it seems like you can only upload one file at a time instead of a batch
If you make a gzipped tar file, you can upload that and it will be unpacked automatically. That is how I usually upload several files at once.
Is there a command-line alternative to working with the wysiwig file manager? Could I sftp into the system?
Our course is hosted on the MAA servers, and they don't provide ssh access to those, so no, you don't have command-line or sftp access to the course. If you ran your own server at your own college or university, you might be able to arrange for that.
what is the minimum code necessary to download to be able to test a .pg file (and not necessarily do anything else, like creating a homework, etc.)
The mechanisms that I know all rely on having a full WeBWorK installation, and I don't see an easy way to avoid that. I suppose it would be possible to make a command-line script that pulls in the required components of PG and WeBWorK that would compile the problem and return any error messages, or would allow you pass a collection of answers to pass to the answer checkers, and would return the results, but I don't know of anyone who has done that outside of a full installation with a server backend for processing the problems.