Remove chef gem as dependency.

It mucks with the full-stack install of chef in all sorts of bad ways by
overriding commands like `chef-client' and `knife'.
Update Berksfile to include Homebrew.

The URL for the Homebrew installer changed, so this is really important.
Note that `chef-client' creates `client.pem'.
Add a couple todos.
Graphviz is already added.
Emacs doesn't need to be installed with homebrew.
Modify iTerm todos.
Update todos.
Add autojump to brew packages.