Javascript works with HTML but not in Rails

Question

I am trying to use a free bootstrap template (http://ironsummitmedia.github.io/startbootstrap-agency/) in my Rails 4 application (https://github.com/IronSummitMedia/startbootstrap-agency). When I copy the Javascript files to my app/assets/javascripts, cbpAnimatedHeader.js complains that "classie" is not defined:

/**
 * cbpAnimatedHeader.js v1.0.0
 * http://www.codrops.com
 *
 * Licensed under the MIT license.
 * http://www.opensource.org/licenses/mit-license.php
 * 
 * Copyright 2013, Codrops
 * http://www.codrops.com
 */
var cbpAnimatedHeader = (function() {

    var docElem = document.documentElement,
        header = document.querySelector( '.navbar-default' ),
        didScroll = false,
        changeHeaderOn = 300;

    function init() {
        window.addEventListener( 'scroll', function( event ) {
            if( !didScroll ) {
                didScroll = true;
                setTimeout( scrollPage, 250 );
            }
        }, false );
    }

    function scrollPage() {
        var sy = scrollY();
        if ( sy >= changeHeaderOn ) {
            classie.add( header, 'navbar-shrink' );
        }
        else {
            classie.remove( header, 'navbar-shrink' );
        }
        didScroll = false;
    }

    function scrollY() {
        return window.pageYOffset || docElem.scrollTop;
    }

    init();

})();

When I looked at classie.js I saw that var classie = {...} is defined inside a function:

/*!
 * classie - class helper functions
 * from bonzo https://github.com/ded/bonzo
 * 
 * classie.has( elem, 'my-class' ) -> true/false
 * classie.add( elem, 'my-new-class' )
 * classie.remove( elem, 'my-unwanted-class' )
 * classie.toggle( elem, 'my-class' )
 */

/*jshint browser: true, strict: true, undef: true */
/*global define: false */

( function( window ) {

'use strict';

// class helper functions from bonzo https://github.com/ded/bonzo

function classReg( className ) {
  return new RegExp("(^|\\s+)" + className + "(\\s+|$)");
}

// classList support for class management
// altho to be fair, the api sucks because it won't accept multiple classes at once
var hasClass, addClass, removeClass;

if ( 'classList' in document.documentElement ) {
  hasClass = function( elem, c ) {
    return elem.classList.contains( c );
  };
  addClass = function( elem, c ) {
    elem.classList.add( c );
  };
  removeClass = function( elem, c ) {
    elem.classList.remove( c );
  };
}
else {
  hasClass = function( elem, c ) {
    return classReg( c ).test( elem.className );
  };
  addClass = function( elem, c ) {
    if ( !hasClass( elem, c ) ) {
      elem.className = elem.className + ' ' + c;
    }
  };
  removeClass = function( elem, c ) {
    elem.className = elem.className.replace( classReg( c ), ' ' );
  };
}

function toggleClass( elem, c ) {
  var fn = hasClass( elem, c ) ? removeClass : addClass;
  fn( elem, c );
}

var classie = {
  // full names
  hasClass: hasClass,
  addClass: addClass,
  removeClass: removeClass,
  toggleClass: toggleClass,
  // short names
  has: hasClass,
  add: addClass,
  remove: removeClass,
  toggle: toggleClass
};

// transport
if ( typeof define === 'function' && define.amd ) {
  // AMD
  define( classie );
} else {
  // browser global
  window.classie = classie;
}

})( window );

I understand why it is complaining. But then my question is why does everything work fine in it's original HTML format (http://ironsummitmedia.github.io/startbootstrap-agency/)? How can I fix this problem? Thanks.