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. 

{
public:
    DatabaseOrdinary(const String & name_, const String & metadata_path_, ContextPtr context);
    DatabaseOrdinary(
        const String & name_, const String & metadata_path_, const String & data_path_,
        const String & logger, ContextPtr context_);
    String getEngineName() const override { return "Ordinary"; }
    void loadStoredObjects(ContextMutablePtr context, LoadingStrictnessLevel mode, bool skip_startup_tables) override;
    bool supportsLoadingInTopologicalOrder() const override { return true; }
    void loadTablesMetadata(ContextPtr context, ParsedTablesMetadata & metadata, bool is_startup) override;
    void loadTableFromMetadata(ContextMutablePtr local_context, const String & file_path, const QualifiedTableName & name, const ASTPtr & ast,
        LoadingStrictnessLevel mode) override;
    void startupTables(ThreadPool & thread_pool, LoadingStrictnessLevel mode) override;
    void alterTable(
        ContextPtr context,
        const StorageID & table_id,
        const StorageInMemoryMetadata & metadata) override;
protected:
    virtual void commitAlterTable(
        const StorageID & table_id,
        const String & table_metadata_tmp_path,
        const String & table_metadata_path,
        const String & statement,
        ContextPtr query_context);
};
}