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. 

bool create_default_db_if_not_exists = !default_database_name.empty();
    bool metadata_dir_for_default_db_already_exists = databases.contains(default_database_name);
    if (create_default_db_if_not_exists && !metadata_dir_for_default_db_already_exists)
    {
        checkUnsupportedVersion(context, default_database_name);
        databases.emplace(default_database_name, std::filesystem::path(path) / escapeForFileName(default_database_name));
    }
    TablesLoader::Databases loaded_databases;
    for (const auto & [name, db_path] : databases)
    {
        loadDatabase(context, name, db_path, has_force_restore_data_flag);
        loaded_databases.insert({name, DatabaseCatalog::instance().getDatabase(name)});
    }
    auto mode = getLoadingStrictnessLevel( true,  true, has_force_restore_data_flag);
    TablesLoader loader{context, std::move(loaded_databases), mode};
    loader.loadTables();
    loader.startupTables();
    if (has_force_restore_data_flag)
    {
        try
        {
            fs::remove(force_restore_data_flag_file);
        }
        catch (...)
        {
            tryLogCurrentException("Load metadata", "Can't remove force restore file to enable data sanity checks");
        }
    }
}
static void loadSystemDatabaseImpl(ContextMutablePtr context, const String & database_name, const String & default_engine)