Ordinary database engine is deprecated but there is no simple mean to change database engine to Atomic for existing databases.

Possible options:
- ALTER DATABASE MODIFY ENGINE query.
- Flag that triggers migration at ClickHouse startup.

The latter should be easier to implement. 

Poco::Util::AbstractConfiguration & config,
    const Strings & listen_hosts,
    const Strings & interserver_listen_hosts,
    bool listen_try,
    Poco::ThreadPool & server_pool,
    AsynchronousMetrics & async_metrics,
    std::vector<ProtocolServerAdapter> & servers,
    bool start_servers)
{
    const Settings & settings = global_context->getSettingsRef();
    Poco::Timespan keep_alive_timeout(config.getUInt("keep_alive_timeout", 10), 0);
    Poco::Net::HTTPServerParams::Ptr http_params = new Poco::Net::HTTPServerParams;
    http_params->setTimeout(settings.http_receive_timeout);
    http_params->setKeepAliveTimeout(keep_alive_timeout);
    for (const auto & listen_host : listen_hosts)
    {