Bring Vagrant Berkshelf up to snuff

Issues:
- Fixes #14 
- Fixes #17 
- Fixes #26 
- Fixes #57 
- Fixes #66 
- Fixes #81 
- Fixes #90 
- Fixes #91 
- Fixes #107 
- Fixes #108 
- Fixes #117 
- Fixes #123 
- Fixes #186 
- Fixes #221 
- Fixes #223 

PRs:
- Closes #231 
- Closes #225 
- Closes #130 
- Closes #94 

TODO:
- [x] Update docs
The tests also explain the new logic.