[increment] running global passes 5-6")
 
-        # Load all members for pass 5
+        # Rebuild full tables for global pass 5-6 (pass1 populates members from scratch)
         tables_for_global = GraphTables()
-        _load_existing_members(conn, tables_for_global)
-
-        # Rebuild asts for global scope (need for pass5/6)
         global_asts = pass1_parse(source_root, tables_for_global, verbose=verbose)
 
         pass5_imperative_edges(tables_for_global, global_asts, source_root=source_root, verbose=verbose)
@@ -3656,7 +3661,25 @@ def _fallback_to_full(source_root: Path, kuzu_path: Path, verbose: bool, t_start
 
 
 def _write_clients_producers_and_calls(conn: kuzu.Connection, tables: GraphTables) -> None:
-    """Write Client, Producer, and cross-service edges to Kuzu."""
+    """Write Route, Client, Producer, and cross-service edges to Kuzu.
+
+    Used by the incremental rebuild's global pass 5-6 step. Writes phantom
+    Route nodes (created by pass5 for cross-service calls) that wouldn't
+    otherwise exist in Kuzu.
+    """
+    # Write phantom routes that don't already exist (pass5 creates these for cross-service calls)
+    for row in tables.routes_rows:
+        # MERGE to avoid duplicates with routes written during scoped step
+        conn.execute(
+            "MERGE (r:Route {id: $id}) "
+            "SET r.kind = $kind, r.framework = $framework, r.method = $method, "
+            "r.path = $path, r.path_template = $path_template, r.path_regex = $path_regex, "
+            "r.topic = $topic, r.broker = $broker, r.feign_name = $feign_name, r.feign_url = $feign_url, "
+            "r.microservice = $microservice, r.module = $module, r.filename = $filename, "
+            "r.start_line = $start_line, r.end_line = $end_line, r.resolved = $resolved",
+            asdict(row),
+        )
+
     # Build node_id lookup for members and types
     member_by_id = {m.node_id: m for m in tables.members}
 

java_codebase_rag/cli.py

@@ -356,7 +356,6 @@ def work() -> int:
             # Parse stdout to check for full_fallback mode
             # The incremental_rebuild function returns a JSON payload with mode field
             try:
-                import json
                 result = json.loads(g.stdout.strip())
                 if result.get("mode") == "full_fallback":
                     print(