fix: preserve edge direction in merge-graphs

graphify/build.py

@@ -1450,15 +1450,20 @@ def prefix_graph_for_global(G: nx.Graph, repo_tag: str) -> nx.Graph:
     """Return a copy of G with all node IDs prefixed with repo_tag::.
 
     Labels are preserved unchanged (for display). A 'local_id' attribute
-    is added to each node so the original ID can be recovered. Edges are
-    rewritten to match the new prefixed IDs. The 'repo' attribute is set
-    on every node.
+    is added to each node so the original ID can be recovered. Edges and
+    their directional attributes (_src/_tgt) are rewritten to match the new
+    prefixed IDs. The 'repo' attribute is set on every node.
     """
     relabel = {n: f"{repo_tag}::{n}" for n in G.nodes}
     H = nx.relabel_nodes(G, relabel, copy=True)
     for node, data in H.nodes(data=True):
         data["repo"] = repo_tag
         data.setdefault("local_id", node.split("::", 1)[1])
+    for u, v, data in H.edges(data=True):
+        if "_src" in data and data["_src"] in relabel:
+            data["_src"] = relabel[data["_src"]]
+        if "_tgt" in data and data["_tgt"] in relabel:
+            data["_tgt"] = relabel[data["_tgt"]]
     return H
 
 

graphify/cli.py

@@ -2093,6 +2093,15 @@ def dispatch_command(cmd: str) -> None:
             # via node_link_data but older runs may have used "edges" (#738).
             if "links" not in data and "edges" in data:
                 data = dict(data, links=data["edges"])
+            # Preserve stored edge direction across undirected node_link_graph (#2261).
+            # Mirrors cli.py's query pattern and export.py's _src/_tgt restoration.
+            data = dict(
+                data,
+                links=[
+                    {**link, "_src": link.get("source"), "_tgt": link.get("target")}
+                    for link in data.get("links", [])
+                ],
+            )
             try:
                 G = _jg.node_link_graph(data, edges="links")
             except TypeError:
@@ -2129,6 +2138,13 @@ def dispatch_command(cmd: str) -> None:
             out_data = _jg.node_link_data(merged, edges="links")
         except TypeError:
             out_data = _jg.node_link_data(merged)
+        # Restore original edge direction from _src/_tgt markers (same pattern as export.py #563/#2261)
+        for link in out_data.get("links", []):
+            tsrc = link.pop("_src", None)
+            ttgt = link.pop("_tgt", None)
+            if tsrc is not None and ttgt is not None:
+                link["source"] = tsrc
+                link["target"] = ttgt
         out_path.parent.mkdir(parents=True, exist_ok=True)
         from graphify.paths import write_json_atomic as _wja
         _wja(out_path, out_data, indent=2)

tests/test_global_graph.py

@@ -66,6 +66,22 @@ def test_prefix_graph_rewrites_edges():
     assert not H.has_edge("a", "b")
 
 
+def test_prefix_graph_rewrites_edge_directional_attributes():
+    """prefix_graph_for_global must update directional edge attributes (_src/_tgt)
+    so they stay aligned with the prefixed node IDs (#2261)."""
+    from graphify.build import prefix_graph_for_global
+    G = _make_graph(
+        [{"id": "rota", "label": "rota.js"}, {"id": "collections", "label": "collections.js"}],
+        [{"source": "rota", "target": "collections", "relation": "imports_from", "_src": "rota", "_tgt": "collections"}],
+    )
+    H = prefix_graph_for_global(G, "repoA")
+    assert H.has_edge("repoA::rota", "repoA::collections")
+    data = H.get_edge_data("repoA::rota", "repoA::collections")
+    assert data["_src"] == "repoA::rota"
+    assert data["_tgt"] == "repoA::collections"
+
+
+
 def test_prune_repo_removes_correct_nodes():
     from graphify.build import prune_repo_from_graph
     G = nx.Graph()

tests/test_merge_graphs_cli.py

@@ -92,3 +92,78 @@ def test_distinct_repo_tags_unit(tmp_path):
         Path("c/src/graphify-out/graph.json"),
     ])
     assert len(set(tags3)) == 3, tags3
+
+
+def test_merge_graphs_preserves_import_edge_direction(tmp_path):
+    # #2261: merge-graphs loaded graph.json into an undirected nx.Graph without
+    # stashing _src/_tgt directional markers, causing node_link_data to re-serialize
+    # edges based on arbitrary node ordering and reversing import edge direction whenever
+    # target node index < source node index (turning imports into self-imports/reversed links).
+    a = tmp_path / "repo1" / "graphify-out" / "graph.json"
+    b = tmp_path / "repo2" / "graphify-out" / "graph.json"
+    a.parent.mkdir(parents=True, exist_ok=True)
+    b.parent.mkdir(parents=True, exist_ok=True)
+
+    # Note: collections comes BEFORE rota in nodes list, so collections has a smaller index
+    a.write_text(json.dumps({
+        "directed": False,
+        "multigraph": False,
+        "nodes": [
+            {"id": "collections", "label": "collections.js"},
+            {"id": "empresa", "label": "empresa.js"},
+            {"id": "logger", "label": "logger.js"},
+            {"id": "rota", "label": "rota.js"},
+        ],
+        "links": [
+            {"source": "rota", "target": "collections", "relation": "imports_from", "context": "import"},
+            {"source": "rota", "target": "empresa", "relation": "imports_from", "context": "import"},
+            {"source": "rota", "target": "logger", "relation": "imports_from", "context": "import"},
+        ],
+    }))
+
+    b.write_text(json.dumps({
+        "directed": False,
+        "multigraph": False,
+        "nodes": [
+            {"id": "main", "label": "main.js"},
+            {"id": "utils", "label": "utils.js"},
+        ],
+        "links": [
+            {"source": "main", "target": "utils", "relation": "imports_from", "context": "import"},
+        ],
+    }))
+
+    out = tmp_path / "merged.json"
+    r = _run(["merge-graphs", str(a), str(b), "--out", str(out)], tmp_path)
+    assert r.returncode == 0, f"merge failed: {r.stderr}"
+
+    data = json.loads(out.read_text(encoding="utf-8"))
+
+    # 1. Node count & edge count correct
+    assert len(data["nodes"]) == 6
+    assert len(data["links"]) == 4
+
+    # 2. Repo prefixes applied
+    node_ids = {n["id"] for n in data["nodes"]}
+    expected_ids = {
+        "repo1::collections", "repo1::empresa", "repo1::logger", "repo1::rota",
+        "repo2::main", "repo2::utils"
+    }
+    assert node_ids == expected_ids
+
+    # 3. Import relationships preserve original direction (source=rota, target=collections/empresa/logger)
+    #    and no import edge becomes a self-import or reversed.
+    repo1_links = [l for l in data["links"] if l["source"].startswith("repo1::") or l["target"].startswith("repo1::")]
+    assert len(repo1_links) == 3
+
+    for link in repo1_links:
+        src = link["source"]
+        tgt = link["target"]
+        assert src != tgt, f"import edge became a self-import: {link}"
+        assert src == "repo1::rota", f"expected source repo1::rota, got {src} in link {link}"
+        assert tgt in {"repo1::collections", "repo1::empresa", "repo1::logger"}, f"unexpected target {tgt} in link {link}"
+
+    repo2_link = [l for l in data["links"] if l["source"].startswith("repo2::")][0]
+    assert repo2_link["source"] == "repo2::main"
+    assert repo2_link["target"] == "repo2::utils"
+