Ok that was super easy! I obviously still had the setup on the computer as described in the thread on upgrading the shapeshifter from linux.
For some reason I had commented out some lines in the etc/udev/rules.d/51-rainmaker.rules, so although “quartus_pgm --auto” ran all green with no errors, the programming failed. I re-enabled those lines and rebooted the computer (to make sure the rules were correctly read).
Then I copied the shapeshifter firmware jic to the base of the quartus binary (/path/to/intelFPGA/19.1/qprogrammer/bin/). This to make sure no path confusion was involved. It seems that (maybe because I didn’t install the quartus software, just downloaded and unbacked it) I need to be quartus binary folder for it to find the various other commands included with the programmer for the final step to work.
Then just ran the following to upload the firmware:
quartus_pgm -m jtag -o "pi;shapeshifter_v2.04_jan16_2020.jic"
All green text indicated success, placed the shapeshifter back in the rack, and confirmed it’s now displaying 2.04.