So I have looked into it.
PFBA is now part of PEMU, along with PSNES and PNES.
Of course, most of my changes to make it work on the Pandora didn't applied anymore, so I spent last weekend plus this saturday to get a working PFBA (and PSNES and PNES).
The problem is the Cyclone M68K cpu emulator doesn't seems supported anymore (sources are still there, but no platform uses it, so I assume it's no more working), meaning arcade machines with numerous M68K-type cpu will be slower than in previous build.
Frameskip was also completly removed, so I hacked some limited frameskip (only 1 frameskip maximum).
And, last but not least, this build use openGL 2.0 with Shaders, so you may need to use latest SGX driver, and it may (or may not) works on CC models.
Because of so many changes, I'm putting the new PFBA only here:
PFBA.PND. Please test and report.
I'll push PSNES and PNES on the repo if there are some reports on how this new PFBA is working.