refactor: save preprocessed data into one .hdf5 file as default

[gcroci2]

Now the preprocessed data are saved into one hdf5 as default. The user can always decide to keep them in separated files using combine_files parameter in preprocess function.

This is the current order of arguments in preprocess:

def preprocess(
    queries: List[Query],
    prefix: Optional[str] = None,
    process_count: Optional[int] = None,
    combine_files: bool = True,
    feature_modules: Union[List[ModuleType], str] = "all"
    ):

Now the user can fill in the arguments like this: preprocess(queries, prefix) in the default case (that is supposed to be the most used one, especially when starting using the package; the possibility to select only some features from the beginning should be used by "expert" users that already have lots of insights on the features themselves). So if we put it in a position different from the last ones --same applies to combine_files-- , then it will be always needed to specify the arguments like this: preprocess(queries=queries, prefix=prefix).

But we can think about changing such order @DaniBodor