It was originally a fork of prboom maintained by someone completely
independently of prboom. It later moved into the prboom SVN, but is still
managed as a separate project. I think there is some cross-pollination
and code flows between the two. However, prboom+ make large, sweeping and
perhaps 'risky' changes which prboom don't immediately incorporate. IIRC
prboom+'s main focus is absolute DOOM.EXE/DOOM2.EXE compatibility, including
some crazy/brilliant ideas like simulating the behaviour of buffer overflows
and underruns from the DOS environment, so old demos playback perfectly. It
has turned out that prboom+ is more actively developed and releases more
often than prboom. When I first looked at it, before it moved into the same
SVN, it was awkward to build in Linux (the developer being Windows-focussed).
That has no doubt changed.