Spent most of the day working on the HTML diagnostics, which I think are now done, at least in the XSLT 2.0 version. I've split the build into multiple targets and it runs quite smoothly. While I originally used regexes to see if a file exists locally, I've decided to just do it by sequence checking (i.e. $fileSequence[.=$thisFile]). After a certain point the regex becomes too slow whereas this is consistently quick.
Ran this on MoEML (15 minutes) and Graves (1.5 minutes) and the results are interesting. MoEML has a ton of broken links, particularly in the Ajax pages, that MH and I will need to discuss; Graves also has some broken links, but only on the gallery pages. From what I can tell, the titles are being processed by templates, but no appendix content is being created; we could decide to either just take the text, apply templates to the title in a different mode, or add an appendix to these pages.