fix(extract): don't classify a deliberately-declined data JSON as failed (#2879)

A data-shaped JSON that extract_json intentionally declines (returning a `skipped`
marker, not an `error`) was counted as a failed extraction, so it was kept out of the
incremental manifest and re-processed on every run. Treat the `skipped` decline as a
valid empty outcome, disjoint from genuine failures (which still return `error` and are
still reported).

graphify/extract.py

@@ -5512,7 +5512,7 @@ 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"):
+        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))
@@ -5544,6 +5544,12 @@ def extract(
                 _failed_sources.append(_key)
                 _failed_seen.add(_key)
             continue
+        if _res.get("skipped"):
+            # The extractor declined this file by design (data JSON, #1224), so
+            # zero nodes is the intended outcome rather than a failure. Marking
+            # it failed keeps it out of the incremental manifest and re-queues
+            # it on every subsequent run, forever (#2879).
+            continue
         if (not _res.get("nodes")) and _get_extractor(_p) is not None:
             if _key not in _failed_seen:
                 _failed_sources.append(_key)

tests/test_extract.py

@@ -3966,3 +3966,42 @@ def test_inferred_uses_edge_dropped_for_module_top_level_reference(tmp_path):
     uses = _inferred_uses(result)
 
     assert not any(tgt == "helpers_helper" for _, tgt in uses)
+
+
+def test_extract_declined_data_json_is_not_failed(tmp_path, capsys):
+    """#2879: data JSON is declined by design (#1224), not failed.
+
+    A `.json` extractor is registered, so a declined file used to satisfy both
+    halves of the failed-source test (zero nodes + extractor exists) and was
+    re-queued on every incremental run because the CLI never stamped it as
+    processed.
+    """
+    pytest.importorskip("tree_sitter_json")
+    data = tmp_path / "meta.json"
+    data.write_text('{"pages": ["a", "b"], "title": "Docs"}\n')
+    cfg = tmp_path / "package.json"
+    cfg.write_text('{"dependencies": {"left-pad": "^1.0.0"}}\n')
+
+    result = extract([data, cfg], cache_root=tmp_path)
+    err = capsys.readouterr().err
+
+    assert result.get("failed_sources") == []
+    # ...and no "produced zero nodes" noise for a deliberate decline (#1666).
+    assert "zero nodes" not in err
+    # the config JSON still extracts normally
+    assert any(str(n.get("label", "")).startswith("package.json") for n in result["nodes"])
+
+
+def test_extract_genuinely_empty_json_still_failed(tmp_path, monkeypatch):
+    """#2879 guard: only an explicit `skipped` marker is exempt."""
+    pytest.importorskip("tree_sitter_json")
+    import graphify.extract as _ex
+
+    monkeypatch.setattr(
+        _ex, "_get_extractor",
+        lambda p: (lambda _p: {"nodes": [], "edges": []}) if p.suffix == ".json" else None,
+    )
+    p = tmp_path / "meta.json"
+    p.write_text("{}\n")
+    result = _ex.extract([p], cache_root=tmp_path)
+    assert [Path(x).name for x in result.get("failed_sources", [])] == ["meta.json"]