Hi Chris.
I probably could have been nicer about that but with 51 unread emails and a massive head cold (like everyone else in Melbourne at the moment) I just wanted to answer your question ASAP.
So regarding the FPGA firmware. I imagine since its HDL and written for a Spartan 6 the final file flashed to the FPGA's external flash memory it's a .bit file (going from my memory of VHDL programming). If it is online, it would be probably be stored on GitHub.
Because of the nature of the FPGA firmware, I imagine this will not be available for public release. I will let Fergus confirm that.
In terms of the relevance of the FPGA firmware, unless you are building your own board, it probably isn't neseccary. All the acquisition management etc. takes place on the STM32F4 so most of the functionality changes that would ever be required can be done by modifying the STM32F4 firmware.
I hope this is helpful. If anything doesn't make sense, I blame the head cold.
Cheers,
Liam