diff --git a/user_guide_src/source/_themes/sphinx_rtd_theme/layout.html b/user_guide_src/source/_themes/sphinx_rtd_theme/layout.html
index 5f9ef21..1203b2f 100644
--- a/user_guide_src/source/_themes/sphinx_rtd_theme/layout.html
+++ b/user_guide_src/source/_themes/sphinx_rtd_theme/layout.html
@@ -90,7 +90,7 @@
 
       <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
         {% block menu %}
-          {% set toctree = toctree(maxdepth=2, collapse=False, includehidden=True) %}
+          {% set toctree = toctree(maxdepth=2, collapse=False, includehidden=False) %}
           {% if toctree %}
               {{ toctree }}
           {% else %}
diff --git a/user_guide_src/source/contributing/index.rst b/user_guide_src/source/contributing/index.rst
index 3548dbc..427a067 100644
--- a/user_guide_src/source/contributing/index.rst
+++ b/user_guide_src/source/contributing/index.rst
@@ -2,6 +2,12 @@
 Contributing to CodeIgniter
 ###########################
 
+.. toctree::
+	:titlesonly:
+
+	../documentation/index
+	../DCO
+
 CodeIgniter is a community driven project and accepts contributions of code
 and documentation from the community. These contributions are made in the form
 of Issues or `Pull Requests <http://help.github.com/send-pull-requests/>`_ on
@@ -28,7 +34,7 @@
 
 If you are having trouble using a feature of CodeIgniter, ask for help on the forum.
 
-If you are wondering if you are using 
+If you are wondering if you are using
 something correctly or if you have found a bug, ask on the forum first.
 
 ****************************
@@ -132,10 +138,10 @@
 
 	Signed-off-by: John Q Public <john.public@example.com>
 
-If you are using Tower there is a "Sign-Off" checkbox in the commit window. You 
-could even alias git commit to use the -s flag so you don’t have to think about 
+If you are using Tower there is a "Sign-Off" checkbox in the commit window. You
+could even alias git commit to use the -s flag so you don’t have to think about
 it.
 
-By signing your work in this manner, you certify to a "Developer's Certificate 
+By signing your work in this manner, you certify to a "Developer's Certificate
 or Origin". The current version of this certificate is in the :doc:`/DCO` file
-in the root of this documentation.
\ No newline at end of file
+in the root of this documentation.
diff --git a/user_guide_src/source/index.rst b/user_guide_src/source/index.rst
index d8f60e3..8d8aa94 100644
--- a/user_guide_src/source/index.rst
+++ b/user_guide_src/source/index.rst
@@ -13,7 +13,10 @@
 Welcome
 *******
 
-- :doc:`general/welcome`
+.. toctree::
+	:titlesonly:
+
+	general/welcome
 
 **********
 Basic Info
@@ -25,32 +28,31 @@
 ************
 Installation
 ************
+.. toctree::
+	:includehidden:
+	:maxdepth: 2
+	:titlesonly:
 
-- :doc:`installation/downloads`
-- :doc:`installation/index`
-- :doc:`installation/upgrading`
-- :doc:`installation/troubleshooting`
+	installation/index
 
 ************
 Introduction
 ************
 
-- :doc:`overview/getting_started`
-- :doc:`overview/at_a_glance`
-- :doc:`overview/features`
-- :doc:`overview/appflow`
-- :doc:`overview/mvc`
-- :doc:`overview/goals`
+.. toctree::
+	:titlesonly:
+
+	overview/index
 
 ********
 Tutorial
 ********
 
-- :doc:`tutorial/index`
-- :doc:`tutorial/static_pages`
-- :doc:`tutorial/news_section`
-- :doc:`tutorial/create_news_items`
-- :doc:`tutorial/conclusion`
+.. toctree::
+	:includehidden:
+	:titlesonly:
+
+	tutorial/index
 
 **************
 General Topics
@@ -59,7 +61,7 @@
 .. toctree::
 	:glob:
 	:titlesonly:
-	
+
 	general/index
 
 *****************
@@ -69,7 +71,7 @@
 .. toctree::
 	:glob:
 	:titlesonly:
-	
+
 	libraries/index
 
 ******************
@@ -79,7 +81,7 @@
 .. toctree::
 	:glob:
 	:titlesonly:
-	
+
 	database/index
 
 ****************
@@ -89,7 +91,7 @@
 .. toctree::
 	:glob:
 	:titlesonly:
-	
+
 	helpers/index
 
 ***************************
@@ -99,16 +101,14 @@
 .. toctree::
 	:glob:
 	:titlesonly:
-	
+
 	contributing/index
-	documentation/index
-	DCO
 
 .. toctree::
 	:glob:
 	:titlesonly:
 	:hidden:
-	
+
 	*
 	overview/index
 	general/requirements
diff --git a/user_guide_src/source/installation/index.rst b/user_guide_src/source/installation/index.rst
index 7f75f78..50493bb 100644
--- a/user_guide_src/source/installation/index.rst
+++ b/user_guide_src/source/installation/index.rst
@@ -47,8 +47,11 @@
 to begin learning how to build dynamic PHP applications. Enjoy!
 
 .. toctree::
-	:glob:
 	:hidden:
 	:titlesonly:
-	
-	*
\ No newline at end of file
+
+	downloads
+	self
+	upgrading
+	troubleshooting
+
diff --git a/user_guide_src/source/installation/upgrading.rst b/user_guide_src/source/installation/upgrading.rst
index 6d2e788..366aa13 100644
--- a/user_guide_src/source/installation/upgrading.rst
+++ b/user_guide_src/source/installation/upgrading.rst
@@ -5,33 +5,35 @@
 Please read the upgrade notes corresponding to the version you are
 upgrading from.
 
--  :doc:`Upgrading from 2.1.4 to 3.0.0 <upgrade_300>`
--  :doc:`Upgrading from 2.1.3 to 2.1.4 <upgrade_214>`
--  :doc:`Upgrading from 2.1.2 to 2.1.3 <upgrade_213>`
--  :doc:`Upgrading from 2.1.1 to 2.1.2 <upgrade_212>`
--  :doc:`Upgrading from 2.1.0 to 2.1.1 <upgrade_211>`
--  :doc:`Upgrading from 2.0.3 to 2.1.0 <upgrade_210>`
--  :doc:`Upgrading from 2.0.2 to 2.0.3 <upgrade_203>`
--  :doc:`Upgrading from 2.0.1 to 2.0.2 <upgrade_202>`
--  :doc:`Upgrading from 2.0 to 2.0.1 <upgrade_201>`
--  :doc:`Upgrading from 1.7.2 to 2.0 <upgrade_200>`
--  :doc:`Upgrading from 1.7.1 to 1.7.2 <upgrade_172>`
--  :doc:`Upgrading from 1.7.0 to 1.7.1 <upgrade_171>`
--  :doc:`Upgrading from 1.6.3 to 1.7.0 <upgrade_170>`
--  :doc:`Upgrading from 1.6.2 to 1.6.3 <upgrade_163>`
--  :doc:`Upgrading from 1.6.1 to 1.6.2 <upgrade_162>`
--  :doc:`Upgrading from 1.6.0 to 1.6.1 <upgrade_161>`
--  :doc:`Upgrading from 1.5.4 to 1.6.0 <upgrade_160>`
--  :doc:`Upgrading from 1.5.3 to 1.5.4 <upgrade_154>`
--  :doc:`Upgrading from 1.5.2 to 1.5.3 <upgrade_153>`
--  :doc:`Upgrading from 1.5.0 or 1.5.1 to 1.5.2 <upgrade_152>`
--  :doc:`Upgrading from 1.4.1 to 1.5.0 <upgrade_150>`
--  :doc:`Upgrading from 1.4.0 to 1.4.1 <upgrade_141>`
--  :doc:`Upgrading from 1.3.3 to 1.4.0 <upgrade_140>`
--  :doc:`Upgrading from 1.3.2 to 1.3.3 <upgrade_133>`
--  :doc:`Upgrading from 1.3.1 to 1.3.2 <upgrade_132>`
--  :doc:`Upgrading from 1.3 to 1.3.1 <upgrade_131>`
--  :doc:`Upgrading from 1.2 to 1.3 <upgrade_130>`
--  :doc:`Upgrading from 1.1 to 1.2 <upgrade_120>`
--  :doc:`Upgrading from Beta 1.0 to Beta 1.1 <upgrade_b11>`
+.. toctree::
+	:titlesonly:
 
+	Upgrading from 2.1.4 to 3.0.0 <upgrade_300>
+	Upgrading from 2.1.3 to 2.1.4 <upgrade_214>
+	Upgrading from 2.1.2 to 2.1.3 <upgrade_213>
+	Upgrading from 2.1.1 to 2.1.2 <upgrade_212>
+	Upgrading from 2.1.0 to 2.1.1 <upgrade_211>
+	Upgrading from 2.0.3 to 2.1.0 <upgrade_210>
+	Upgrading from 2.0.2 to 2.0.3 <upgrade_203>
+	Upgrading from 2.0.1 to 2.0.2 <upgrade_202>
+	Upgrading from 2.0 to 2.0.1 <upgrade_201>
+	Upgrading from 1.7.2 to 2.0 <upgrade_200>
+	Upgrading from 1.7.1 to 1.7.2 <upgrade_172>
+	Upgrading from 1.7.0 to 1.7.1 <upgrade_171>
+	Upgrading from 1.6.3 to 1.7.0 <upgrade_170>
+	Upgrading from 1.6.2 to 1.6.3 <upgrade_163>
+	Upgrading from 1.6.1 to 1.6.2 <upgrade_162>
+	Upgrading from 1.6.0 to 1.6.1 <upgrade_161>
+	Upgrading from 1.5.4 to 1.6.0 <upgrade_160>
+	Upgrading from 1.5.3 to 1.5.4 <upgrade_154>
+	Upgrading from 1.5.2 to 1.5.3 <upgrade_153>
+	Upgrading from 1.5.0 or 1.5.1 to 1.5.2 <upgrade_152>
+	Upgrading from 1.4.1 to 1.5.0 <upgrade_150>
+	Upgrading from 1.4.0 to 1.4.1 <upgrade_141>
+	Upgrading from 1.3.3 to 1.4.0 <upgrade_140>
+	Upgrading from 1.3.2 to 1.3.3 <upgrade_133>
+	Upgrading from 1.3.1 to 1.3.2 <upgrade_132>
+	Upgrading from 1.3 to 1.3.1 <upgrade_131>
+	Upgrading from 1.2 to 1.3 <upgrade_130>
+	Upgrading from 1.1 to 1.2 <upgrade_120>
+	Upgrading from Beta 1.0 to Beta 1.1 <upgrade_b11>