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. 

ContextMutablePtr context,
        const ASTCreateQuery & query,
        DatabaseOrdinary & database,
        const String & database_name,
        const String & metadata_path,
        bool force_restore)
    {
        try
        {
            auto [table_name, table] = createTableFromAST(
                query,
                database_name,
                database.getTableDataPath(query),
                context,
                force_restore);
            database.attachTable(context, table_name, table, database.getTableDataPath(query));
        }
        catch (Exception & e)
        {
            e.addMessage(
                "Cannot attach table " + backQuote(database_name) + "." + backQuote(query.getTable()) + " from metadata file " + metadata_path
                + " from query " + serializeAST(query));
            throw;
        }
    }
}
DatabaseOrdinary::DatabaseOrdinary(const String & name_, const String & metadata_path_, ContextPtr context_)