I've tidied up most of the remaining issues with my attempt at an updated Jaguar SDK, and documented the outstanding problems in github issues. Here it is:
See the README.md for cloning, setup, and general getting started instructions. If you have a skunkboard or a BJL cable and know enough to run bash scripts and make, you should be up and running "hello world" built from source in a few minutes. Beyond that, you're on your own.