Include JRE classes in banDuplicateClasses

[joachim-durchholz-six]

banDuplicateClasses currently ignores classes that override those in the JRE.
Sometimes that's intentional, but sometimes it is not (most notably many instances of Xalan and Xerces dependencies which should have gone long ago).

So I'm suggesting adding an option to have the JRE included in the list of dependencies to check for duplicate classes, off by default to be backwards compatible.