Numerous changes

All connections closed. Opt files not saved are deleted on close as well
as Opt log files. MIP files will not delete. Progress bar centered. Opt
context menu updated.
Merge https://github.com/jimkell/MOST

Conflicts:
	src/edu/rutgers/MOST/config/LocalConfig.java
	src/edu/rutgers/MOST/data/ReactionsUpdater.java