Admin app PHPCS cleanup & exemption changes

This PR fixes all reportable PHPCS issues in the admin app outside the `components` folder and `application.php` and `framework.php` files in the `includes` folder (as reported at http://mbabker.github.io/jcms-codestyle/).  In doing this, I've also changed the exceptions on the `administrator` folder so that only the files previously specified as not touched (and templates, which are permanently exempted from most rules) are still exempt from specified rules.