Documentation is great and all, but no one ever talks about when theres too much. Maybe because it's rare? At big companies I've seen "architects" churn out page after page of diagrams, design docs, runbooks, checklists, descriptions, etc. There is so much information that it becomes practically useless in aggregate, because no one is reasonably going to read it all. I'm not going to pretend that I have the patience…
In theory it should work like this:
I) "User should be able to do X" II) "X can be achieved by performing steps A, B, and C" III) "A works by using components 1 and 2" etc.
I) generates your index (what can I even do with the software)
II) generates the documentation (how can I do it)
III) and below is for technical use only (extending, modifying, porting)
Stuff like rationales for design decisions can be structured in the same layered way.
I don't know how something like this can be extracted after the fact, but no matter the development model (waterfall/agile), a structure like this should arise naturally anyway and the absolute amount of documentation isn't a problem. Lack of proper structure, however, is.