Lots of script changes (see full message)

- Simplified copyFromSubmitted.sh
- Scripts now use directores for temp files
- Added ability to process more than one netid to checkByNetID.sh
- Scripts now communicate with each other via exit codes
- Added batch mode (outputs program results to a results folder)
- Removed machine-specific library locations
- Other misc changes

This really should've been split up into more commits...