Fix semantic node preservation on incremental rebuild and detach git hooks

watch.py: filter preserved nodes by ID membership in new AST output instead
of file_type — INFERRED/AMBIGUOUS nodes on code files also carry file_type=code
and were being wrongly dropped, triggering the to_json safety check refusal.

hooks.py: detach post-commit and post-checkout rebuilds with nohup + disown
so git commit returns immediately instead of blocking for the full rebuild
duration. Rebuild log written to ~/.cache/graphify-rebuild.log.

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

graphify/hooks.py

@@ -61,7 +61,13 @@ fi
 
 """ + _PYTHON_DETECT + """
 export GRAPHIFY_CHANGED="$CHANGED"
-$GRAPHIFY_PYTHON -c "
+
+# Run rebuild detached so git commit returns immediately.
+# Full repo rebuilds can take hours; blocking the post-commit hook stalls the shell.
+_GRAPHIFY_LOG="${HOME}/.cache/graphify-rebuild.log"
+mkdir -p "$(dirname "$_GRAPHIFY_LOG")"
+echo "[graphify hook] launching background rebuild (log: $_GRAPHIFY_LOG)"
+nohup $GRAPHIFY_PYTHON -c "
 import os, sys
 from pathlib import Path
 
@@ -79,7 +85,8 @@ try:
 except Exception as exc:
     print(f'[graphify hook] Rebuild failed: {exc}')
     sys.exit(1)
-"
+" > "$_GRAPHIFY_LOG" 2>&1 < /dev/null &
+disown 2>/dev/null || true
 # graphify-hook-end
 """
 
@@ -111,8 +118,10 @@ GIT_DIR=$(git rev-parse --git-dir 2>/dev/null)
 [ -f "$GIT_DIR/CHERRY_PICK_HEAD" ] && exit 0
 
 """ + _PYTHON_DETECT + """
-echo "[graphify] Branch switched - rebuilding knowledge graph (code files)..."
-$GRAPHIFY_PYTHON -c "
+_GRAPHIFY_LOG="${HOME}/.cache/graphify-rebuild.log"
+mkdir -p "$(dirname "$_GRAPHIFY_LOG")"
+echo "[graphify] Branch switched - launching background rebuild (log: $_GRAPHIFY_LOG)"
+nohup $GRAPHIFY_PYTHON -c "
 from graphify.watch import _rebuild_code
 from pathlib import Path
 import sys
@@ -121,7 +130,8 @@ try:
 except Exception as exc:
     print(f'[graphify] Rebuild failed: {exc}')
     sys.exit(1)
-"
+" > "$_GRAPHIFY_LOG" 2>&1 < /dev/null &
+disown 2>/dev/null || true
 # graphify-checkout-hook-end
 """
 

graphify/watch.py

@@ -60,20 +60,25 @@ def _rebuild_code(watch_path: Path, *, follow_symlinks: bool = False) -> bool:
         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.
+        # AST-only rebuild replaces nodes for changed files; everything else is kept.
+        # Filter by node ID membership in the new AST output, not by file_type —
+        # INFERRED/AMBIGUOUS nodes extracted from code files also carry file_type="code"
+        # and would be wrongly dropped by a file_type-based filter.
         out = watch_path / "graphify-out"
         existing_graph = out / "graph.json"
         if existing_graph.exists():
             try:
                 existing = json.loads(existing_graph.read_text(encoding="utf-8"))
-                code_ids = {n["id"] for n in existing.get("nodes", []) if n.get("file_type") == "code"}
-                sem_nodes = [n for n in existing.get("nodes", []) if n.get("file_type") != "code"]
-                sem_edges = [e for e in existing.get("links", existing.get("edges", []))
-                             if e.get("confidence") in ("INFERRED", "AMBIGUOUS")
-                             or (e.get("source") not in code_ids and e.get("target") not in code_ids)]
+                new_ast_ids = {n["id"] for n in result["nodes"]}
+                preserved_nodes = [n for n in existing.get("nodes", []) if n["id"] not in new_ast_ids]
+                all_ids = new_ast_ids | {n["id"] for n in preserved_nodes}
+                preserved_edges = [
+                    e for e in existing.get("links", existing.get("edges", []))
+                    if e.get("source") in all_ids and e.get("target") in all_ids
+                ]
                 result = {
-                    "nodes": result["nodes"] + sem_nodes,
-                    "edges": result["edges"] + sem_edges,
+                    "nodes": result["nodes"] + preserved_nodes,
+                    "edges": result["edges"] + preserved_edges,
                     "hyperedges": existing.get("hyperedges", []),
                     "input_tokens": 0,
                     "output_tokens": 0,