make config dump take into account modifications to the config

        # merge dictionaries, overriding from config file

        merge_dicts(cfg, file_cfg)

        self._validate_merged_config(cfg)

        self._dump_keys = list(cfg.keys())

        # set attributes from merged dictionary

        self.__dict__.update(cfg)

        # store the merged config for writing to file later

        self._yaml_dump = self._dump_yaml(cfg)

        # convert to Path

        self.input_path = Path(self.input_path).resolve().absolute()

        self.output_path = Path(self.output_path).resolve().absolute()

        return cfg

    def to_file(self, outfile: str|Path):

        to_dump = self._dump_yaml({k:v for k, v in self.__dict__.items() if k in self._dump_keys})

        with open(outfile, "w") as f:

            yaml.safe_dump(self._yaml_dump, f)

            yaml.safe_dump(to_dump, f)

    def _validate_file_cfg(self, cfg: dict, use_windows_codec_binaries: bool):

        """ensure configuration contains required keys"""