Skip gems packaged with Ruby when packing.

This allows `bundle cache` and the like to work if you are using a gem that
is shipped with Ruby, like minitest 4.7.5.

@indirect This "fixes" https://github.com/bundler/bundler/issues/2864. Given that this is my first time working on Bundler, I'm not sure if this is in the right spot let alone correct. How does it look to you?