simplify/refactor load_* sig/db functions in sourmash_args.py

[ctb]

There's a confusing mess of loading functions in sourmash_args.py that's slowly converging as we simplify and refactor our Index handling code.

In no particular order,

there's query loading code, load_query_signature. This is responsible for loading a single signature. I think it can probably stay.

there's generic file loading code, load_file_as_signatures and load_file_as_index. I think these can be combined pretty easily now, since they are both simple wrappers around another function.

there's subject loading code, load_many_signatures and load_dbs_and_sigs, which I bet could be combined. The main difference seems to be in diagnostic output.

there's utility functions, traverse_find_sigs and load_pathlist_from_file, which can probably be moved under sourmash.index now, or otherwise refactored out of sourmash_args.

and finally the SignatureLoadingProgress class can probably go away, since CLI functions are mostly moving away from loading long lists of signatures.

[ctb]

more generally, per throwaway comment in #1871, would be good to take a holistic look at all the crud in the argument loading/parsing code for commands.py and sig/__main__.py and figure out how much of it can be put in one place. I'm guessing a lot of the signature loading compatibility code can be refactored into a single function.

[ctb]

also relevant: picking query ksize automatically to match provided databases #809

[ctb]

ref #1894 - remove is_database?

[ctb]

ref #1312

[ctb]

ref #1062 and #1060

[ctb]

wow, this has become a tangled mess of interconnected issues with no clear path forward. yay!

the main comment from the issues that resonates most is from #1426:

I'm wondering if the right answer is to track the total number of signatures in a collection (using e.g. manifests) and when doing a search of some kind, provide a generic indicator of what fraction of the collection is actually being searched? This should be straightforward.

[ctb]

PR #2204 cleans up signature load/selection reporting for load_dbs_and_sigs.

[ctb]

moving parts of this comment here -

• load_query_signature is used in only a few places, and is only used for CLI functionality around loading a query signature from a file. It is not very well written.

My current hot take is that

• load_query_signature should become the public API, and it should be better written. start thinking about a standard selector framework for signature search/compatibility #1072 also seems relevant.