added additional pauseflag check -mitch
added additional pauseflag check, added production argument
prejob_processing adds +1 to RunCount
added RunCount - mitch
various small changes, moves around data and renames files
edited opt and pro output redirection and create_job_basename; added check_round, post_job_clean and final_run_cleanup
Merge pull request #6 from mbarts/master

a range of changes