Drupal and Require.js not playing nice - double load of jQuery
I would try option 1. Require JS is pretty demanding in terms of getting all the dependencies right, so unless you want to debug that I'd load the Require JS version.

The place to look is: https://www.drupal.org/node/756722 where all this is explained.

Basically I think you should (for D7) define the Require JS stuff as a library using hook_library like so:



function hook_library() {
      $libraries['vertical-tabs'] = array(
        'title' =&gt; 'MY_STUFF',
        'version' =&gt; '1.0',
        'js' =&gt; array(
          'PATH/require_stuff.js' =&gt; array(),
        ),
        'css' =&gt; array(
          'PATH/bootstrap_stuff.js' =&gt; array(),
        ),
      );
      return $libraries;
    }


And on hook_init add it like so:

drupal_add_library('system', 'vertical-tabs');


And replace the core version of Jquery with hook_js_alter:



function hook_js_alter(&amp;$javascript) { 
  $javascript['misc/jquery.js']['data'] = drupal_get_path('module', 'MY_MODULE') . '/jquery.js'; // Swap out jQuery to use your version.
}


I wouldn't worry too much about sticking with the Drupal version of Jquery as it is very common to use the jquery_update module to replace it anyway.