fix(analyze): keep edge direction in graph_diff

graph_diff keyed undirected edges by their sorted endpoints, so a call
that reversed (a->b became b->a) dropped out of the --update summary.
When both snapshots carry _src/_tgt and they differ, the edge is now
reported as one removed and one new edge, with source/target taken from
the markers. Graphs without the markers diff as before.

The skill's diff step loaded the old graph.json with a plain
node_link_graph call, which drops the stored direction, so it now uses
paths.load_node_link_graph (#4066/#4088). Skills regenerated with
skillgen, and the aider/devin monolith round-trip allows the changed
lines.

Closes #4067

Co-Authored-By: Grok Bot <noreply@x.ai>

graphify/analyze.py

@@ -630,24 +630,39 @@ def graph_diff(G_old: nx.Graph, G_new: nx.Graph) -> dict:
             return (u, v, data.get("relation", ""))
         return (min(u, v), max(u, v), data.get("relation", ""))
 
-    old_edge_keys = {
-        edge_key(G_old, u, v, d)
+    def edge_dir(data: dict) -> tuple | None:
+        # Stored direction of an undirected edge (build_from_json, load_node_link_graph).
+        if "_src" in data and "_tgt" in data:
+            return (data["_src"], data["_tgt"])
+        return None
+
+    old_edge_dirs = {
+        edge_key(G_old, u, v, d): edge_dir(d)
         for u, v, d in G_old.edges(data=True)
     }
-    new_edge_keys = {
-        edge_key(G_new, u, v, d)
+    new_edge_dirs = {
+        edge_key(G_new, u, v, d): edge_dir(d)
         for u, v, d in G_new.edges(data=True)
     }
+    old_edge_keys = set(old_edge_dirs)
+    new_edge_keys = set(new_edge_dirs)
 
-    added_edge_keys = new_edge_keys - old_edge_keys
-    removed_edge_keys = old_edge_keys - new_edge_keys
+    # A reversed edge (a->b became b->a) keeps its undirected key. Report it as
+    # removed + added only when both snapshots carry _src/_tgt and they differ,
+    # so graphs without the markers diff exactly as before (#4067).
+    reversed_edge_keys = {
+        k for k in old_edge_keys & new_edge_keys
+        if old_edge_dirs[k] and new_edge_dirs[k] and old_edge_dirs[k] != new_edge_dirs[k]
+    }
+    added_edge_keys = (new_edge_keys - old_edge_keys) | reversed_edge_keys
+    removed_edge_keys = (old_edge_keys - new_edge_keys) | reversed_edge_keys
 
     new_edges_list = []
     for u, v, d in G_new.edges(data=True):
         if edge_key(G_new, u, v, d) in added_edge_keys:
             new_edges_list.append({
-                "source": u,
-                "target": v,
+                "source": d.get("_src", u),
+                "target": d.get("_tgt", v),
                 "relation": d.get("relation", ""),
                 "confidence": d.get("confidence", ""),
             })
@@ -656,8 +671,8 @@ def graph_diff(G_old: nx.Graph, G_new: nx.Graph) -> dict:
     for u, v, d in G_old.edges(data=True):
         if edge_key(G_old, u, v, d) in removed_edge_keys:
             removed_edges_list.append({
-                "source": u,
-                "target": v,
+                "source": d.get("_src", u),
+                "target": d.get("_tgt", v),
                 "relation": d.get("relation", ""),
                 "confidence": d.get("confidence", ""),
             })

graphify/skill-aider.md

@@ -856,7 +856,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -866,7 +866,7 @@ new_extract = json.loads(Path('.graphify_extract.json').read_text())
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skill-devin.md

@@ -993,7 +993,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -1002,7 +1002,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text()
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/agents/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/amp/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/claude/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/claw/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/codex/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/copilot/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/droid/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/kilo/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/kiro/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/opencode/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/pi/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/trae/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/vscode/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

graphify/skills/windows/references/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tests/test_analyze.py

@@ -347,6 +347,39 @@ def test_graph_diff_empty_diff():
     assert diff["summary"] == "no changes"
 
 
+def _make_marked_graph(src, tgt):
+    """Helper: undirected graph whose one edge stores its direction in _src/_tgt."""
+    G = nx.Graph()
+    G.add_node("n1", label="Alpha")
+    G.add_node("n2", label="Beta")
+    G.add_edge(src, tgt, relation="calls", confidence="EXTRACTED", _src=src, _tgt=tgt)
+    return G
+
+
+def test_graph_diff_reversed_edge_reported():
+    # #4067: n1 calls n2 becoming n2 calls n1 must not vanish from the diff.
+    diff = graph_diff(_make_marked_graph("n1", "n2"), _make_marked_graph("n2", "n1"))
+    assert [(e["source"], e["target"]) for e in diff["new_edges"]] == [("n2", "n1")]
+    assert [(e["source"], e["target"]) for e in diff["removed_edges"]] == [("n1", "n2")]
+    assert diff["summary"] == "1 new edge, 1 edge removed"
+
+
+def test_graph_diff_unchanged_direction_no_changes():
+    diff = graph_diff(_make_marked_graph("n2", "n1"), _make_marked_graph("n2", "n1"))
+    assert diff["new_edges"] == []
+    assert diff["removed_edges"] == []
+    assert diff["summary"] == "no changes"
+
+
+def test_graph_diff_reversed_edge_without_markers_unchanged():
+    # Without _src/_tgt on both sides the edge is keyed by its endpoints, as before.
+    nodes = [("n1", "Alpha"), ("n2", "Beta")]
+    G_old = _make_simple_graph(nodes, [("n1", "n2", "calls", "EXTRACTED")])
+    G_new = _make_simple_graph(nodes, [("n2", "n1", "calls", "EXTRACTED")])
+    assert graph_diff(G_old, G_new)["summary"] == "no changes"
+    assert graph_diff(G_old, _make_marked_graph("n2", "n1"))["summary"] == "no changes"
+
+
 # --- code↔doc INFERRED suppression tests ---
 
 def _make_code_doc_graph():

tools/skillgen/expected/graphify__skill-aider.md

@@ -856,7 +856,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -866,7 +866,7 @@ new_extract = json.loads(Path('.graphify_extract.json').read_text())
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skill-devin.md

@@ -993,7 +993,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -1002,7 +1002,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text()
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__agents__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__amp__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__claude__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__claw__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__codex__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__copilot__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__droid__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__kilo__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__kiro__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__opencode__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__pi__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__trae__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__vscode__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/expected/graphify__skills__windows__references__update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/fragments/core/aider.md

@@ -856,7 +856,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -866,7 +866,7 @@ new_extract = json.loads(Path('.graphify_extract.json').read_text())
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/fragments/core/devin.md

@@ -993,7 +993,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -1002,7 +1002,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text()
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/fragments/references/shared/update.md

@@ -174,7 +174,7 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.analyze import graph_diff
 from graphify.build import build_from_json
-from networkx.readwrite import json_graph
+from graphify.paths import load_node_link_graph
 import networkx as nx
 from pathlib import Path
 
@@ -184,7 +184,7 @@ new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(e
 G_new = build_from_json(new_extract, directed=IS_DIRECTED)
 
 if old_data:
-    G_old = json_graph.node_link_graph(old_data, edges='links')
+    G_old = load_node_link_graph(old_data)
     diff = graph_diff(G_old, G_new)
     print(diff['summary'])
     if diff['new_nodes']:

tools/skillgen/gen.py

@@ -1180,6 +1180,23 @@ def _is_watch_injection_fix_line(line: str) -> bool:
     )
 
 
+def _is_graph_diff_direction_fix_line(line: str) -> bool:
+    """Whether a line is part of the --update graph-diff direction fix (#4067).
+
+    The diff step loaded the old graph.json with a plain ``node_link_graph``,
+    which drops the stored edge direction, so a reversed call showed as "no
+    changes". It now loads through ``paths.load_node_link_graph`` (#4066). Both
+    the removed import/load lines and the added ones match here.
+    """
+    stripped = line.strip()
+    return stripped in (
+        "from networkx.readwrite import json_graph",
+        "G_old = json_graph.node_link_graph(old_data, edges='links')",
+        "from graphify.paths import load_node_link_graph",
+        "G_old = load_node_link_graph(old_data)",
+    )
+
+
 # Every line that may differ between a rendered monolith and its pristine v8
 # baseline. Each predicate documents one sanctioned change-class; a blank line is
 # allowed because the multi-line fix blocks insert spacing. Anything else failing
@@ -1203,6 +1220,7 @@ _SANCTIONED_MONOLITH_DIFFS = (
     _is_community_label_export_fix_line,
     _is_step1_root_marker_fix_line,
     _is_watch_injection_fix_line,
+    _is_graph_diff_direction_fix_line,
 )