--traverse-directory behavior is counterintuitive

[ctb]

Right now, --traverse-directory is a flag that tells various sourmash commands to turn on directory traversal when loading signatures, so that if you give sourmash a directory as a query it will find all the signatures under it. Per #649 this is confusing, and it trips me up conceptually, too.

I'm not sure what a good solution is, but a few thoughts --

• it would be conceptually simplifying if we allowed directories of signatures as both queries and databases, since sourmash supports both internally...
• maybe directory traversal could be on by default - if you provide a directory as an argument, it treats it as a collection of signatures? (See also Would a "Directory" Index be useful? #810.) Then --no-directory-traverse or something could be an option. (That doesn't really make sense, tho; maybe just "don't specify a directory on the command line" is better!)

random thoughts, for now. Just recording the convo.

[ctb]

this came up in #513 (comment) as well.