Use relative includes. Should fix #1.

_includes/head.html

@@ -7,9 +7,8 @@
 
   
     <link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">
-    <link rel="stylesheet" type="text/css" media="screen,projection" href="{{ "/assets/materialize.css" | relative_url }}" />
-    <link rel="stylesheet" type="text/css" media="screen,projection" href="{{ "/assets/main.css" | relative_url }}">
+    <link rel="stylesheet" type="text/css" media="screen,projection" href="assets/materialize.css" />
+    <link rel="stylesheet" type="text/css" media="screen,projection" href="assets/main.css">
     <link rel="canonical" href="{{ page.url | replace:'index.html','' | absolute_url }}" />
-    <link rel="alternate" type="application/rss+xml" title="{{ site.title | escape }}" href="{{ "/feed.xml" | relative_url }}" />
   
 </head>

_includes/script.html

 <!--  Scripts-->                                                                               
-<script src="{{ "js/jquery.min.js" | relative_url }}"></script>
-<script src="{{ "js/materialize.min.js" | relative_url }}"></script>
-<script src="{{ "js/init.js" | relative_url }}"></script>
\ No newline at end of file
+<script src="js/jquery.min.js"></script>
+<script src="js/materialize.min.js"></script>
\ No newline at end of file

js/init.js

-(function($){
-  $(function(){
-
-    $('.button-collapse').sideNav();
-    $('.carousel').carousel();
-
-  }); // end of document ready
-})(jQuery); // end of jQuery name space
\ No newline at end of file