Fixes GH-39: -d flag not working

It appears how I was handling the proc for the dockerfiles_path option was causing user input to be ignored. This commit fixes this issue.
Fixes #38 - Duplicate cookbook defs in Berksfile

If a cookbook appeared more than once in the runlist, it would appear that many times in the Berksfile. Also, the Berksfile wasn't being generated if you had no runlist even if you requested it be generated.
Merge branch 'tduffield/GH-38-39' into release/0.2.x