Update gems

- berkshelf 1.1.2
- chef 10.18.2
- vagrant 1.0.6
Work around issue with Vagrant plugin when "cookbooks" folder exists

See https://github.com/RiotGames/berkshelf/issues/267
Remove Gemfile.lock from skeleton

To know immediately when some change in the overall ecosystem breaks the setup.

See http://yehudakatz.com/2010/12/16/clarifying-the-roles-of-the-gemspec-and-gemfile/