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. 

if (new_projections_str != current_metadata->projections.toString())
            future_metadata_in_zk.projections = new_projections_str;
        String new_constraints_str = future_metadata.constraints.toString();
        if (new_constraints_str != current_metadata->constraints.toString())
            future_metadata_in_zk.constraints = new_constraints_str;
        Coordination::Requests ops;
        size_t alter_path_idx = std::numeric_limits<size_t>::max();
        size_t mutation_path_idx = std::numeric_limits<size_t>::max();
        String new_metadata_str = future_metadata_in_zk.toString();
        ops.emplace_back(zkutil::makeSetRequest(fs::path(zookeeper_path) / "metadata", new_metadata_str, metadata_version));
        String new_columns_str = future_metadata.columns.toString();
        ops.emplace_back(zkutil::makeSetRequest(fs::path(zookeeper_path) / "columns", new_columns_str, -1));
        if (ast_to_str(current_metadata->settings_changes) != ast_to_str(future_metadata.settings_changes))
        {
            
            StorageInMemoryMetadata metadata_copy = *current_metadata;
            metadata_copy.settings_changes = future_metadata.settings_changes;
            changeSettings(metadata_copy.settings_changes, table_lock_holder);
            DatabaseCatalog::instance().getDatabase(table_id.database_name)->alterTable(query_context, table_id, metadata_copy);
        }
        
        
        int new_metadata_version = metadata_version + 1;
        alter_entry->type = LogEntry::ALTER_METADATA;
        alter_entry->source_replica = replica_name;
        alter_entry->metadata_str = new_metadata_str;
        alter_entry->columns_str = new_columns_str;
        alter_entry->alter_version = new_metadata_version;
        alter_entry->create_time = time(nullptr);
        auto maybe_mutation_commands = commands.getMutationCommands(