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. 

const auto & create_query = ast->as<const ASTCreateQuery &>();
        if (create_query.is_dictionary)
        {
            pool.scheduleOrThrowOnError([&]()
            {
                loadTableFromMetadata(local_context, path, name, ast, mode);
                
                logAboutProgress(log, ++dictionaries_processed, metadata.total_dictionaries, watch);
            });
        }
    }
    pool.wait();
    
    for (const auto & name_with_path_and_query : metadata.parsed_tables)
    {
        const auto & name = name_with_path_and_query.first;
        const auto & path = name_with_path_and_query.second.path;
        const auto & ast = name_with_path_and_query.second.ast;
        const auto & create_query = ast->as<const ASTCreateQuery &>();
        if (!create_query.is_dictionary)
        {
            pool.scheduleOrThrowOnError([&]()
            {
                loadTableFromMetadata(local_context, path, name, ast, mode);
                
                logAboutProgress(log, ++tables_processed, total_tables, watch);
            });
        }
    }
    pool.wait();