I’d point to Lacinia as an open-source Clojure project that has excellent documentation, including a tutorial, more semantic manual-style docs, and Codox API docs. re-frame has probably the best docs on this level that I know of.
I’m glad Codox exists, but most of the time I wind up just using it for its pointers to the actual source-code of various functions on GitHub - I tend to find notes and examples in a README to be more helpful.
I am using Zeal plus repl facilities like doc and apropos through inf-clojure.
When I was using cider a bit more, I was using Grimoire integration quite a bit.
I have a shortcut defined in my spacemacs config which calls helm-clojuredocs-at-point. This makes searching in clojuredocs much quicker and convenient.
BTW, one interesting aspect of how these manuals are written is that they’ve built a literate programming environment in which one writes the “book” along with the contracts (basically clojure.specs) for the functions and a set of example forms per procedure to be evaluated automatically in the course of building the documentation. The library that does all this is included in the distribution and can easily be used by tooling to produce rich in-place documentation.
Check out section 4.1.5 of this doc for a nice example.