Fix wiki TypeError on null source_file and skip nested worktrees/ dirs (#1016, #1023)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

graphify/detect.py

@@ -563,7 +563,7 @@ _SKIP_FILES = {
     "composer.lock", "go.sum", "go.work.sum",
 }
 
-def _is_noise_dir(part: str) -> bool:
+def _is_noise_dir(part: str, parent: "Path | None" = None) -> bool:
     """Return True if this directory name looks like a venv, cache, or dep dir."""
     if part in _SKIP_DIRS:
         return True
@@ -572,6 +572,9 @@ def _is_noise_dir(part: str) -> bool:
         return True
     if part.endswith(".egg-info"):
         return True
+    # worktrees/ nested inside a dotted dir (e.g. .claude/worktrees/, .git/worktrees/)
+    if part == "worktrees" and parent is not None and parent.name.startswith("."):
+        return True
     return False
 
 
@@ -912,7 +915,7 @@ def detect(root: Path, *, follow_symlinks: bool | None = None, google_workspace:
                 has_negation = any(p.startswith("!") for _, p in ignore_patterns)
                 dirnames[:] = [
                     d for d in dirnames
-                    if not _is_noise_dir(d)
+                    if not _is_noise_dir(d, dp)
                     and (has_negation or not _is_ignored(dp / d, root, ignore_patterns))
                 ]
             for fname in filenames:

graphify/wiki.py

@@ -54,7 +54,7 @@ def _community_article(
             conf_counts[ed.get("confidence", "EXTRACTED")] += 1
     total_edges = sum(conf_counts.values()) or 1
 
-    sources = sorted({G.nodes[n].get("source_file", "") for n in nodes} - {""})
+    sources = sorted({G.nodes[n].get("source_file") or "" for n in nodes} - {""})
 
     lines: list[str] = []
     lines += [f"# {label}", ""]

tests/test_detect.py

@@ -657,6 +657,19 @@ def test_detect_skips_worktrees_dir(tmp_path):
     assert not any(".worktrees" in f for f in code)
 
 
+def test_detect_skips_nested_worktrees_dir(tmp_path):
+    """Files inside .claude/worktrees/ (nested placement) are never indexed (#1023)."""
+    wt = tmp_path / ".claude" / "worktrees" / "feature-branch"
+    wt.mkdir(parents=True)
+    (wt / "main.py").write_text("x = 1")
+    (tmp_path / "app.py").write_text("y = 2")
+
+    result = detect(tmp_path)
+    code = result["files"]["code"]
+    assert any("app.py" in f for f in code)
+    assert not any("worktrees" in f for f in code)
+
+
 def test_detect_extra_excludes_pattern(tmp_path):
     """extra_excludes patterns exclude matching files from detect() (#947)."""
     (tmp_path / "main.py").write_text("x = 1")

tests/test_wiki.py

@@ -197,3 +197,16 @@ def test_to_wiki_stale_nodes_prints_warning(tmp_path, capsys):
     err = capsys.readouterr().err
     assert "2" in err  # dropped count
     assert "stale" in err.lower()
+
+
+def test_community_article_handles_null_source_file(tmp_path):
+    """source_file=None on a node must not crash sorted() with TypeError (#1016)."""
+    G = nx.Graph()
+    G.add_node("n1", label="parse", file_type="code", source_file=None, community=0)
+    G.add_node("n2", label="validate", file_type="code", source_file="parser.py", community=0)
+    G.add_edge("n1", "n2", relation="calls", confidence="EXTRACTED", weight=1.0)
+    communities = {0: ["n1", "n2"]}
+    labels = {0: "Parsing Layer"}
+    # Must not raise TypeError
+    to_wiki(G, communities, tmp_path, community_labels=labels)
+    assert (tmp_path / "index.md").exists()