Remove getenv

This MR builds on !569 (merged) to allow us to run without the getenv=True option that is being removed from HTCondor.

The diff with !569 (merged) can be seen here.

• The changes are most clear from the changes to the parser.
• There are two new arguments --environment-variables and --getenv that can be used to pass variables that are then written directly into the submit files.
• These also replace --disable-hdf5-locking.
• To not break most workflows I set defaults in utils.py for important variables.
• The same environment variables are sent to all jobs in the dag.