Fix jointcal exit status and doRaise handling

jointcal is giving these warnings since DM-4141 was implemented:

Unable to retrieve exit status ('Struct' object has no attribute 'exitStatus') 

To fix this, I think I need to do the following:

• add this to the start of run: exitStatus = 0 # exit status for shell
• add exitStatus to the returned Struct
• wrap most of run in try: except:
• set exitStatus=1 (or some other number) if doRaise is False and something went wrong.

Anything else I'm missing?