Having a Glossary as an Appendix to the manual would be useful, I believe, in order to make more accessible Scrivener’s unique terminology. I get lost in Scrivener’s terms. Put another way, the glossary would display a Scrivener term, and then explain it. An obvious example would be the Inspector. What’s an Inspector? It’s a term with a simple explanation and an essential role in the Scrivener process. Show me how it works and what it is. Links in the glossary’s definitions might help refer back to explainations in the manual, adding power and usefulness to the 842 pages of instructions Scrivener provides. Wow and ugh. I should add that keeping track of Scrivener’s unique terminology (any unique terminology, actually,) is not one of my strong suits.
I got a good start on a glossary in the early phases of the project, but eventually it tapered off—the process of identifying these things while writing about them are different kinds of thinking in my mind. So while the infrastructure for building a glossary and the few entries I wrote are in the non-compiling section of the project, I haven’t resurrected it.
Of course another problem I was running in to was that 842 page problem. 
It’s worth noting that 180 pages of that are already appendix material. I feel that adding a glossary would require some reciprocal surgery from elsewhere, which of course makes it a lot more difficult than just spamming out ten pages of nouns and definitions.
At any rate, there are two things I tried my best to do, in creating a sort of index or map that could be used to scout out terms you aren’t familiar with and then branch into more detailed explorations of those things as needed:
- The preference and menu appendices. You were wondering what the inspector means (perhaps rhetorically, but it’s a good example), so one could use the search tool in the Help menu to look for inspector. They find the View ▸ Show|Hide Inspector command and maybe try it. Great, but what is it? On page 692 where that very menu command is documented, we find a simple glossary-sized definition for what the inspector is, and where to go to find more about it (chapter 13). The menu appendix goes a lot further than most probably do, and for precisely this reason. This isn’t a File/Save: Saves the project, type formality.
- All right but what about stuff that isn’t a menu command, like draft folder? That’s what Chapter 4, Interface in Overview is all about. The draft folder is found in the binder (and of course if we don’t know that yet, the binder is introduced at the top of that chapter), so we jump down to the subsection on the binder—and there you will find an itemised list going over the three special folders. If the couple of pages of overview there isn’t enough for you, at the bottom of that section is a See Also to the full chapter on the Binder, whereupon we scroll right into a ToC that has a whole subsection dedicated to The Draft Folder.
I.e. there may not be a somewhat redundant copy of this information in a Glossary appendix, but the structure of the principle introductory and reference appendices were very much built in mind to operate as a glossary of sorts.
Is it good enough? Well… that’s for you to say and not me, maybe it needs more, but again I think more would mean less elsewhere (which probably isn’t a bad thing anyhow).
Thanks for your thoughtful reply, Amber. Yes, I just visited this forum exchange after posting it 5 or so years. Wow. Some ideas never die. I would still like to see a toggled window like the Quick Reference panel in the tool bar in the role of glossary. It would look something like two columns: in one, the term in question and, in the other column, citations showing where definitions and explanations reside in the current manual, which can be found on the Scrivener menu under Help.