How do I get a javascript library to work inside the CKEditor module?
Using the code supplied in this associated question, I was able to get the javascript nav-pills to work in the CKEditor instance for Drupal 7. Unfortunately, it will only function in Firefox for PC. In addition, I had to add the following code to the ckeditor.config.js file as well as manually add the script to the admin theme's html.tpl.php file - this seems redundant but it will only work if both files have it.

CKEDITOR.on('instanceReady', function(ev) {
var jqScript = document.createElement('script');
var bsScript = document.createElement('script');

jqScript.src = 'http://code.jquery.com/jquery-2.0.2.js';
bsScript.src = 'http://netdna.bootstrapcdn.com/bootstrap/3.0.0/js/bootstrap.min.js';

var editorHead = ev.editor.document.$.head;
editorHead.appendChild(jqScript);
editorHead.appendChild(bsScript);

jqScript.onload = function() { editorHead.appendChild(bsScript); }; 
});