Installing

1. Close Emacs.
2. Delete ~/.emacs or ~/.emacs.d if they exist. (Windows users, your emacs files will probably live in C:\Users\your_user_name\AppData\Roaming\. So, for example, you would delete C:\Users\skeletor\AppData\Roaming\.emacs.d.) This is where Emacs looks for configuration files, and deleting these files and directories will ensure that you start with a clean slate.
3. Clone and rename dir to ~/.emacs.d`.

Then open Emacs.

Organization

I've tried to separate everything logically and document the purpose of every line. init.el acts as a kind of table of contents. It's a good idea to eventually go through init.el and the files under the customizations directory so that you know exactly what's going on.