fix(commonlisp): derive node ids from the full path stem

The Common Lisp extractor minted its id prefix from the bare path.stem instead of the
canonical _file_stem used by every other extractor, so two same-basename .lisp files in
different directories collided (one file's nodes vanished on merge) and nested .lisp files
tripped a spurious legacy-id nudge. Use _make_id(_file_stem(path)) to match the shared
convention; cross-file rewire is unaffected (it matches on label, not id).

graphify/extractors/commonlisp.py

@@ -4,7 +4,7 @@ from __future__ import annotations
 import warnings
 from pathlib import Path
 
-from graphify.extractors.base import _make_id
+from graphify.extractors.base import _file_stem, _make_id
 
 
 # Standard CL definer forms that introduce data/type/variable bindings
@@ -84,7 +84,11 @@ def extract_commonlisp(path: Path) -> dict:
     except Exception as e:
         return {"nodes": [], "edges": [], "error": str(e)}
 
-    stem = path.stem
+    # Path-qualified, not the bare `path.stem`: same-named .lisp files in
+    # different directories must not collide (#1504). Pre-collapsed through
+    # `_make_id` because `_cl_id` would otherwise map the `/` separators to
+    # `_slash` via _CL_CHAR_MAP.
+    stem = _make_id(_file_stem(path))
     str_path = str(path)
     nodes: list[dict] = []
     edges: list[dict] = []

tests/test_languages.py

@@ -3974,3 +3974,25 @@ def test_zig_enum_and_union_methods_are_extracted(tmp_path):
         for e in r["edges"] if e["relation"] == "calls"
     }
     assert (".area()", "helper()") in calls, "call from union method body dropped"
+
+
+@_needs_commonlisp
+def test_cl_ids_are_path_qualified_across_directories(tmp_path):
+    """Two same-named .lisp files in DIFFERENT directories must mint distinct
+    ids (#1504). The prefix was derived from the bare `path.stem`, so both
+    `a/sample.lisp` and `b/sample.lisp` minted `sample` / `sample_init`; when
+    they land in separate extract batches (what `graphify update` does) build()
+    merges them and one file's nodes are dropped."""
+    a = tmp_path / "a" / "sample.lisp"
+    b = tmp_path / "b" / "sample.lisp"
+    for p in (a, b):
+        p.parent.mkdir(parents=True)
+        p.write_text("(defun init (x) (+ x 1))\n")
+
+    ids_a = {n["id"] for n in extract_commonlisp(a)["nodes"]}
+    ids_b = {n["id"] for n in extract_commonlisp(b)["nodes"]}
+
+    assert not (ids_a & ids_b), (
+        f"same-named .lisp files in different dirs must not share ids, "
+        f"got overlap {sorted(ids_a & ids_b)}"
+    )