Прописал все пути от корня

_layouts/main.html

@@ -6,11 +6,11 @@
   <meta charset="utf-8">
   <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
 
-  <link rel="stylesheet" href="stylesheets/stylesheet.css" media="screen"/>
-  <link rel="stylesheet" href="stylesheets/pygment_trac.css"/>
+  <link rel="stylesheet" href="/stylesheets/stylesheet.css" media="screen"/>
+  <link rel="stylesheet" href="/stylesheets/pygment_trac.css"/>
   <script type="text/javascript" src="http://yandex.st/jquery/2.0.0/jquery.min.js"></script>
   <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML"></script>
-  <script type="text/javascript" src="javascripts/script.js"></script>
+  <script type="text/javascript" src="/javascripts/script.js"></script>
 
   <title>Космическая эра: 1861</title>
   <meta name="description" content="">

chargen.html

@@ -2,7 +2,7 @@
 layout: main
 ---
 <script type="text/javascript" src="javascripts/chargen.js"></script>
-  <link rel="stylesheet" href="stylesheets/chargen.css"/>
+<link rel="stylesheet" href="/stylesheets/chargen.css" />
 <div id="wrapper_overview">
 	<div class="group" id="specials"></div>
 	<div class="group" id="derived"></div>