fix(build): exclude global MCP ids from legacy-id detection (#2408)

tests/test_build.py

@@ -1302,6 +1302,65 @@ def test_graph_has_legacy_ids_detects_old_scheme():
     assert graph_has_legacy_ids(go_symbol, root=".") is False
 
 
+# ── #2408: globally-scoped MCP node ids are not file-stem derived ──────────────
+
+@pytest.mark.parametrize("mcp_kind, nid", [
+    ("mcp_command", "mcp_command_npx"),
+    ("mcp_package", "mcp_package_google_cloud_cloud_run_mcp"),
+    ("env_var", "env_var_google_cloud_project"),
+])
+def test_graph_has_legacy_ids_ignores_global_mcp_ids(mcp_kind, nid):
+    """MCP ingest stamps every node with L1 (JSON has no line info), so global ids
+    would otherwise be read as file-level. Under `sub/.mcp.json` the old bare stem
+    is `mcp`, which these ids legitimately start with (#2408)."""
+    from graphify.build import graph_has_legacy_ids
+    node = {
+        "id": nid,
+        "source_file": "sub/.mcp.json",
+        "source_location": "L1",
+        "metadata": {"mcp_kind": mcp_kind},
+    }
+    assert graph_has_legacy_ids([node], root=".") is False
+
+
+def test_graph_has_legacy_ids_still_checks_file_scoped_mcp_nodes():
+    """The exemption is narrow: file-derived MCP kinds stay under detection, and a
+    missing/malformed metadata blob doesn't exempt anything (or crash)."""
+    from graphify.build import graph_has_legacy_ids
+    for kind in ("mcp_config_file", "mcp_server"):
+        stale = {"id": "mcp_mcp_server_x", "source_file": "sub/.mcp.json",
+                 "source_location": "L1", "metadata": {"mcp_kind": kind}}
+        assert graph_has_legacy_ids([stale], root=".") is True
+    for meta in (None, "not-a-dict", {}, {"mcp_kind": None}):
+        stale = {"id": "mcp_mcp_server_x", "source_file": "sub/.mcp.json",
+                 "source_location": "L1", "metadata": meta}
+        assert graph_has_legacy_ids([stale], root=".") is True
+
+
+@pytest.mark.parametrize("mcp_dir", ["", "sub"])
+def test_fresh_mcp_graph_is_not_flagged_legacy(tmp_path, monkeypatch, mcp_dir):
+    """End-to-end: a freshly extracted graph containing a .mcp.json — nested or at
+    the repo root — must not nudge the user to rebuild (#2408)."""
+    from graphify.build import graph_has_legacy_ids
+    from graphify.extract import extract
+
+    (tmp_path / "main.py").write_text("def main():\n    return 1\n")
+    mcp_parent = tmp_path / mcp_dir if mcp_dir else tmp_path
+    mcp_parent.mkdir(parents=True, exist_ok=True)
+    (mcp_parent / ".mcp.json").write_text(json.dumps({"mcpServers": {"cloud-run": {
+        "command": "npx",
+        "args": ["-y", "@google-cloud/cloud-run-mcp"],
+        "env": {"GOOGLE_CLOUD_PROJECT": "x"},
+    }}}))
+
+    monkeypatch.chdir(tmp_path)
+    rel = Path(mcp_dir, ".mcp.json") if mcp_dir else Path(".mcp.json")
+    result = extract([Path("main.py"), rel], root=Path("."), parallel=False)
+    ids = {n["id"] for n in result["nodes"]}
+    assert "mcp_command_npx" in ids  # guard: the ingest actually ran
+    assert graph_has_legacy_ids(result["nodes"], root=".") is False
+
+
 def test_semantic_rekey_relative_vs_absolute_source_file():
     """Re-key contract: a relative source_file is migrated; an absolute one is left
     untouched (it can't be relativized, so its on-disk path must not leak into IDs)."""