Restructure directories

I've changed the directory structure so ember is now at the root. I did this for a few reasons

1. It makes more sense. You'll be working more with the ember commands than cordova so there's one less directory you need to cd into. 
2. It will help in turning this into an addon. This way I can blueprint out the cordova directory and not have ember inside of it's own folder. It just wouldn't work.