Petar, I am not sure whether your patch really solves
MASSEMBLY-342. You are simply avoiding the NPE in the FileSetManager but as far as I understand, the NPE is adequate: A required parameter is missing and I wouldn't consider a FileSet without base directory a valid object. The Assembly Plugin is responsible to properly configure the FileSet before passing it down to the FileSetManager, so that needs fixing. In particular, consider the POM snippet given over at the MASSEMBLY-342
which suggests that the user wants the FileSet to use the project's base directory. This is a completely different semantics than just returning an empty result list.
To summarize: I think this issue itself should be closed as "Won't fix". To real work is over in the Assembly Plugin.