Hi,
Two problems:
1. I can't figure out how to add mega style menu's to your menu system because I can't inject main-menu class attributes.
2. I have a workaround, but I can't get the scrollto function to work.

1. I was struggling to find a workaround for your current menu system. My issue is that you re-wrote the menu to allow for menu attributions that support links and direct to anchors. This could have been done without re-writing the menu in your module.

2. However, I found a work around. But if you could make the menu support mega style menu's, that would be great.

My workaround:
I created a mini-panel block using your code for the logo and navigation wrapper div's. My issue now is that even though the structure of my code is almost exact to yours after rewriting it, I can't get the scrollto jquery function to work. I see that in your md-alpine/js/scripts.js file, you have a function the makes this happen (line 233]. I can't get it to work with my current navigation (below). I copied the whole block just in case you would like to see it.

<div class="block block-panels-mini contextual-links-region" id="block-panels-mini-main-header-navigation">
<div class="container">
<div class="section-title text-center">
<div class="contextual-links-wrapper contextual-links-processed"><a href="#" class="contextual-links-trigger contextual-links-trigger-active">Configure</a><ul class="contextual-links"><li class="block-configure first last"><a href="/admin/structure/block/manage/panels_mini/main_header_navigation/configure?destination=node">Configure block</a></li>
</ul></div> </div>
</div>
<div class="content">
<div id="mini-panel-main_header_navigation" class="panel-display panel-1col clearfix">
<div class="panel-panel panel-col">
<div><div class="panel-pane pane-custom pane-1">

<div class="pane-content">
<div id="navigation-sticky-wrapper" class="sticky-wrapper" style="height: 100px;"><div id="navigation" class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="navbar-inner">
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
<span class="sr-only">Toggle navigation</span>
<i class="icon fontello icon-menu icon-2x"></i>
</button>
<a id="brand" class="navbar-brand" href="/#home"> <img src="/sites/default/themes/md_alpine/img/logo.png" alt=""> </a>
</div>
<div class="navbar-collapse collapse">
<ul class="menu clearfix nav navbar-nav navbar-right"><li class="first collapsed"><a class="active menu-minipanel menu-minipanel-1770 minipanel-processed" title="" href="/#about">Overview</a></li>
<li class="leaf"><a title="" href="/why-do-our-clients-choose-us">Services</a></li>
<li class="leaf"><a title="" href="/blog/inner-circle">Blog</a></li>
<li class="leaf"><a title="" href="/open-positions"><i aria-hidden="true" class="icon fontello icon-location"></i>Jobs</a></li>
<li class="last collapsed"><a title="" href="/ContactUs">Contact</a></li>
</ul> </div>
</div>
</div></div> </div>

</div>
</div>
</div>
</div>
</div>
</div>

Your help is greatly appreciated. BTW, great job with the theme.
E.