Fix four bugs from community PRs

- cache: skip directory source_file in save_cached to prevent IsADirectoryError (#444)
- report: skip structural-only communities with no real nodes (#443)
- hooks: allow @ in python path allowlist for Homebrew paths (#474)
- watch: keep source_file paths project-relative after rebuild (#434)

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

graphify/cache.py

@@ -75,8 +75,15 @@ def save_cached(path: Path, result: dict, root: Path = Path(".")) -> None:
 
     Stores as graphify-out/cache/{hash}.json where hash = SHA256 of current file contents.
     result should be a dict with 'nodes' and 'edges' lists.
+
+    No-ops if `path` is not a regular file. Subagent-produced semantic fragments
+    occasionally carry a directory path in `source_file`; skipping them prevents
+    IsADirectoryError from aborting the whole batch.
     """
-    h = file_hash(path, root)
+    p = Path(path)
+    if not p.is_file():
+        return
+    h = file_hash(p, root)
     entry = cache_dir(root) / f"{h}.json"
     tmp = entry.with_suffix(".tmp")
     try:

graphify/hooks.py

@@ -21,7 +21,7 @@ if [ -n "$GRAPHIFY_BIN" ]; then
     # Allowlist: only keep characters valid in a filesystem path to prevent
     # injection if the shebang contains shell metacharacters
     case "$GRAPHIFY_PYTHON" in
-        *[!a-zA-Z0-9/_.-]*) GRAPHIFY_PYTHON="" ;;
+        *[!a-zA-Z0-9/_.@-]*) GRAPHIFY_PYTHON="" ;;
     esac
     if [ -n "$GRAPHIFY_PYTHON" ] && ! "$GRAPHIFY_PYTHON" -c "import graphify" 2>/dev/null; then
         GRAPHIFY_PYTHON=""

graphify/report.py

@@ -111,6 +111,8 @@ def generate(
         score = cohesion_scores.get(cid, 0.0)
         # Filter method/function stubs from display - they're structural noise
         real_nodes = [n for n in nodes if not _ifn(G, n)]
+        if not real_nodes:
+            continue
         display = [G.nodes[n].get("label", n) for n in real_nodes[:8]]
         suffix = f" (+{len(real_nodes)-8} more)" if len(real_nodes) > 8 else ""
         lines += [

graphify/watch.py

@@ -12,11 +12,35 @@ _WATCHED_EXTENSIONS = CODE_EXTENSIONS | DOC_EXTENSIONS | PAPER_EXTENSIONS | IMAG
 _CODE_EXTENSIONS = CODE_EXTENSIONS
 
 
+def _report_root_label(watch_path: Path) -> str:
+    if watch_path.is_absolute():
+        return watch_path.name or str(watch_path)
+    return Path.cwd().name if watch_path == Path(".") else str(watch_path)
+
+
+def _relativize_source_files(payload: dict, root: Path) -> None:
+    for bucket in ("nodes", "edges", "hyperedges"):
+        for item in payload.get(bucket, []):
+            source = item.get("source_file")
+            if not source:
+                continue
+            source_path = Path(source)
+            if not source_path.is_absolute():
+                continue
+            try:
+                item["source_file"] = str(source_path.resolve().relative_to(root))
+            except ValueError:
+                continue
+
+
 def _rebuild_code(watch_path: Path, *, follow_symlinks: bool = False) -> bool:
     """Re-run AST extraction + build + cluster + report for code files. No LLM needed.
 
     Returns True on success, False on error.
     """
+    watch_root = watch_path.resolve()
+    project_root = Path.cwd().resolve() if not watch_path.is_absolute() else watch_root
+    report_root = _report_root_label(watch_path)
     try:
         from graphify.extract import extract
         from graphify.detect import detect
@@ -33,7 +57,7 @@ def _rebuild_code(watch_path: Path, *, follow_symlinks: bool = False) -> bool:
             print("[graphify watch] No code files found - nothing to rebuild.")
             return False
 
-        result = extract(code_files, cache_root=watch_path)
+        result = extract(code_files, cache_root=watch_root)
 
         # Preserve semantic nodes/edges from a previous full run.
         # AST-only rebuild replaces code nodes; doc/paper/image nodes are kept.
@@ -57,6 +81,8 @@ def _rebuild_code(watch_path: Path, *, follow_symlinks: bool = False) -> bool:
             except Exception:
                 pass  # corrupt graph.json - proceed with AST-only
 
+        _relativize_source_files(result, project_root)
+
         detection = {
             "files": {"code": [str(f) for f in code_files], "document": [], "paper": [], "image": []},
             "total_files": len(code_files),
@@ -74,7 +100,7 @@ def _rebuild_code(watch_path: Path, *, follow_symlinks: bool = False) -> bool:
         out.mkdir(exist_ok=True)
 
         report = generate(G, communities, cohesion, labels, gods, surprises, detection,
-                          {"input": 0, "output": 0}, str(watch_path), suggested_questions=questions)
+                          {"input": 0, "output": 0}, report_root, suggested_questions=questions)
         (out / "GRAPH_REPORT.md").write_text(report, encoding="utf-8")
         to_json(G, communities, str(out / "graph.json"))