Changed some exceptions to print statements and exit to give cleaner output to user.
Changed some exceptions to print statements and exit to give cleaner
output to user.

Fixed bug where self.counter was updated instead of self.expt.counter.

Check PAYU_CURRENT_RUN isn't set before trying to find counter value.

Still fails to output to correctly named output and restart dirs.

marshallward/payu,aidanheerdegen/payu,marshallward/payu,aidanheerdegen/payu