Update to Clean_Entromics_1.0.sh

Updated Clean_Entromics_1.0.sh:
- Application will now zip the output folder
- Updated pep9 and romkes Clean_Entromics_1.0.sh

Also spoke with Senthil and his responce to the current PittGrid issue:
"Looks like it is IO issue, since the version of software we have keep the files opened until jobs are complete.
If possible try to use the same log file for all the cmd files instead of unique log file for each job (e.g. segment-12_03_82-1065.Nicol.log), something like entromics.log and see if it fixes the problem.
I think it should fix the problem ,if not try to reduce to 1000 jobs instead of 2000.
Let me know, how it goes."

Will make these updates today and run another test tonight.