fix: suppress warnings for intentionally skipped files

graphify/extract.py

@@ -4529,7 +4529,11 @@ def extract(
     _empty_sources: list[str] = []
     for i, _p in enumerate(paths):
         _res = per_file[i] or {}
-        if _res.get("nodes") or _res.get("error"):
+        # Some extractors deliberately return no graph data for recognized input
+        # (for example, JSON records rather than a config/manifest).  Their
+        # explicit ``skipped`` marker distinguishes that expected outcome from
+        # the anomalous empty extraction this warning is meant to surface.
+        if _res.get("nodes") or _res.get("error") or _res.get("skipped"):
             continue
         if _get_extractor(_p) is not None:
             _empty_sources.append(str(_p))

tests/test_zero_node_no_cache.py

@@ -52,3 +52,15 @@ def test_no_warning_when_all_files_produce_nodes(tmp_path, capsys):
     ex.extract([f], cache_root=tmp_path / "out", parallel=False)
     err = capsys.readouterr().err
     assert "zero nodes" not in err
+
+
+def test_intentionally_skipped_data_json_does_not_warn(tmp_path, capsys):
+    """A recognized data document is empty by design, not an extractor failure."""
+    f = tmp_path / "records.json"
+    f.write_text('[{"id": 1, "name": "Ada"}]')
+
+    result = ex.extract([f], cache_root=tmp_path / "out", parallel=False)
+
+    assert result["nodes"] == []
+    err = capsys.readouterr().err
+    assert "zero nodes" not in err, err