A few touch and go fixes/comments/ and file updates you might consider looking into

index.html

@@ -38,7 +38,7 @@
 <![endif]-->
 
 <!-- JavaScript -->
-<script src="js/modernizr-2.0.6.min.js"></script>
+<script src="js/vendor/modernizr-2.5.3.min.js"></script>
 
 <!-- For iPhone 4 -->
 <!-- <link rel="apple-touch-icon-precomposed" sizes="114x114" href="img/h/apple-touch-icon.png"> -->
@@ -110,17 +110,22 @@ <h2 class="h3">&#8216;320 and Up&#8217; contains:</h2>
 <small>&#8216;320 and Up&#8217; wouldn&#8217;t be possible without <a href="http://html5boilerplate.com/">HTML5 Boilerplate</a>, <a href="http://framelessgrid.com/">Frameless grid</a> and <a href="http://twitter.github.com/bootstrap/">Bootstrap</a>. Licensed under the <a href="http://creativecommons.org/licenses/MIT/">Creative Commons MIT</a> license.</small>
 </footer>
 
+<!-- Grab Google CDN's jQuery, with a protocol relative URL; fall back to local if offline -->
 <script src="//ajax.googleapis.com/ajax/libs/jquery/1.7.1/jquery.min.js"></script>
-<script>window.jQuery || document.write('<script src="js/jquery-1.7.1.min.js"><\/script>')</script>
+<script>window.jQuery || document.write('<script src="js/vendor/jquery-1.7.2.min.js"><\/script>')</script>
 
+<!-- Scripts concatenated and minified via build script -->
 <script src="js/plugins.js"></script>
-<script src="js/script.js"></script>
+<script src="js/main.js"></script>
 <script src="js/helper.js"></script>
+
+<!-- Asynchronous Google Analytics snippet. Change UA-XXXXX-X to be your site's ID. -->
 <script>
 var _gaq=[["_setAccount","UA-XXXXX-X"],["_trackPageview"]];
 (function(d,t){var g=d.createElement(t),s=d.getElementsByTagName(t)[0];g.async=1;
 g.src=("https:"==location.protocol?"//ssl":"//www")+".google-analytics.com/ga.js";
 s.parentNode.insertBefore(g,s)}(document,"script"));
 </script>
+
 </body>
 </html>