Pito
Yes indeed the *.cxx question is not answered directly in the FAQ. It is indirectly answered in "I have modified my Arduino setup and... "
But to give you some background:
I don't compile *.cxx files XD
My plugin uses avr eclipse that uses cdt, win avr and GNU compiler. CDT uses eclipse
It is cdt (which is a C/C++ plugin for eclipse) that compiles *.cxx
If you have read the "How to keep the IDE and plugin compatible" you must have seen how to add *.pde file as to be handled by the compiler.
Unfortunately you can not remove *.cxx files as they are supported by default.
In my humble opinion it is better to avoid mixing files of different sources. Having the *.cxx somewhere else may fix your problem.
Best regards
Jantje