Okey @piotrpasich , Now I get it.. I just saw your PR #236 and I see that you've introduced a bug that I have considered. 
Since locateResource() returns resources in alphabetical order and the getSkeletonDirs()-function should return resources in prioritized order you will get some problems with overriding the skeleton files when not adding the SensioGeneratorBundle at the end of the $skeletonDirs. 

@fabpot Do you have any thoughts on this?