Removed older files which relied in the fixed model of 2 fatty acid chains only.
Removed unused dependencies
Cleaned and commented LipidFactory.
Refactored classes to util package.
Adds BinaryCounter interface and deprecates IntegerListIterators not in use.
Changed the file level to avoid additional directory.
Commented most of the mass package and removed many unnecessary classes.
Commented the rule package.
Commented the util package.
Comments added on exec package.
More comments on the exec package.