Updated vagrantfile and chef cookbooks for a generalized my-dev-box

@rppatel1007 @craigschneider @ChrisPetr0 

So I've cleaned up unused cookbooks and added needed cookbooks for HC. I updated the vagrantfile accordingly. I moved all the custom recipes to site-cookbooks per chef practices so that we can update third-party cookbooks can be updated without losing custom code. I also updated the berksfile so that it can be run if necessary and will pull in all dependencies and cookbooks necessary including custom cookbooks from site-cookbooks. However it shouldn't be necessary as all cookbooks are currently contained within the repo. Finally I updated the readme.