What is the best way to upgrade the Kraken software, using git pull or some other method?
Easiest way is to just burn the latest SD card image.
If you are familiar with git, doing a git pull in the krakensdr_doa/krakensdr_doa directory should also work fine. So just deleting the krakensdr_doa/krakensdr_doa and cloning from source again.
If you update Heimdall, you will need to double check that the Makefile settings are correct for your machine. E.g. on the Pi 4/5 images the Makefile is slightly modified for those systems by uncommenting the line with compiler flags. Then when you have the Makefile right, run ‘make’.