JTAG
There are three options for jtag programming of the Bifferboard.
RDC Windows software can be obtained to do the programming. You can find it on the net from some dodgy sites I'm sure. I cannot legally distribute it here, although I have the 'official' copy from MRT Communications. I think there is an official JTAG adapter as well, but there's no point going to the extraordinary lengths you'd have to to purchase one. You may as well make up one yourself as it would be quicker.
There is some jtag software in the tools directory. You will need to construct a parallel port JTAG adapter to use this. It looks like this:
Who knows if modern Linux still allows direct IO port access as the Python attempts to do. YMMV. It was used on Slackware circa 2009, but relatively recent motherboards have at least pin headers for Parallel ports so it may be possible to make it work.
Also, there is the at-biffjtag program that allows a suitably hacked Bifferboard to program another Bifferboard. This requires the removal of R19 on the 'programmer' Bifferboard, which allows you to use the JTAG pins as GPIO, unfortunately then preventing the board from itself being programmed by JTAG. The five pin header (GND and four IO pins) must be connected to the equivalent pins on the target board to be programmed. This requires a straight ribbon cable. Make sure you do not connect the 3.3v and join the two board supplies, just the GND and 4 data pins are all you should connect. Then it's simply a matter of switching on the target board and running the other biffjtag program.