First pass at ToC remediation
diff --git a/user_guide_src/source/_themes/eldocs/layout.html b/user_guide_src/source/_themes/eldocs/layout.html
index 4b1a022..01db07c 100644
--- a/user_guide_src/source/_themes/eldocs/layout.html
+++ b/user_guide_src/source/_themes/eldocs/layout.html
@@ -9,6 +9,9 @@
 {%- if project == 'ExpressionEngine' %}{% set project_abbreviation = 'ee' %}{% set project_domain = 'expressionengine.com' %}{% endif -%}
 {%- if project == 'CodeIgniter' %}{% set project_abbreviation = 'ci' %}{% set project_domain = 'codeigniter.com' %}{% endif -%}
 {%- if project == 'MojoMotor' %}{% set project_abbreviation = 'mm' %}{% set project_domain = 'mojomotor.com' %}{% endif -%}
+{%- set exclude_comments = ['index', 'license', 'changelog',
+							'development/index', 'development/extension_hooks/index',
+							'development/guidelines/template'] %}
 
 <html>
 	<head>
@@ -85,10 +88,6 @@
 		<div id="brand" class="{{ project_abbreviation }}">
 			<a href="http://{{ project_domain }}/"><img src="{{ pathto('_static/asset/img/' + project_abbreviation + '-logo.gif', 1) }}" alt="{{ project }}"></a>
 			<p>{{ release }} User Guide</p>
-			{%- if show_source and has_source and sourcename %}
-		    <p><a href="{{ pathto('_sources/' + sourcename, true)|e }}"
-			           rel="nofollow">{{ _('Show Source') }}</a></p>
-			{%- endif %}
 		</div><!-- /#brand -->
 
 		<div id="header">
@@ -101,15 +100,16 @@
 			</form>
 			<ul>
 				{%- block rootrellink %}
-				<li><a href="{{ pathto(master_doc) }}">Home</a>&nbsp;&nbsp;{{ reldelim1 }}</li>
-				<li><a id="toc-link" href="{{ pathto(master_doc) }}">Table of Contents</a>&nbsp;&nbsp;{{ reldelim1 }}</li>
+				<li><a href="{{ pathto(master_doc) }}">User Guide Home</a>{%- if pagename != 'index' %}&nbsp;&nbsp;{{ reldelim1 }}{%- endif %}</li>
 				{%- endblock %}
 				
 				{%- for parent in parents %}
 				<li><a href="{{ parent.link|e }}" {% if loop.last %}{{ accesskey("U") }}{% endif %}>{{ parent.title }}</a>&nbsp;&nbsp; {{ reldelim1 }}</li>
 		        {%- endfor %}
 
+				{%- if pagename != 'index' %}
 				<li><strong>{{ title }}</strong></li>
+				{%- endif %}
 			</ul>
 		</div><!-- /#header -->
 
@@ -124,49 +124,9 @@
 	
 	{%- block footer %}			
 		<div id="footer">
-			<p class="top">
-				{% if prev %}
-				<span class="prev">Previous Topic: <a href="{{ prev.link }}">{{ prev.title }}</a></span>
-				{% endif %}
-				{% if next %}
-				<span class="next">Next Topic: <a href="{{ next.link }}">{{ next.title }}</a></span>
-				{% endif %}
-				<a href="#header" title="Return to top">Return to top</a>
-			</p>
-			<p><a href="{{ project_url }}">{{ project }}</a> &ndash; Copyright &copy; {{ copyright }}</a> &ndash; Last updated: {{ last_updated }}</p>
+			<p class="top"><a href="#header" title="Return to top">Return to top</a></p>
+			<p><a href="{{ project_url }}">{{ project }}</a> &ndash; Copyright &copy; {{ copyright }}</a></p>
 		</div><!-- /#footer -->
 	{%- endblock %}
-	
-	<script src="{{ pathto('_static/asset/js/jquery-ui-min.js', 1) }}" type="text/javascript" charset="utf-8" async></script>
-	<script type="text/javascript" charset="utf-8">
-		$('#toc-link').click(function(){
-			$('#table-contents').animate({ left: '0' },1000);
-			return false;
-		});
-		$('html').click(function(){
-			if ($('#table-contents').css("left") == '0px'){
-				$('#table-contents').animate({ left: '-520' },1000);
-			}
-		});
-		$('#table-contents').click(function(event){
-			event.stopPropagation();
-		});
-/*		$('*:not(#table-contents,#toc-link)').click(function(){
-			if ($('#table-contents').css("left") == '0px'){
-				$('#table-contents').animate({ left: '-520' },1000);
-			}
-		});
-/*		$("#toc-link").click(function () {
-			$('#table-contents').show("slide", { direction: "left" }, 100);
-			event.stopPropagation();
-			return false;
-		});
-		$('*:not(#table-contents,#toc-link)').click(function () {
-			if ($('#table-contents').is(":visible")) {
-				$('#table-contents').hide("slide", { direction: "left" }, 100);
-				event.stopPropagation();	
-			}
-		}); */
-	</script>
 	</body>
-</html>
\ No newline at end of file
+</html>
diff --git a/user_guide_src/source/_themes/eldocs/static/asset/css/common.css b/user_guide_src/source/_themes/eldocs/static/asset/css/common.css
index 66768ba..6cabda0 100644
--- a/user_guide_src/source/_themes/eldocs/static/asset/css/common.css
+++ b/user_guide_src/source/_themes/eldocs/static/asset/css/common.css
@@ -49,7 +49,9 @@
 
 h1{ font-size: 28px; }
 
-h2{ font-size: 24px; }
+h2{ font-size: 24px; font-weight: normal; }
+
+h1, h2, h3, h4, h5, h6{ margin-bottom: 20px; }
 
 h2, h3{ border-bottom: 2px solid #EEEEEE; padding: 0 0 3px; }	
 
@@ -73,6 +75,10 @@
 	li > ol{ margin: 0; margin-left: 40px; }
 
 	dl > dd{ margin-left: 20px; }
+	
+	li > p { margin: 0; }
+
+#expressionengine-user-guide li em { font-style: normal; }
 
 p, li, dd, dt, pre{ line-height: 1.5; }
 
@@ -141,39 +147,31 @@
 fieldset{ border: 0; }
 
 .top{ float: right; }
-.next{ padding: 0 20px 0 10px; }
-.prev{ padding-right: 10px; }
 
-.highlight-ci,
+.admonition,
 .highlight-ee,
+.highlight-ci,
 .highlight-rst,
 .highlight-bash,
 .highlight-perl,
+.highlight-php,
 .cp-path,
-.important,
-.note{ 
-	background-color: #F5FBFF; 
+.codeblock{ 
+	background-color: #F9FEFF; 
 	border: 1px solid #C8DEF0; 
-	margin: 20px 0 20px 20px; 
+	-moz-box-shadow: 4px 4px 0 rgba(0,0,0,0.03);
+	-webkit-box-shadow: 4px 4px 0 rgba(0,0,0,0.03);
+	box-shadow: 4px 4px 0 rgba(0,0,0,0.03);
+	margin: 20px 0; 
 	padding: 10px 10px 8px; 
 }
 
-	.highlight-ci,
-	.highlight-ee,
-	.highlight-rst,
-	.highlight-bash,
-	.highlight-perl{
-		-moz-box-shadow: 4px 4px 0 rgba(0,0,0,0.03);
-		-webkit-box-shadow: 4px 4px 0 rgba(0,0,0,0.03);
-		box-shadow: 4px 4px 0 rgba(0,0,0,0.03);
-	}
-
-	.cp-path{ background-color: #FFFDED; border-color: #D1CDB0; }
-	.important, .note{ background-color: #F2FFE8; border-color: #B9D3A6; }
-	.highlight-rst{ background-color: #F9FEFE; border-color: #AACFCF; }
+	.admonition p{ margin: 0; }
 	
-	.important p,
-	.note p{ margin: 0; }
+	.codeblock{ margin: 10px 0; }
+	
+	.cp-path{ background-color: #FAFFF6; border-color: #D1CDB0; }
+	.important, .note{ background-color: #FFFFF2; border-color: #C8C8A5; }
 	
 .admonition-title{ 
 	float: left;
@@ -295,6 +293,43 @@
 
 	#footer p{ margin: 0; }
 
+#comments,
+#feedLink{ background: #FCFCFC; padding: 1px 40px 20px; }
+
+	#comments{ border-top: 1px solid #CCCCCC; }
+	#comments h3{ margin: 20px 0; }
+
+.comments td.avatar{ min-width: 100px; }
+
+.comments td.column1,
+.comments td.post{ background-color: #FFFFFF; padding: 10px; }
+
+.comments td.staffeven{ border-left: 10px solid #C8DEF0; }
+
+#comment_form p,
+.comments p{ margin: 0; }
+
+	.comments p{ margin-bottom: 10px; }
+
+#comment_form textarea{
+	-moz-box-sizing: border-box;
+	-webkit-box-sizing: border-box;
+	box-sizing: border-box;
+	margin-bottom: 10px;
+	resize: none; 
+	width: 100%; 
+}
+
+#comment_form input[type="submit"]{ margin-top: 10px; }
+
+	#comment_form textarea:focus{ background-color: #FFFFF2; border: 1px solid #666666; outline: 0; }
+
+	#commentFormInstructions{ font-size: 12px; margin: 20px 0; }
+
+	#feedLink a{ font-size: 16px; }
+
+	#feedLink a img{ float: left; margin-right: 5px; }
+
 @media (max-width:800px){
 	#footer .top,
 	#header form{ float: none; margin-bottom: 10px; }
@@ -310,4 +345,4 @@
 
 @media screen and (-webkit-min-device-pixel-ratio:0){
 	#header input[type="submit"]{ padding-bottom: 7px; }
-}
\ No newline at end of file
+}
diff --git a/user_guide_src/source/general/welcome.rst b/user_guide_src/source/general/welcome.rst
new file mode 100644
index 0000000..b28c3bc
--- /dev/null
+++ b/user_guide_src/source/general/welcome.rst
@@ -0,0 +1,32 @@
+######################
+Welcome to CodeIgniter
+######################
+
+CodeIgniter is an Application Development Framework - a toolkit - for
+people who build web sites using PHP. Its goal is to enable you to
+develop projects much faster than you could if you were writing code
+from scratch, by providing a rich set of libraries for commonly needed
+tasks, as well as a simple interface and logical structure to access
+these libraries. CodeIgniter lets you creatively focus on your project
+by minimizing the amount of code needed for a given task.
+
+***********************
+Who is CodeIgniter For?
+***********************
+
+CodeIgniter is right for you if:
+
+-  You want a framework with a small footprint.
+-  You need exceptional performance.
+-  You need broad compatibility with standard hosting accounts that run
+   a variety of PHP versions and configurations.
+-  You want a framework that requires nearly zero configuration.
+-  You want a framework that does not require you to use the command
+   line.
+-  You want a framework that does not require you to adhere to
+   restrictive coding rules.
+-  You are not interested in large-scale monolithic libraries like PEAR.
+-  You do not want to be forced to learn a templating language (although
+   a template parser is optionally available if you desire one).
+-  You eschew complexity, favoring simple solutions.
+-  You need clear, thorough documentation.
diff --git a/user_guide_src/source/index.rst b/user_guide_src/source/index.rst
index 6cdeb24..c89b41c 100644
--- a/user_guide_src/source/index.rst
+++ b/user_guide_src/source/index.rst
@@ -1,34 +1,95 @@
-Welcome to CodeIgniter
-======================
+######################
+CodeIgniter User Guide
+######################
 
-CodeIgniter is an Application Development Framework - a toolkit - for
-people who build web sites using PHP. Its goal is to enable you to
-develop projects much faster than you could if you were writing code
-from scratch, by providing a rich set of libraries for commonly needed
-tasks, as well as a simple interface and logical structure to access
-these libraries. CodeIgniter lets you creatively focus on your project
-by minimizing the amount of code needed for a given task.
+- :doc:`License Agreement <license>`
+- :doc:`Change Log <changelog>`
 
-Who is CodeIgniter For?
-=======================
+.. contents::
+   :local:
+   :depth: 2
 
-CodeIgniter is right for you if:
+*******
+Welcome
+*******
 
--  You want a framework with a small footprint.
--  You need exceptional performance.
--  You need broad compatibility with standard hosting accounts that run
-   a variety of PHP versions and configurations.
--  You want a framework that requires nearly zero configuration.
--  You want a framework that does not require you to use the command
-   line.
--  You want a framework that does not require you to adhere to
-   restrictive coding rules.
--  You are not interested in large-scale monolithic libraries like PEAR.
--  You do not want to be forced to learn a templating language (although
-   a template parser is optionally available if you desire one).
--  You eschew complexity, favoring simple solutions.
--  You need clear, thorough documentation.
+- :doc:`general/welcome`
 
+**********
+Basic Info
+**********
+
+- :doc:`general/requirements`
+- :doc:`general/credits`
+
+************
+Installation
+************
+
+- :doc:`installation/downloads`
+- :doc:`installation/index`
+- :doc:`installation/upgrading`
+- :doc:`installation/troubleshooting`
+
+************
+Introduction
+************
+
+- :doc:`overview/getting_started`
+- :doc:`overview/at_a_glance`
+- :doc:`overview/cheatsheets`
+- :doc:`overview/features`
+- :doc:`overview/appflow`
+- :doc:`overview/mvc`
+- :doc:`overview/goals`
+
+********
+Tutorial
+********
+
+- :doc:`tutorial/index`
+- :doc:`tutorial/static_pages`
+- :doc:`tutorial/news_section`
+- :doc:`tutorial/create_news_items`
+- :doc:`tutorial/conclusion`
+
+**************
+General Topics
+**************
+
+.. toctree::
+	:glob:
+	:titlesonly:
+	
+	general/index
+
+*****************
+Library Reference
+*****************
+
+.. toctree::
+	:glob:
+	:titlesonly:
+	
+	libraries/index
+
+****************
+Driver Reference
+****************
+
+- :doc:`libraries/caching`
+- :doc:`database/index`
+- :doc:`libraries/javascript`
+
+****************
+Helper Reference
+****************
+
+.. toctree::
+	:glob:
+	:titlesonly:
+	
+	helpers/index
 
 .. toctree::
 	:glob: