After much struggle, finally got a working eXist 1.4 up on the server, and so far so good: uploads/indexing are going very quickly, and the site seems to be working perfectly without the need for all the re-indexing we had to do before. I found a bug immediately in my code which creates id attributes for page-breaks: there was an <fw> tag with no content, which tripped up my function for creating an id. That's now fixed.

I also noticed that footnote popups and reference popups were typically on top of each other, so I've moved the footnote popup down the page a bit. We should also add a close button to both of those.

Finally, I've made the menu position: fixed, because I was getting sick of scrolling back up the page to get to it...