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. 

global_context->setUserScriptsPath(user_scripts_path);
        fs::create_directories(user_scripts_path);
    }
    {
        std::string user_defined_path = config().getString("user_defined_path", path / "user_defined/");
        global_context->setUserDefinedPath(user_defined_path);
        fs::create_directories(user_defined_path);
    }
    
    {
        const std::string & top_level_domains_path = config().getString("top_level_domains_path", path / "top_level_domains/");
        TLDListsHolder::getInstance().parseConfig(fs::path(top_level_domains_path) / "", config());
    }
    {
        fs::create_directories(path / "data/");
        fs::create_directories(path / "metadata/");
        
        fs::create_directories(path / "metadata_dropped/");
    }
#if USE_ROCKSDB
    
    if (config().has("merge_tree_metadata_cache"))
    {
        fs::create_directories(path / "rocksdb/");
        size_t size = config().getUInt64("merge_tree_metadata_cache.lru_cache_size", 256 << 20);
        bool continue_if_corrupted = config().getBool("merge_tree_metadata_cache.continue_if_corrupted", false);
        try
        {
            LOG_DEBUG(
                log, "Initiailizing merge tree metadata cache lru_cache_size:{} continue_if_corrupted:{}", size, continue_if_corrupted);