Add regression test for dangling edge pruning consistency

group_skipped feeds the dangling reference pruning pass and the write
loop must agree with it on whether a recovered group is written or
skipped. This proves an edge between two nodes inside the same
recovered group survives instead of being pruned as referencing a
supposedly skipped id.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_017qfdzgbA5KedGEjD1AayNh

tests/test_semantic_cache_basename_recovery.py

@@ -30,6 +30,31 @@ def test_malformed_but_basename_unique_path_recovers(tmp_path):
     assert {n["id"] for n in cached["nodes"]} == {"n1"}
 
 
+def test_recovered_group_edges_are_not_pruned_as_dangling(tmp_path):
+    # group_skipped (used by the dangling-reference pruning pass) and the
+    # write loop must agree a recovered group is WRITTEN, not skipped --
+    # otherwise an edge between two nodes in that same recovered group would
+    # be wrongly pruned as referencing a "skipped" id.
+    real = tmp_path / "sub" / "weird_named_file.py"
+    real.parent.mkdir(parents=True)
+    real.write_text("def f(): pass\ndef g(): pass\n")
+
+    nodes = [
+        {"id": "n1", "label": "f", "source_file": "lost_dir/weird_named_file.py"},
+        {"id": "n2", "label": "g", "source_file": "lost_dir/weird_named_file.py"},
+    ]
+    edges = [
+        {"source": "n1", "target": "n2", "relation": "calls",
+         "source_file": "lost_dir/weird_named_file.py"},
+    ]
+    saved = save_semantic_cache(nodes, edges, root=tmp_path, allowed_source_files=[real])
+    assert saved == 1
+
+    cached = load_cached(real, root=tmp_path, kind="semantic")
+    assert cached is not None
+    assert len(cached["edges"]) == 1
+
+
 def test_ambiguous_basename_stays_skipped(tmp_path):
     a = tmp_path / "pkg_a" / "shared.py"
     b = tmp_path / "pkg_b" / "shared.py"