Add test for upgrade

This adds a test for the upgrade studies dumper. I had to make a few changes along the way:

• In ca-make-test-file, add an option to put all branches in the test file
  • Some other miscellaneous cleanup in that file
• Fix a bug in the upgrade config: the deprecated jvt_cut field was being specified and ignored, rather than the minimum_jvt that we use now.

Closes #60 (closed).