diff --git a/_includes/main_title.html b/_includes/main_title.html
index 8e22ced110926139022b54a201d66a46c34d491d..d007abae203592c924f78bd178f2d22538214e07 100644
--- a/_includes/main_title.html
+++ b/_includes/main_title.html
@@ -1,4 +1,4 @@
 {% comment %}
   Main title for lesson pages.
 {% endcomment %}
-<h1 class="maintitle"><a href="{{ page.root }}/">{{ site.title }}</a>{% if page.title %}: {{ page.title }}{% endif %}</h1>
+<h1 class="maintitle"><a href="{{ page.root }}{% link index.md %}">{{ site.title }}</a>{% if page.title %}: {{ page.title }}{% endif %}</h1>
diff --git a/_includes/navbar.html b/_includes/navbar.html
index 7e2560d1498514ec183fa31184691b50224fe2fc..31b2c65b755c9f5a834be824f29088b18c813df0 100644
--- a/_includes/navbar.html
+++ b/_includes/navbar.html
@@ -12,33 +12,35 @@
       </button>
 
       {% comment %} Select what logo to display. {% endcomment %}
-      {% if site.carpentry == "swc" %}
+      {% if page.carpentry == "swc" %}
       <a href="{{ site.swc_site }}" class="pull-left">
         <img class="navbar-logo" src="{{ page.root }}/assets/img/swc-icon-blue.svg" alt="Software Carpentry logo" />
       </a>
-      {% elsif site.carpentry == "dc" %}
+      {% elsif page.carpentry == "dc" %}
       <a href="{{ site.dc_site }}" class="pull-left">
         <img class="navbar-logo" src="{{ page.root }}/assets/img/dc-icon-black.svg" alt="Data Carpentry logo" />
       </a>
-      {% elsif site.carpentry == "lc" %}
+      {% elsif page.carpentry == "lc" %}
       <a href="{{ site.lc_site }}" class="pull-left">
         <img class="navbar-logo" src="{{ page.root }}/assets/img/lc-icon-black.png" alt="Library Carpentry logo" />
       </a>
       {% endif %}
 
       {% comment %} Always show link to home page. {% endcomment %}
-      <a class="navbar-brand" href="{{ page.root }}/">Home</a>
+      <a class="navbar-brand" href="{{ page.root }}{% link index.md %}">Home</a>
 
     </div>
     <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
       <ul class="nav navbar-nav">
 
 	{% comment %} Always show code of conduct. {% endcomment %}
-        <li><a href="{{ page.root }}/conduct/">Code of Conduct</a></li>
+        <li><a href="{{ page.root }}{% link CONDUCT.md %}">Code of Conduct</a></li>
 
-	{% comment %} Show setup instructions, reference guide, and lesson episodes for lessons. {% endcomment %}
         {% if site.kind == "lesson" %}
-        <li><a href="{{ page.root }}/setup/">Setup</a></li>
+	{% comment %} Show setup instructions. {% endcomment %}
+        <li><a href="{{ page.root }}{% link setup.md %}">Setup</a></li>
+
+        {% comment %} Show lesson episodes for lessons. {% endcomment %}
         <li class="dropdown">
           <a href="{{ page.root }}/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Episodes <span class="caret"></span></a>
           <ul class="dropdown-menu">
@@ -46,7 +48,7 @@
             <li><a href="{{ page.root }}{{ episode.url }}">{{ episode.title }}</a></li>
             {% endfor %}
 	    <li role="separator" class="divider"></li>
-            <li><a href="{{ page.root }}/aio/">All in one page (Beta)</a></li>
+            <li><a href="{{ page.root }}{% link aio.md %}">All in one page (Beta)</a></li>
           </ul>
         </li>
 	{% endif %}
@@ -56,7 +58,7 @@
         <li class="dropdown">
           <a href="{{ page.root }}/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Extras <span class="caret"></span></a>
           <ul class="dropdown-menu">
-            <li><a href="{{ page.root }}/reference/">Reference</a></li>
+            <li><a href="{{ page.root }}{% link reference.md %}">Reference</a></li>
             {% for extra in site.extras %}
             <li><a href="{{ page.root }}{{ extra.url }}">{{ extra.title }}</a></li>
             {% endfor %}
@@ -65,7 +67,7 @@
 	{% endif %}
 
 	{% comment %} Always show license. {% endcomment %}
-        <li><a href="{{ page.root }}/license/">License</a></li>
+        <li><a href="{{ page.root }}{% link LICENSE.md %}">License</a></li>
 	{% if page.source %}
 	{% if page.source == "Rmd" %}
 	<li><a href="{{site.github.repository_url}}/edit/gh-pages/{{page.path|replace: "_episodes", "_episodes_rmd" | replace: ".md", ".Rmd"}}">Improve this page <span class="glyphicon glyphicon-pencil" aria-hidden="true"></span></a></li>
diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py
index fc7baf7d8d0d5223b0547e53cc3ae494fb019499..bf0ba17c5b1a85eff07be16a53d753d125bab2b2 100755
--- a/bin/lesson_initialize.py
+++ b/bin/lesson_initialize.py
@@ -222,9 +222,10 @@ start_time: 0
 collections:
   episodes:
     output: true
-    permalink: /:path/
+    permalink: /:path/index.html
   extras:
     output: true
+    permalink: /:path/index.html
 
 # Set the default layout for things in the episodes collection.
 defaults:
@@ -249,6 +250,7 @@ ROOT_INDEX_MD = '''\
 ---
 layout: lesson
 root: .
+permalink: index.html  # Is the only page that don't follow the partner /:path/index.html
 ---
 FIXME: home page introduction
 
@@ -261,7 +263,6 @@ FIXME: home page introduction
 ROOT_REFERENCE_MD = '''\
 ---
 layout: reference
-permalink: /reference/
 ---
 
 ## Glossary
@@ -273,7 +274,6 @@ ROOT_SETUP_MD = '''\
 ---
 layout: page
 title: Setup
-permalink: /setup/
 ---
 FIXME
 '''
@@ -281,7 +281,6 @@ FIXME
 ROOT_AIO_MD = '''\
 ---
 layout: page 
-permalink: /aio/
 ---
 <script>
   window.onload = function() {
@@ -335,7 +334,6 @@ EXTRAS_ABOUT_MD = '''\
 ---
 layout: page
 title: About
-permalink: /about/
 ---
 {% include carpentries.html %}
 '''
@@ -344,7 +342,6 @@ EXTRAS_DISCUSS_MD = '''\
 ---
 layout: page
 title: Discussion
-permalink: /discuss/
 ---
 FIXME
 '''
@@ -353,7 +350,6 @@ EXTRAS_FIGURES_MD = '''\
 ---
 layout: page
 title: Figures
-permalink: /figures/
 ---
 {% include all_figures.html %}
 '''
@@ -362,7 +358,6 @@ EXTRAS_GUIDE_MD = '''\
 ---
 layout: page
 title: "Instructor Notes"
-permalink: /guide/
 ---
 FIXME
 '''