Finally got urjtag working under Linux and am currently packaging up urjtag and the Logic Analyzer into an easy to use package. Getting urjtag to work under Linux took longer than expected because of a bug that causes svf files to load too fast under linux.
I finally found a forum thread that described the problem I was having. I was able to program a svf file if I changed the programming frequency to 300kHz but not at the default 1MHz that works fine in Windows. Turned out the precompiled version of urjtag that I was using for Windows was patched to fix the problem. I was able to track down the patch and apply it for Linux and all is well and working now.
Once this is finished I will be moving on to documenting the Butterfly Platform specification and asking for people to look it over. My goal is to have that finished by the end of the week.