fix Husky 9 hook path, skill.md INPUT_PATH literal, per-worker exception isolation

- hooks.py: add _user_hooks_dir() to target .husky/ instead of .husky/_ on Husky 9 repos (#987)
- skill.md: replace unsubstituted 'INPUT_PATH' literal with '.' in generate() calls (#986)
- extract.py: wrap future.result() per-future so a single worker failure prints a warning instead of falling back to full sequential re-extraction (#943)

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

graphify/extract.py

@@ -7434,8 +7434,15 @@ def _extract_parallel(
                 pool.submit(_extract_single_file, item): item[0] for item in work_items
             }
             for future in concurrent.futures.as_completed(futures):
-                idx, result = future.result()
-                per_file[idx] = result
+                try:
+                    idx, result = future.result()
+                    per_file[idx] = result
+                except Exception as exc:
+                    idx = futures[future]
+                    print(
+                        f"  warning: worker failed for {work_items[idx][1]}: {exc}",
+                        file=sys.stderr, flush=True,
+                    )
                 done_count += 1
                 if (
                     total_files >= _PROGRESS_INTERVAL

graphify/hooks.py

@@ -259,13 +259,26 @@ def _uninstall_hook(hooks_dir: Path, name: str, marker: str, marker_end: str) ->
     return f"graphify removed from {name} at {hook_path} (other hook content preserved)"
 
 
+def _user_hooks_dir(hooks_dir: Path) -> Path:
+    """Return the user-editable hooks directory.
+
+    Husky 9 sets core.hooksPath to .husky/_ (wrapper scripts auto-generated by
+    Husky), while user-editable hooks live in the parent .husky/. Return the
+    parent when the resolved dir ends in '_' so install/status/uninstall target
+    the correct location (#987).
+    """
+    if hooks_dir.name == "_":
+        return hooks_dir.parent
+    return hooks_dir
+
+
 def install(path: Path = Path(".")) -> str:
     """Install graphify post-commit and post-checkout hooks in the nearest git repo."""
     root = _git_root(path)
     if root is None:
         raise RuntimeError(f"No git repository found at or above {path.resolve()}")
 
-    hooks_dir = _hooks_dir(root)
+    hooks_dir = _user_hooks_dir(_hooks_dir(root))
 
     commit_msg = _install_hook(hooks_dir, "post-commit", _HOOK_SCRIPT, _HOOK_MARKER)
     checkout_msg = _install_hook(hooks_dir, "post-checkout", _CHECKOUT_SCRIPT, _CHECKOUT_MARKER)
@@ -279,7 +292,7 @@ def uninstall(path: Path = Path(".")) -> str:
     if root is None:
         raise RuntimeError(f"No git repository found at or above {path.resolve()}")
 
-    hooks_dir = _hooks_dir(root)
+    hooks_dir = _user_hooks_dir(_hooks_dir(root))
     commit_msg = _uninstall_hook(hooks_dir, "post-commit", _HOOK_MARKER, _HOOK_MARKER_END)
     checkout_msg = _uninstall_hook(hooks_dir, "post-checkout", _CHECKOUT_MARKER, _CHECKOUT_MARKER_END)
 
@@ -291,7 +304,7 @@ def status(path: Path = Path(".")) -> str:
     root = _git_root(path)
     if root is None:
         return "Not in a git repository."
-    hooks_dir = _hooks_dir(root)
+    hooks_dir = _user_hooks_dir(_hooks_dir(root))
 
     def _check(name: str, marker: str) -> str:
         p = hooks_dir / name

graphify/skill.md

@@ -537,7 +537,7 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
 # Placeholder questions - regenerated with real labels in Step 5
 questions = suggest_questions(G, communities, labels)
 
-report = generate(G, communities, cohesion, labels, gods, surprises, detection, tokens, 'INPUT_PATH', suggested_questions=questions)
+report = generate(G, communities, cohesion, labels, gods, surprises, detection, tokens, '.', suggested_questions=questions)
 Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
 to_json(G, communities, 'graphify-out/graph.json')
 
@@ -591,7 +591,7 @@ labels = LABELS_DICT
 # Regenerate questions with real community labels (labels affect question phrasing)
 questions = suggest_questions(G, communities, labels)
 
-report = generate(G, communities, cohesion, labels, analysis['gods'], analysis['surprises'], detection, tokens, 'INPUT_PATH', suggested_questions=questions)
+report = generate(G, communities, cohesion, labels, analysis['gods'], analysis['surprises'], detection, tokens, '.', suggested_questions=questions)
 Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
 Path('graphify-out/.graphify_labels.json').write_text(json.dumps({str(k): v for k, v in labels.items()}, ensure_ascii=False), encoding=\"utf-8\")
 print('Report updated with community labels')