As far as the piece of fah go, I'll take a stab at what I think (rightly or wrongly) they do. Fah6 is the CEO, it handles all the connections in and out of the computer, and dictates when work needs to be done. mpiexec is the middle manager and directs the cores to fold when handed a work assignment by the CEO, fah6. The a1 and a2 (and now a3) cores are the grunts who do all the work. For whatever reason, the middle manager and the grunts like to give the CEO the finger when told to stop working (hmm this sorta makes sense in a weird way actually). The qd stuff is a bulletin board that has all the info about the work assignments that the grunts are working on. client.cfg contains info about the owner, and how the work should be done. FAHlog.txt is the equivalent of a surveillance camera telling what the grunts have been up to. I have no idea what machinedependant.dat is, mine is just a short line of gibberish. queue.dat is information on what has already been done, and what is currently being worked on. unitinfo is a short summary of what is currently being worked on. I think that was added by PG for some of the monitoring clients out there. The work directory is mainly all the info that the cores need to actually process the work unit.
AFAIU, the machinedependant.dat file uniquely identifies your machine for Stanford. It's gibberish because it contains binary data, not text.
