Using real database instead of using `.json` files as database

Advanced of #1894

I found a performance bottleneck: `atomicWrite` of `sites.json`.
This is significant when seeding many sites + sites frequency update.

When using `.json` files as database, if one row updates, whole file need to rewrite.
When using real database, if one row updates, only related disk sector need to rewrite.

该 issue 只提到 atomicWrite 和 sites.json，没有提供仓库文件或测试。首先定位这条写入路径，以及负责播种和频率更新的调用方；在实现之前明确数据库选择、迁移范围和可衡量的完成标准。

由索引模型根据 Issue 内容生成。