provide better docs and/or examples for command line loading of signatures

[ctb]

per #1090, confusions abound now that #1059 has been merged. we say in the docs,

Note that as of sourmash v3.4, most commands will load signatures from indexed databases (the SBT and LCA formats) as well as from signature files.

but this isn't very prominent.

--

• commands that take multiple input signatures can do so from databases!
• --query-from-file should contain a list of files you want to load from
• --query typically supports multiple files
• query signatures support loading from databases, etc., but you gotta pick just one (for e.g. search and gather). multigather will let you load many!

other things to mention:

• big LCA databases may take a while to load, while SBTs may be slower

[ctb]

big question is, what do we write and/or focus on?

• example queries, either in the specific command sections or in their own section
• better documentation in the specific commands
• high level documentation under "advanced command line usage" or something

not sure where our energies are best spent.

[ctb]

(right now I'm leaning towards an 'advanced usage' section that also lays out our design considerations.)

[ctb]

https://twitter.com/ctitusbrown/status/1281620331006799872

[ctb]

Looking at command-line.md, "advanced-command-line-usage", I'm actually pretty happy with what we have there. No plans to change prior to 4.0.

[ctb]

this is largely fixed in the docs by #2025 and others, I think. We could probably use more examples but that's always gonna be true