You dont need all the fragmented appframework js and css files, you can just include 2 css and 1 js file, here is updated code, it works as cordova app on android, I built Cordova app with Intel XDK.
<!DOCTYPE html>
<html>
<head>
<title>XDK</title>
<meta name="viewport" content="initial-scale=1.0, maximum-scale=1.0, minimum-scale=1.0, user-scalable=0;" />
<link rel="stylesheet" type="text/css" href="css/af.ui.css" />
<link rel="stylesheet" type="text/css" href="css/icons.css" />
<script type="text/javascript" charset="utf-8" src="js/appframework.ui.min.js"></script>
<script>
$.ui.ready(function () {
console.log("UI Ready!!!");
});
$(document).ready(function() {
console.log('Document Ready...');
alert('Document Ready...');
});
</script>
</head>
<body>
<div id="afui">
<div id="header">
</div>
<div id="content">
<div title="Home" class="panel" id="main" selected="true">
<span>THIS is the HOME Page!</span>
</div>
<div title="Second Page" class="panel" id="second">
</div>
</div>
<nav>
<div class="title">Nav Home</div>
<ul class="list">
<li><a class="icon home mini" href="#main">Home Link</a></li>
<li><a class="icon mini" href="#second">Second Link</a></li>
</ul>
</nav>
</div>
<script type="text/javascript" src="cordova.js"></script>
</body>
</html>