I think elclanrs's comment is the answer you are looking for.
In coffeescript do ($) ->
will compile to (function($){ … })($)
.
But do ($ = jQuery) ->
will compile to (function($){ … })(jQuery)
.
There really isn't any cleaner way of doing it than this. It's one line at the top of the file and makes it very clear what you are doing.
do ($ = jQuery) ->
class App