Add --force flag and GRAPHIFY_FORCE env var to graphify update

Bypasses the node-count safety check in to_json for refactors that
legitimately shrink the graph (renames, package deletions). Also
honored by post-commit and post-checkout hooks via GRAPHIFY_FORCE=1.

Implements the approach from #639 (targeted at v5) adapted for v6.

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

graphify/__main__.py

@@ -1009,6 +1009,8 @@ def main() -> None:
         print("    --dir <path>            target directory (default: ./raw)")
         print("  watch <path>            watch a folder and rebuild the graph on code changes")
         print("  update <path>           re-extract code files and update the graph (no LLM needed)")
+        print("    --force                 overwrite graph.json even if the rebuild has fewer nodes")
+        print("                            (also: GRAPHIFY_FORCE=1 env var; use after refactors that delete code)")
         print("  cluster-only <path>     rerun clustering on an existing graph.json and regenerate report")
         print("  query \"<question>\"       BFS traversal of graph.json for a question")
         print("    --dfs                   use depth-first instead of breadth-first")
@@ -1423,8 +1425,13 @@ def main() -> None:
         print(f"Done — {len(communities)} communities. GRAPH_REPORT.md, graph.json and graph.html updated.")
 
     elif cmd == "update":
-        if len(sys.argv) > 2:
-            watch_path = Path(sys.argv[2])
+        force = os.environ.get("GRAPHIFY_FORCE", "").lower() in ("1", "true", "yes")
+        argv = list(sys.argv)
+        if "--force" in argv[2:]:
+            force = True
+            argv = [a for a in argv if a != "--force"]
+        if len(argv) > 2:
+            watch_path = Path(argv[2])
         else:
             # Try to recover the scan root saved by the last full build
             saved = Path("graphify-out/.graphify_root")
@@ -1437,7 +1444,7 @@ def main() -> None:
             sys.exit(1)
         from graphify.watch import _rebuild_code
         print(f"Re-extracting code files in {watch_path} (no LLM needed)...")
-        ok = _rebuild_code(watch_path)
+        ok = _rebuild_code(watch_path, force=force)
         if ok:
             print("Code graph updated. For doc/paper/image changes run /graphify --update in your AI assistant.")
             if not os.environ.get("MOONSHOT_API_KEY") and not os.environ.get("GRAPHIFY_NO_TIPS"):

graphify/hooks.py

@@ -80,8 +80,10 @@ if not changed:
 print(f'[graphify hook] {len(changed)} file(s) changed - rebuilding graph...')
 
 try:
+    import os as _os
     from graphify.watch import _rebuild_code
-    _rebuild_code(Path('.'))
+    _force = _os.environ.get('GRAPHIFY_FORCE', '').lower() in ('1', 'true', 'yes')
+    _rebuild_code(Path('.'), force=_force)
 except Exception as exc:
     print(f'[graphify hook] Rebuild failed: {exc}')
     sys.exit(1)
@@ -124,9 +126,10 @@ echo "[graphify] Branch switched - launching background rebuild (log: $_GRAPHIFY
 nohup $GRAPHIFY_PYTHON -c "
 from graphify.watch import _rebuild_code
 from pathlib import Path
-import sys
+import os, sys
 try:
-    _rebuild_code(Path('.'))
+    _force = os.environ.get('GRAPHIFY_FORCE', '').lower() in ('1', 'true', 'yes')
+    _rebuild_code(Path('.'), force=_force)
 except Exception as exc:
     print(f'[graphify] Rebuild failed: {exc}')
     sys.exit(1)

graphify/watch.py

@@ -33,9 +33,13 @@ def _relativize_source_files(payload: dict, root: Path) -> None:
                 continue
 
 
-def _rebuild_code(watch_path: Path, *, follow_symlinks: bool = False) -> bool:
+def _rebuild_code(watch_path: Path, *, follow_symlinks: bool = False, force: bool = False) -> bool:
     """Re-run AST extraction + build + cluster + report for code files. No LLM needed.
 
+    When ``force`` is True the node-count safety check in ``to_json`` is bypassed
+    so the rebuilt graph overwrites graph.json even if it has fewer nodes.
+    Use this after refactors that legitimately delete code.
+
     Returns True on success, False on error.
     """
     watch_root = watch_path.resolve()
@@ -105,7 +109,7 @@ def _rebuild_code(watch_path: Path, *, follow_symlinks: bool = False) -> bool:
         out.mkdir(exist_ok=True)
         (out / ".graphify_root").write_text(str(watch_root), encoding="utf-8")
 
-        json_written = to_json(G, communities, str(out / "graph.json"))
+        json_written = to_json(G, communities, str(out / "graph.json"), force=force)
         if not json_written:
             return False