Processing from yaml requires --clean

Mineo-san writes:

There is a known issue: you have to use --clean option when converting the yaml to shell script. Otherwise, a single directory will have outputs from calibBlocks of the same type with different names, and pfsIngestCalibs.py fails.

This is an unfortunate limitation that we should fix.

I wonder if this is mostly a problem with the fiberProfiles (shell script to combine odd/even pairs?). Can we deal with this by using separate reruns based on the calib block names?