Report unclassified files from graphify update too

graphify extract has printed this since #1692, but the update and
watch rebuild path never did, so a corpus with no extractor for its
language, Lean 4 in the reported case, rebuilt successfully with
those files completely absent and nothing said about it. Prints the
same wording from the extract command, and threads the count into
the local detection summary the rebuild path already builds for
GRAPH_REPORT.md, which previously dropped it. Fixes #3511.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_017qfdzgbA5KedGEjD1AayNh
(cherry picked from commit 120405673f)

graphify/watch.py

@@ -1428,6 +1428,20 @@ def _rebuild_code(
         )
         code_files = [Path(f) for f in detected['files']['code']]
 
+        # #3511: `graphify extract` has surfaced files it saw but could not
+        # classify since #1692; this update/watch rebuild path never did,
+        # so a corpus in a language with no extractor (no supported
+        # extension or shebang) rebuilt "successfully" with those files
+        # silently absent from the graph. Same wording as the extract path.
+        _unclassified = detected.get("unclassified", []) if isinstance(detected, dict) else []
+        if _unclassified:
+            _names = ", ".join(sorted({Path(p).name for p in _unclassified})[:6])
+            _more = f" (+{len(_unclassified) - 6} more)" if len(_unclassified) > 6 else ""
+            print(
+                f"[graphify watch] {len(_unclassified)} file(s) not classified "
+                f"(no supported extension or shebang), skipped: {_names}{_more}"
+            )
+
         # #2495: hand reconcile the same ignore decisions the detect() call
         # above made, so a newly-ignored file that still exists on disk is
         # purged from the graph instead of preserved forever by the fail-closed
@@ -1876,6 +1890,7 @@ def _rebuild_code(
             "files": {"code": [str(f) for f in code_files], "document": [], "paper": [], "image": []},
             "total_files": len(code_files),
             "total_words": detected.get("total_words", 0),
+            "unclassified": detected.get("unclassified", []),
         }
 
         # Inherit the existing graph's directed flag (#2342) so `graphify

tests/test_watch.py

@@ -133,6 +133,25 @@ def test_doc_only_deletion_full_rebuild_evicts_md_nodes(tmp_path):
     assert "run()" in labels
 
 
+def test_rebuild_code_reports_unclassified_files(tmp_path, capsys):
+    """#3511: `graphify extract` has surfaced files it saw but could not
+    classify (no supported extension/shebang) since #1692; the update/watch
+    rebuild path never did, so a corpus mostly in an unsupported language
+    (e.g. Lean, per the report) rebuilt "successfully" with those files
+    silently absent and nothing said about it."""
+    corpus = tmp_path / "corpus"
+    corpus.mkdir()
+    (corpus / "app.py").write_text("def run(): pass\n", encoding="utf-8")
+    (corpus / "Main.lean").write_text("def main := 0\n", encoding="utf-8")
+    (corpus / "Util.lean").write_text("def util := 1\n", encoding="utf-8")
+
+    assert _rebuild_code(corpus, acquire_lock=False) is True
+    out = capsys.readouterr().out
+    assert "2 file(s) not classified" in out
+    assert "Main.lean" in out
+    assert "Util.lean" in out
+
+
 # --- watch() import error without watchdog ---
 
 def test_check_update_no_flag_returns_true(tmp_path):