fix: mark virtual workspace Cargo.toml manifests as skipped, not zero-node

graphify/manifest_ingest.py

@@ -92,6 +92,14 @@ def extract_package_manifest(path: Path) -> dict[str, Any]:
     except Exception as exc:  # noqa: BLE001 — a malformed manifest must not abort extraction
         return {"nodes": [], "edges": [], "error": f"manifest parse error: {exc}"}
     if not info or not info.get("name"):
+        # A virtual workspace root (Cargo `[workspace]`, no `[package]`) is a
+        # legitimate zero-node result, not a failure (#1833): mark it
+        # "skipped" so extract.py's #1666 empty-source detector doesn't print
+        # a persistent "produced zero nodes" warning for a manifest that was
+        # never supposed to emit a package node. A manifest missing a name
+        # for any other reason keeps warning, since that IS unexplained.
+        if info and info.get("workspace_only"):
+            return {"nodes": [], "edges": [], "skipped": True}
         return {"nodes": [], "edges": []}
 
     name = info["name"]
@@ -237,6 +245,8 @@ def _parse_cargo(text: str) -> dict | None:
     # package of its own — emit nothing rather than a fabricated node. ``name`` is
     # never workspace-inheritable in Cargo, but guard on the type anyway.
     if not isinstance(name, str) or not name:
+        if isinstance(data.get("workspace"), dict):
+            return {"name": None, "workspace_only": True, "deps": []}
         return None
     # ``version`` may be workspace-inherited (``version.workspace = true``), which
     # parses to a table; keep only a concrete string version.

tests/test_manifest_ingest.py

@@ -144,6 +144,21 @@ def test_cargo_virtual_workspace_manifest_emits_no_package(tmp_path):
     assert _pkg_nodes(r) == []
 
 
+def test_cargo_virtual_workspace_manifest_is_marked_skipped(tmp_path):
+    # #1833: a virtual workspace root (no [package]) legitimately emits zero
+    # nodes by design. Without an explicit "skipped" marker, extract.py's
+    # #1666 empty-source detector treats this as an unexplained failure and
+    # prints a persistent "produced zero nodes" warning on every run. A
+    # manifest with no [workspace] table either (i.e. genuinely malformed,
+    # missing a name) must NOT be marked skipped — that would hide a real
+    # problem.
+    ws = _write(tmp_path / "ws" / "Cargo.toml", '[workspace]\nmembers = ["a"]\n')
+    assert extract_package_manifest(ws).get("skipped") is True
+
+    broken = _write(tmp_path / "broken" / "Cargo.toml", '[dependencies]\nserde = "1"\n')
+    assert extract_package_manifest(broken).get("skipped") is not True
+
+
 def test_cargo_target_conditional_deps_are_collected(tmp_path):
     # Platform-gated deps under [target.'cfg(...)'.dependencies] are common in
     # real crates and must not be dropped just because they are conditional.