I spent some time recently documenting a large clojure project.  The
approach I used was a combination of doc-strings, comments throughout
my code, and a project-wide emacs-org-mode file summarizing the point
of each file, the important functions in each file categorized by
purpose, and an overview of how to use those functions effectively.
It worked, but I'm not entirely pleased with the result.  There was a
lot of duplication between the org-mode file and the comments within
the files, and I have a feeling it will be hard to maintain the
documentation as the project evolves.

autodoc doesn't work on Windows, but even if it does, I'm not certain
it would be sufficient for me.  As far as I know, it's main purpose is
to show an alphabetized API of all the public functions and
docstrings, which is a good start, but doesn't allow for the kind of
categorization and usage notes I think would be ideal.  A couple years
ago, when I was doing a lot of Actionscript coding, I fell in love
with Natural Docs (http://www.naturaldocs.org/) and this is really the
kind of thing I would most enjoy using if I'm going the route of
automatically extracting comments and doc strings, because it gives
good control over how the API is organized, and the extra annotations
are quite readable in the code.

The recent post of the website that displays the clojure API
categorized by purpose is a good example of the kind of thing I'm
looking for.  Recently, there was a thread about Literate Programming,
including org-babel and Mark Fredrickson's changeling lein plugin,
which also raised interesting possibilities.  So I'm guessing a lot of
people are interested in versatile doc tools and are working on and
exploring the options.

So this seems like a good time to ask:  what is the current
state-of-the-art in Clojure documentation tools?

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