Use a div instead of alert for version warning

With this change, it is also no longer necessary to display the version in the
navigation bar. The accidently removed doctype is also brought back.

config/jsdoc/api/template/tmpl/navigation.tmpl

@@ -3,7 +3,6 @@ var self = this;
 ?>
 <div class="navigation">
     <div class="search">
-        <h4 class='package-version'>v<?js= self.version ?></h4>
         <input id="search" type="text" class="form-control input-sm" placeholder="Search Documentation">
     </div>
     <ul class="list">