1. The first thing I notice is that I get this strange notice about
the INSTALL file:
Ah, tha'ts something new - that part of INSTALL is now auto-generated from the CMakeLists.txt file. I fixed it - see r49553 for the correct way to edit a build option docstring.
2. The second thing I notice is that I cannot get the build system to
recognize that I have the prereqs for a pdf build.
Um. I'm guessing they are present on your system? I had intentionally turned OFF pdf building by default because it is so time intensive - you need to set BRLCAD_EXTRADOCS_PDF=ON to get the PDF build, even if everything is present...
I've tweaked your changes some - does the current version work if you add -DBRLCAD_EXTRADOCS_PDF=ON?