Exceptions in Module Dependency Diagrams

Generally your own exceptions might be interesting, but system exceptions are probably not. Remember, the primary purpose of an MDD is to communicate or discover something (usually a thesis related to the design of the system and coupling) -- you should include classes which are relevant to that thesis, and avoid cluttering it otherwise. For example, it's not very interesting to see in an MDD that every class depends (in some way) on Integer, because I can usually assume that java.lang.Integer is fixed and will not change (thus there is no point to removing or worrying about dependencies on it). On the other hand, if I were an engineer at Sun contemplating a potential change to java.lang.Integer, its presence in my MDD would be very important. Same goes for java.lang.Throwable, java.lang.Exception and the same reasoning for inclusion or exclusion applies to your own exception types.