I really love the autofromat feature. I makes your code more readable and in case of JavaScript tells you, when there are synatcs errors (missing brackets etc.).
However
Try to make an empty comment after each line:
define([ // 'jquery', // 'aloha', // 'aloha/plugin', // 'ui/ui', // 'ui/scopes', // 'ui/button', // 'ui/toggleButton', // ...
Not nice, but I think it will work.