fix(markdown): keep owner evidence when the edge already exists

The review bot flagged a real hazard in the owner-evidence bookkeeping: a
mention whose `references` edge is already in the graph returned early, so
the document never recorded that it cites the target. A later bare method
mention in the same document then lost its owner and was dropped.

`_add` now records the cited target before it decides whether the edge has
to be written, so the evidence survives an edge that is already there.

The pipeline cannot reach that state today (the resolver is handed a fresh
edge list, and the incremental context only carries contains/method/
inherits/imports edges), so this is hardening rather than a fix for a
reachable failure. The regression test drives the resolver directly with a
pre-existing class edge.

graphify/markdown_resolution.py

@@ -229,7 +229,14 @@ def resolve_markdown_mentions(
 
     def _add(rc: dict, target: str | None, confidence: str, score: float) -> None:
         caller = str(rc.get("caller_nid", ""))
-        if target is None or target == caller or (caller, target) in existing:
+        if target is None or target == caller:
+            return
+        doc = _posix(str(rc.get("source_file", "")))
+        if (caller, target) in existing:
+            # The edge is already in the graph, but this document still CITES that
+            # target, so it stays on record as owner evidence for a later method
+            # mention in the same document (#4609 review finding).
+            cited_targets.setdefault(doc, set()).add(target)
             return
         existing.add((caller, target))
         all_edges.append({
@@ -243,7 +250,7 @@ def resolve_markdown_mentions(
             "source_location": rc.get("source_location"),
             "weight": 1.0,
         })
-        cited_targets.setdefault(_posix(str(rc.get("source_file", ""))), set()).add(target)
+        cited_targets.setdefault(doc, set()).add(target)
 
     # Pass 1: explicit evidence resolves on its own — a cited path, a dotted
     # qualifier chain, or a trailing (). Record those targets per document.

tests/test_markdown_code_spans.py

@@ -346,3 +346,39 @@ def test_owner_cited_in_another_document_does_not_count(tmp_path):
 
     b = _node(r, "B")
     assert {t for (s, t) in _references(r) if s == b["id"]} == set()
+
+
+def test_owner_evidence_survives_an_edge_that_already_exists():
+    """A mention whose edge is already in the graph still counts as citing its target.
+
+    The resolver skips an edge that is already there, but the document has still
+    cited that symbol, so the evidence must stay on record for a later method
+    mention in the same document (#4609, review finding on the PR).
+    """
+    from graphify.markdown_resolution import resolve_markdown_mentions
+
+    per_file = [{"raw_calls": [
+        {"caller_nid": "doc_notes", "callee": "HandlerResult", "language": "markdown",
+         "context": "HandlerResult", "source_file": "notes.md", "source_location": "L3"},
+        {"caller_nid": "doc_notes", "callee": "successWithWarnings", "language": "markdown",
+         "context": "successWithWarnings", "source_file": "notes.md", "source_location": "L3"},
+    ]}]
+    nodes = [
+        {"id": "doc_notes", "label": "Notes", "file_type": "document",
+         "source_file": "notes.md"},
+        {"id": "handler_handlerresult", "label": "HandlerResult", "file_type": "code",
+         "_callable": True, "_callable_class": True, "source_file": "handler.py"},
+        {"id": "handler_handlerresult_successwithwarnings", "label": ".successWithWarnings()",
+         "file_type": "code", "_callable": True, "source_file": "handler.py"},
+    ]
+    edges = [
+        {"source": "handler_handlerresult",
+         "target": "handler_handlerresult_successwithwarnings", "relation": "method"},
+        # The class reference edge is already in the graph.
+        {"source": "doc_notes", "target": "handler_handlerresult", "relation": "references"},
+    ]
+
+    resolve_markdown_mentions(per_file, nodes, edges)
+
+    assert ("doc_notes", "handler_handlerresult_successwithwarnings") in {
+        (e["source"], e["target"]) for e in edges if e.get("relation") == "references"}