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. 

ops.emplace_back(zkutil::makeCreateRequest(zookeeper_path + "/temp", "",
            zkutil::CreateMode::Persistent));
        ops.emplace_back(zkutil::makeCreateRequest(zookeeper_path + "/replicas", "last added replica: " + replica_name,
            zkutil::CreateMode::Persistent));
        
        ops.emplace_back(zkutil::makeCreateRequest(zookeeper_path + "/quorum", "",
            zkutil::CreateMode::Persistent));
        ops.emplace_back(zkutil::makeCreateRequest(zookeeper_path + "/quorum/last_part", "",
            zkutil::CreateMode::Persistent));
        ops.emplace_back(zkutil::makeCreateRequest(zookeeper_path + "/quorum/failed_parts", "",
            zkutil::CreateMode::Persistent));
        ops.emplace_back(zkutil::makeCreateRequest(zookeeper_path + "/mutations", "",
            zkutil::CreateMode::Persistent));
        
        ops.emplace_back(zkutil::makeCreateRequest(replica_path, "",
            zkutil::CreateMode::Persistent));
        ops.emplace_back(zkutil::makeCreateRequest(replica_path + "/host", "",
            zkutil::CreateMode::Persistent));
        ops.emplace_back(zkutil::makeCreateRequest(replica_path + "/log_pointer", "",
            zkutil::CreateMode::Persistent));
        ops.emplace_back(zkutil::makeCreateRequest(replica_path + "/queue", "",
            zkutil::CreateMode::Persistent));
        ops.emplace_back(zkutil::makeCreateRequest(replica_path + "/parts", "",
            zkutil::CreateMode::Persistent));
        ops.emplace_back(zkutil::makeCreateRequest(replica_path + "/flags", "",
            zkutil::CreateMode::Persistent));
        ops.emplace_back(zkutil::makeCreateRequest(replica_path + "/is_lost", "0",
            zkutil::CreateMode::Persistent));
        ops.emplace_back(zkutil::makeCreateRequest(replica_path + "/metadata", metadata_str,
            zkutil::CreateMode::Persistent));