bug: gather --save-prefetch-csv does not save all matches

[ctb]

when @bluegenes was digging into some classification results, she discovered that gather was not outputting all of the prefetch results (as evaluated by comparing to sourmash prefetch -o ...).

(IMO they should always be the same.)

This is a bug / behavior change introduced in #2116, merged into latest in #2111, and released in sourmash v4.4.2.

In brief,

• in [MRG] subtantial refactoring of CounterGather and related Index code. #2116, I changed CounterGather over to using a dict with md5sum as key to store signatures;
• this means that when sketches with identical contents are encountered, only one is stored;
• and then when the list of all signatures is retrieved with CounterGather.signatures() duplicates are omitted;

The relevant code in commands.py::gather is:

        for db in databases:
            counter = None
            try:
                counter = db.counter_gather(prefetch_query, args.threshold_bp)
            except ValueError:
                # catch "no signatures to search" ValueError if empty db.       
                continue

            save_prefetch.add_many(counter.signatures())

            if prefetch_csvout_fp:
                for found_sig in counter.signatures():
                    ... # write info to CSV

and here .signatures() is not returning all signatures.

I'm not 100% sure how to resolve this. One option would be to adjust CounterGather to save prefetch results internally; possible, but maybe messy? Another would be to store all the signatures in a list, too.

Ideally any solution would result in the same code being used in commands.py::gather and commands.py::prefetch so that this doesn't happen again ;). And of course we'll want some tests.