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. 

server.stop();
            current_connections += server.currentConnections();
        }
        if (!current_connections)
            break;
        sleep_current_ms += sleep_one_ms;
        if (sleep_current_ms < sleep_max_ms)
            std::this_thread::sleep_for(std::chrono::milliseconds(sleep_one_ms));
        else
            break;
    }
    return current_connections;
}
}
namespace DB
{
namespace ErrorCodes
{
    extern const int NO_ELEMENTS_IN_CONFIG;
    extern const int SUPPORT_IS_DISABLED;
    extern const int ARGUMENT_OUT_OF_BOUND;
    extern const int EXCESSIVE_ELEMENT_IN_CONFIG;
    extern const int INVALID_CONFIG_PARAMETER;
    extern const int SYSTEM_ERROR;
    extern const int FAILED_TO_GETPWUID;
    extern const int MISMATCHING_USERS_FOR_PROCESS_AND_DATA;
    extern const int NETWORK_ERROR;
    extern const int CORRUPTED_DATA;
}
static std::string getCanonicalPath(std::string && path)