And here it is!

I used Atmel Studio to compile the firmware, but all flashing was done with the Raspberry Pi.
BOM:
One Raspberry Pi (with SD card and support devices, keyboard, mouse, etc)
One GPIO header ribbon cable
Six hookup wires
One JTAG 5 by 2 (10 pin) ribbon cable
One (or more) Bitforce SC devices

I used Luke-Jr's instructions at https://bitcointalk.org/index.php?topic=262558.0 and modified to suit the Raspberry Pi environment and using the GPIO pins.

Full details:
http://randomcontent.wolfnexus.net/RandomSite/reflashing-a-butterfly-labs-jalapeno-with-only-a-raspberry-pi/