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 AlterCommands & commands, ContextPtr query_context, AlterLockHolder & table_lock_holder)
{
    assertNotReadonly();
    auto table_id = getStorageID();
    if (commands.isSettingsAlter())
    {
        
        
        StorageInMemoryMetadata future_metadata = getInMemoryMetadata();
        commands.apply(future_metadata, query_context);
        merge_strategy_picker.refreshState();
        changeSettings(future_metadata.settings_changes, table_lock_holder);
        DatabaseCatalog::instance().getDatabase(table_id.database_name)->alterTable(query_context, table_id, future_metadata);
        return;
    }
    auto ast_to_str = [](ASTPtr query) -> String
    {
        if (!query)
            return "";
        return queryToString(query);
    };
    const auto zookeeper = getZooKeeperAndAssertNotReadonly();
    std::optional<ReplicatedMergeTreeLogEntryData> alter_entry;
    std::optional<String> mutation_znode;
    while (true)
    {