Fix blocking I/O on event loop, cache graphviz, optimize DB sync

Move all save_json/load_json/sync_to_db/DB calls off the event loop
with asyncio.to_thread to prevent UI freezes. Cache graphviz SVG by
DOT source hash (bounded LRU of 20). Replace DELETE-all/re-INSERT in
sync_to_db with UPSERT + targeted DELETE. Add DB indexes, COUNT query,
and reduce graph poll interval to 0.5s.

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

utils.py

@@ -184,11 +184,11 @@ def sync_to_db(db, project_name: str, file_path: Path, data: dict) -> None:
         # Use a single transaction for atomicity
         db.conn.execute("BEGIN IMMEDIATE")
         try:
+            now = time.time()
             df = db.get_data_file(proj["id"], file_name)
             top_level = {k: v for k, v in data.items()
                          if k not in (KEY_BATCH_DATA, KEY_HISTORY_TREE)}
             if not df:
-                now = time.time()
                 cur = db.conn.execute(
                     "INSERT INTO data_files (project_id, name, data_type, top_level, created_at, updated_at) "
                     "VALUES (?, ?, ?, ?, ?, ?)",
@@ -198,7 +198,6 @@ def sync_to_db(db, project_name: str, file_path: Path, data: dict) -> None:
             else:
                 df_id = df["id"]
                 # Update top_level metadata
-                now = time.time()
                 db.conn.execute(
                     "UPDATE data_files SET top_level = ?, updated_at = ? WHERE id = ?",
                     (json.dumps(top_level), now, df_id),
@@ -207,23 +206,31 @@ def sync_to_db(db, project_name: str, file_path: Path, data: dict) -> None:
             # Sync sequences
             batch_data = data.get(KEY_BATCH_DATA, [])
             if isinstance(batch_data, list):
-                db.conn.execute("DELETE FROM sequences WHERE data_file_id = ?", (df_id,))
+                new_seq_nums = set()
                 for item in batch_data:
                     if not isinstance(item, dict):
                         continue
                     seq_num = int(item.get(KEY_SEQUENCE_NUMBER, 0))
-                    now = time.time()
+                    new_seq_nums.add(seq_num)
                     db.conn.execute(
                         "INSERT INTO sequences (data_file_id, sequence_number, data, updated_at) "
                         "VALUES (?, ?, ?, ?) "
                         "ON CONFLICT(data_file_id, sequence_number) DO UPDATE SET data=excluded.data, updated_at=excluded.updated_at",
                         (df_id, seq_num, json.dumps(item), now),
                     )
+                # Remove sequences that no longer exist
+                if new_seq_nums:
+                    placeholders = ','.join('?' * len(new_seq_nums))
+                    db.conn.execute(
+                        f"DELETE FROM sequences WHERE data_file_id = ? AND sequence_number NOT IN ({placeholders})",
+                        (df_id, *new_seq_nums),
+                    )
+                else:
+                    db.conn.execute("DELETE FROM sequences WHERE data_file_id = ?", (df_id,))
 
             # Sync history tree
             history_tree = data.get(KEY_HISTORY_TREE)
             if history_tree and isinstance(history_tree, dict):
-                now = time.time()
                 db.conn.execute(
                     "INSERT INTO history_trees (data_file_id, tree_data, updated_at) "
                     "VALUES (?, ?, ?) "