Only add js/css if the output is HTML

Coming from #1279226-92: jQuery and Drupal JavaScript libraries and settings are output even when no JS is added to the page and quoting catch:

htmlshiv isn't the only file that gets needlessly added for non-HTML pages, we also need to move module css/js additions out of system_init().

For the moment all css/js is added inside system_init, but it isn't needed unless the output is HTML and sometimes for AJAX (if a new js/css file gets added).