2. I found out that "see xyz" and "see also" have bespoke markup in Docbook -- <glosssee> and <glossseealso>. I changed some glossentries to use those, removing some glossdefs and changing a couple of paras to glossseealsos. I also removed all "id" properties from glossentries that are just <glosssee>, because I think it's a mistake to have references to entries that will make the reader look up a different term; for me as a reader that's annoying, and I don't like to annoy people.
+1 These structural enhancements are great. I'm fine with removing the id from just-glossee, and glad that we're keeping the entry to aid discovery.
I rewrote the definition for "atomic" once again. Made it two glossdefs, because I can. If you don't like this, I can undo.
+1 Splitting this into two definitions, one for each context, is the most sensible thing and I don't know why I didn't do that in the first place.