Improvements to Logger module.
Improvements to Logger module.

1) If something is wrong with the log file, we throw a RuntimeException,
   which will be uncaught and will cause the java to exit with a stack trace.
   This is probably better than ignoring the problem.

2) logStackTrace(e) now uses ERROR level instead of INFO

3) I've made a new method Logger.flush() which will flush the log file.
   This can be called when you want to make sure the log file is up to date,
   eg. you're about to do something time-consuming, or you've just reported
   an error. This is called automatically after ERRORs and CRITICALs.

jwallen/RMG-Java,connie/RMG-Java,KEHANG/RMG-Java,enochd/RMG-Java,rwest/RMG-Java,ReactionMechanismGenerator/RMG-Java,keceli/RMG-Java,connie/RMG-Java,keceli/RMG-Java,faribas/RMG-Java,jwallen/RMG-Java,jwallen/RMG-Java,faribas/RMG-Java,enochd/RMG-Java,enochd/RMG-Java,nyee/RMG-Java,nyee/RMG-Java,faribas/RMG-Java,rwest/RMG-Java,enochd/RMG-Java,ReactionMechanismGenerator/RMG-Java,ReactionMechanismGenerator/RMG-Java,ReactionMechanismGenerator/RMG-Java,ReactionMechanismGenerator/RMG-Java,KEHANG/RMG-Java,jwallen/RMG-Java,rwest/RMG-Java,keceli/RMG-Java,enochd/RMG-Java,faribas/RMG-Java,keceli/RMG-Java,nyee/RMG-Java,KEHANG/RMG-Java,KEHANG/RMG-Java,nyee/RMG-Java,jwallen/RMG-Java,enochd/RMG-Java,connie/RMG-Java,KEHANG/RMG-Java,connie/RMG-Java,KEHANG/RMG-Java,connie/RMG-Java,keceli/RMG-Java,rwest/RMG-Java,jwallen/RMG-Java,rwest/RMG-Java,nyee/RMG-Java,nyee/RMG-Java,keceli/RMG-Java