Use a package manager.

Use [Cask](http://cask.github.io/) and [Pallet](https://github.com/rdallasgray/pallet) to manage packages and their dependencies.  

- Delete all submodules that could be replaced with packages from `list-packages`.
- Disable some packages and related setup modules that are infrequently or no longer used.
- Replace or update some older packages.
- Install and configure some new packages stumbled upon in [MELPA](http://melpa.milkbox.net/#/).