Replace celeri with commander.js for CLI and clean up implementation

There are 3 things that happened in the PR:
* Replace celeri with the better supported [commander.js](https://github.com/visionmedia/commander.js/). Doing this removed a considerable amount of code.
* Add index.js file to the root of the project as it is the entry point specified in the `package.json`
* Correct a handful of jshint errors. Sorry that would have been in another PR but I couldn't commit without fixing them.