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>

db.py

@@ -47,6 +47,9 @@ CREATE TABLE IF NOT EXISTS history_trees (
     tree_data     TEXT NOT NULL DEFAULT '{}',
     updated_at    REAL NOT NULL
 );
+
+CREATE INDEX IF NOT EXISTS idx_data_files_project_id ON data_files(project_id);
+CREATE INDEX IF NOT EXISTS idx_sequences_data_file_id ON sequences(data_file_id);
 """
 
 
@@ -146,6 +149,14 @@ class ProjectDB:
         ).fetchall()
         return [dict(r) for r in rows]
 
+    def count_data_files(self, project_id: int) -> int:
+        """Return the number of data files for a project."""
+        row = self.conn.execute(
+            "SELECT COUNT(*) AS cnt FROM data_files WHERE project_id = ?",
+            (project_id,),
+        ).fetchone()
+        return row["cnt"]
+
     def get_data_file(self, project_id: int, name: str) -> dict | None:
         row = self.conn.execute(
             "SELECT id, project_id, name, data_type, top_level, created_at, updated_at "