What happened?

resolve_markdown_mentions links a bare code span (no (), no qualifier) to the corpus's single _callable that carries that label, and methods qualify. A word that is prose, not a reference, then becomes heading --references--> SomeClass.word() at INFERRED 0.95.

Expected: no edge. A parenthesis-less lowercase word in a code span (redis the server, data, message, request, current) is not evidence of a reference to a method on whichever unrelated class happens to define it.

On a real corpus (about 1,400 classes, 12 READMEs) 44 of 1,906 resolved mention edges were words of this kind: data, message, request, previous, current, integrations, signature, moved.

Steps to reproduce

d=$(mktemp -d)
printf 'class Cache:\n    def redis(self):\n        return "connection"\n' > $d/cache.py
printf '# Queue\n\nJobs run on `redis` (the server, not our code).\n' > $d/README.md
python - <<PY
from pathlib import Path
from graphify.extract import extract
d = Path("$d")
r = extract([d / "cache.py", d / "README.md"], parallel=False, cache_root=d / "cache", root=d)
labels = {n["id"]: n["label"] for n in r["nodes"]}
print([(labels[e["source"]], labels[e["target"]], e["confidence"]) for e in r["edges"] if e.get("relation") == "references"])
PY

Error output or graph output

[('Queue', '.redis()', 'INFERRED')]

Proposed fix

In the bare branch of resolve_markdown_mentions (graphify/markdown_resolution.py), when the span has no trailing () and no qualifiers and the candidate is a method (not _callable_class), keep the match only if the method's owner class (the method edge's source) is itself the target of a mention in the same document. successWithWarnings written next to HandlerResult keeps its edge; redis with no owner cited does not. The raw call already carries the span text in context, so the resolver can tell redis from redis().

A stricter alternative is to require parentheses for any method match.

I have this running downstream as a post-pass and can open a PR with a regression test if you prefer that to a patch from the maintainers.

Related: #3561 (the feature that added code-span mentions).

Graphify version 0.9.93 (also 0.9.92), macOS, Python 3.14, installed with uv tool.