xml generation fixes

This is on the way to implement #910 (closed), but it also fixes some bugs brought up in #802 (closed). What this does:

1. It turns out our math wasn't actually being turned into valid JATS! Now it is. Oops!
2. Supplementary files now have the file name they were given when uploaded.
3. Some fixes for crashes in zip file generation when things aren't exactly as we expect them to be. This includes the situation, for example, when a pasted-in image in Wax isn't actually in the image store but is remote; there should be a deeper fix for this, but we're not crashing any more if it happens.

This does not add SVGs into the output zip, but it won't be hard to get there from here.