several sourmash sig commands do not use 'modern' signature output methods

[ctb]

I noticed that several functions in src/sourmash/sig/__main__.py use sourmash.save_signatures(...) insteads of sourmash_args.SaveSignaturesToLocation(...). This means they only output JSON signatures, and will not save to .zip, directories, etc.

To resolve this issue, replace all of the uses of sourmash.save_signatures(...) with sourmash_args.SaveSignaturesToLocation(...).

You can use the code in sourmash sig inflate (#1889) as an example of how to do it. Note that you'll need to set the default value for -o/--output to stdin ('-') to get the right stdout behavior.