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. 

{
    LOG_INFO(log, "Restoring replica metadata");
    if (!is_readonly)
        throw Exception(ErrorCodes::BAD_ARGUMENTS, "Replica must be readonly");
    if (getZooKeeper()->exists(replica_path))
        throw Exception(ErrorCodes::BAD_ARGUMENTS,
                        "Replica path is present at {} - nothing to restore. "
                        "If you are sure that metadata is lost and that replica path contains some garbage, "
                        "then use SYSTEM DROP REPLICA query first.", replica_path);
    if (has_metadata_in_zookeeper.has_value() && *has_metadata_in_zookeeper)
        throw Exception(ErrorCodes::LOGICAL_ERROR, "Replica has metadata in ZooKeeper: "
                                                   "it's either a bug or it's a result of manual intervention to ZooKeeper");
    if (are_restoring_replica.exchange(true))
        throw Exception(ErrorCodes::CONCURRENT_ACCESS_NOT_SUPPORTED, "Replica restoration in progress");
    SCOPE_EXIT({ are_restoring_replica.store(false); });
    auto metadata_snapshot = getInMemoryMetadataPtr();
    const DataPartsVector all_parts = getAllDataPartsVector();
    Strings active_parts_names;