Do you use a content management system to generate all those
pages? Which one? How does it work?

I wrote the CMS from scratch, which is why it took me so long (about 20
months) to get this new version of the site online. None of the other
CMS software out there would do most of the things I wanted --
taxonomic hierarchy, common names integrated everywhere, glossary terms
with clickable definitions, book citations almost automatic, etc. It
was a lot of work but it pays off now that this site is so easy to
improve and add to.