Documentation is currently undergoing revision, albeit in fits and starts.
Quick Start guides for Relying Party and CA on Ubuntu Xenial are here
The User's Manual. This is old, and corresponds, roughly,
to the old-trunk branch. Portions of it are now obsolete, but it
may still be useful as a general guide to some of the more obscure
bits of the software.
If you find a place where the code and the manual disagree, the code is probably right.
Content salvaged from old trac.rpki.net wiki. This is mostly for archival, although some pieces of it may still be directly useful.
Not written yet. At one point we experimented with Doxygen, but the results were not particularly useful. But that was years ago, and Doxygen has undergone a lot of development since that time, so it might be worth another try.