Don't extend the js/elgg view. This is frowned upon now.

When developing for 1.9 you should define your JS as an AMD module in a .js view (not .php) and use elgg_require_js to load it.

See the guide for more information: http://learn.elgg.org/en/1.x/guides/javascript.html

Also, you should register the vendor as an AMD module as well:

elgg_define_js("jquery.wookmark", array(
  "src" => "/mod/pin_theme/vendors/js/jquery.wookmark.min.js",
));

Then in your JS you can just require it:

// views/default/js/pin_theme.js
define(function(require) {
  var $ = require("jquery"); require("jquery.wookmark");

  $(function() { /* doc ready behavior */ });
});

If you want to load your JS on every page, just do:

elgg_require_js('pin_theme');

Worked like a charm. Thanks for the guiding.