diff --git a/system/application/config/autoload.php b/application/config/autoload.php
similarity index 95%
rename from system/application/config/autoload.php
rename to application/config/autoload.php
index e7c6f0d..35ad628 100644
--- a/system/application/config/autoload.php
+++ b/application/config/autoload.php
@@ -31,7 +31,7 @@
 |  Auto-load Libraries
 | -------------------------------------------------------------------
 | These are the classes located in the system/libraries folder
-| or in your system/application/libraries folder.
+| or in your application/libraries folder.
 |
 | Prototype:
 |
@@ -100,4 +100,4 @@
 
 
 /* End of file autoload.php */
-/* Location: ./system/application/config/autoload.php */
\ No newline at end of file
+/* Location: ./application/config/autoload.php */
\ No newline at end of file
diff --git a/system/application/config/config.php b/application/config/config.php
similarity index 99%
rename from system/application/config/config.php
rename to application/config/config.php
index 1c961b4..bd1429a 100644
--- a/system/application/config/config.php
+++ b/application/config/config.php
@@ -326,4 +326,4 @@
 
 
 /* End of file config.php */
-/* Location: ./system/application/config/config.php */
\ No newline at end of file
+/* Location: ./application/config/config.php */
\ No newline at end of file
diff --git a/system/application/config/constants.php b/application/config/constants.php
similarity index 96%
rename from system/application/config/constants.php
rename to application/config/constants.php
index 86ebdbb..1551cbc 100644
--- a/system/application/config/constants.php
+++ b/application/config/constants.php
@@ -38,4 +38,4 @@
 
 
 /* End of file constants.php */
-/* Location: ./system/application/config/constants.php */
\ No newline at end of file
+/* Location: ./application/config/constants.php */
\ No newline at end of file
diff --git a/system/application/config/database.php b/application/config/database.php
similarity index 97%
rename from system/application/config/database.php
rename to application/config/database.php
index fcdefda..a3226b1 100644
--- a/system/application/config/database.php
+++ b/application/config/database.php
@@ -59,4 +59,4 @@
 
 
 /* End of file database.php */
-/* Location: ./system/application/config/database.php */
\ No newline at end of file
+/* Location: ./application/config/database.php */
\ No newline at end of file
diff --git a/system/application/config/doctypes.php b/application/config/doctypes.php
similarity index 100%
rename from system/application/config/doctypes.php
rename to application/config/doctypes.php
diff --git a/system/application/config/foreign_chars.php b/application/config/foreign_chars.php
similarity index 96%
rename from system/application/config/foreign_chars.php
rename to application/config/foreign_chars.php
index 8d70a2f..59a7d23 100644
--- a/system/application/config/foreign_chars.php
+++ b/application/config/foreign_chars.php
@@ -61,4 +61,4 @@
 
 
 /* End of file foreign_chars.php */
-/* Location: ./system/application/config/foreign_chars.php */
\ No newline at end of file
+/* Location: ./application/config/foreign_chars.php */
\ No newline at end of file
diff --git a/system/application/config/hooks.php b/application/config/hooks.php
similarity index 89%
rename from system/application/config/hooks.php
rename to application/config/hooks.php
index 5e98a9b..a4ad2be 100644
--- a/system/application/config/hooks.php
+++ b/application/config/hooks.php
@@ -13,4 +13,4 @@
 
 
 /* End of file hooks.php */
-/* Location: ./system/application/config/hooks.php */
\ No newline at end of file
+/* Location: ./application/config/hooks.php */
\ No newline at end of file
diff --git a/system/application/config/index.html b/application/config/index.html
similarity index 100%
rename from system/application/config/index.html
rename to application/config/index.html
diff --git a/system/application/config/mimes.php b/application/config/mimes.php
similarity index 100%
rename from system/application/config/mimes.php
rename to application/config/mimes.php
diff --git a/system/application/config/profiler.php b/application/config/profiler.php
similarity index 89%
rename from system/application/config/profiler.php
rename to application/config/profiler.php
index f30432d..f8a5b1a 100644
--- a/system/application/config/profiler.php
+++ b/application/config/profiler.php
@@ -14,4 +14,4 @@
 
 
 /* End of file profiler.php */
-/* Location: ./system/application/config/profiler.php */
\ No newline at end of file
+/* Location: ./application/config/profiler.php */
\ No newline at end of file
diff --git a/system/application/config/routes.php b/application/config/routes.php
similarity index 95%
rename from system/application/config/routes.php
rename to application/config/routes.php
index 4d9f340..57af985 100644
--- a/system/application/config/routes.php
+++ b/application/config/routes.php
@@ -36,4 +36,4 @@
 
 
 /* End of file routes.php */
-/* Location: ./system/application/config/routes.php */
\ No newline at end of file
+/* Location: ./application/config/routes.php */
\ No newline at end of file
diff --git a/system/application/config/smileys.php b/application/config/smileys.php
similarity index 98%
rename from system/application/config/smileys.php
rename to application/config/smileys.php
index 7f3aba5..31a60c6 100644
--- a/system/application/config/smileys.php
+++ b/application/config/smileys.php
@@ -63,4 +63,4 @@
 		);
 
 /* End of file smileys.php */
-/* Location: ./system/application/config/smileys.php */
\ No newline at end of file
+/* Location: ./application/config/smileys.php */
\ No newline at end of file
diff --git a/system/application/config/user_agents.php b/application/config/user_agents.php
similarity index 98%
rename from system/application/config/user_agents.php
rename to application/config/user_agents.php
index a1c0b14..3be2009 100644
--- a/system/application/config/user_agents.php
+++ b/application/config/user_agents.php
@@ -174,4 +174,4 @@
 				);
 
 /* End of file user_agents.php */
-/* Location: ./system/application/config/user_agents.php */
\ No newline at end of file
+/* Location: ./application/config/user_agents.php */
\ No newline at end of file
diff --git a/system/application/controllers/index.html b/application/controllers/index.html
similarity index 100%
rename from system/application/controllers/index.html
rename to application/controllers/index.html
diff --git a/system/application/controllers/welcome.php b/application/controllers/welcome.php
similarity index 76%
rename from system/application/controllers/welcome.php
rename to application/controllers/welcome.php
index 20d4885..bd134e7 100644
--- a/system/application/controllers/welcome.php
+++ b/application/controllers/welcome.php
@@ -14,4 +14,4 @@
 }
 
 /* End of file welcome.php */
-/* Location: ./system/application/controllers/welcome.php */
\ No newline at end of file
+/* Location: ./application/controllers/welcome.php */
\ No newline at end of file
diff --git a/system/application/core/index.html b/application/core/index.html
similarity index 100%
rename from system/application/core/index.html
rename to application/core/index.html
diff --git a/system/application/errors/error_404.php b/application/errors/error_404.php
similarity index 100%
rename from system/application/errors/error_404.php
rename to application/errors/error_404.php
diff --git a/system/application/errors/error_db.php b/application/errors/error_db.php
similarity index 100%
rename from system/application/errors/error_db.php
rename to application/errors/error_db.php
diff --git a/system/application/errors/error_general.php b/application/errors/error_general.php
similarity index 100%
rename from system/application/errors/error_general.php
rename to application/errors/error_general.php
diff --git a/system/application/errors/error_php.php b/application/errors/error_php.php
similarity index 100%
rename from system/application/errors/error_php.php
rename to application/errors/error_php.php
diff --git a/system/application/errors/index.html b/application/errors/index.html
similarity index 100%
rename from system/application/errors/index.html
rename to application/errors/index.html
diff --git a/system/application/helpers/index.html b/application/helpers/index.html
similarity index 100%
rename from system/application/helpers/index.html
rename to application/helpers/index.html
diff --git a/system/application/hooks/index.html b/application/hooks/index.html
similarity index 100%
rename from system/application/hooks/index.html
rename to application/hooks/index.html
diff --git a/system/application/index.html b/application/index.html
similarity index 100%
rename from system/application/index.html
rename to application/index.html
diff --git a/system/application/language/english/index.html b/application/language/english/index.html
similarity index 100%
rename from system/application/language/english/index.html
rename to application/language/english/index.html
diff --git a/system/application/libraries/index.html b/application/libraries/index.html
similarity index 100%
rename from system/application/libraries/index.html
rename to application/libraries/index.html
diff --git a/system/application/models/index.html b/application/models/index.html
similarity index 100%
rename from system/application/models/index.html
rename to application/models/index.html
diff --git a/system/application/third_party/index.html b/application/third_party/index.html
similarity index 100%
rename from system/application/third_party/index.html
rename to application/third_party/index.html
diff --git a/system/application/views/index.html b/application/views/index.html
similarity index 100%
rename from system/application/views/index.html
rename to application/views/index.html
diff --git a/system/application/views/welcome_message.php b/application/views/welcome_message.php
similarity index 90%
rename from system/application/views/welcome_message.php
rename to application/views/welcome_message.php
index 653b62c..b66fb3f 100644
--- a/system/application/views/welcome_message.php
+++ b/application/views/welcome_message.php
@@ -48,10 +48,10 @@
 <p>The page you are looking at is being generated dynamically by CodeIgniter.</p>
 
 <p>If you would like to edit this page you'll find it located at:</p>
-<code>system/application/views/welcome_message.php</code>
+<code>application/views/welcome_message.php</code>
 
 <p>The corresponding controller for this page is found at:</p>
-<code>system/application/controllers/welcome.php</code>
+<code>application/controllers/welcome.php</code>
 
 <p>If you are exploring CodeIgniter for the very first time, you should start by reading the <a href="user_guide/">User Guide</a>.</p>
 
diff --git a/user_guide/general/helpers.html b/user_guide/general/helpers.html
index ef24e8c..5ba1674 100644
--- a/user_guide/general/helpers.html
+++ b/user_guide/general/helpers.html
@@ -69,7 +69,7 @@
 <p>CodeIgniter does not load Helper Files by default, so the first step in using
 a Helper is to load it.  Once loaded, it becomes globally available in your <a href="../general/controllers.html">controller</a> and <a href="../general/views.html">views</a>.</p>
 
-<p>Helpers are typically stored in your <dfn>system/helpers</dfn>, or <dfn>system/application/helpers </dfn>directory.	CodeIgniter will look first in your <dfn>system/application/helpers</dfn>
+<p>Helpers are typically stored in your <dfn>system/helpers</dfn>, or <dfn>application/helpers </dfn>directory.	CodeIgniter will look first in your <dfn>application/helpers</dfn>
 directory.  If the directory does not exist or the specified helper is not located there CI will instead look in your global
 <dfn>system/helpers</dfn> folder.</p>
 
diff --git a/user_guide/general/managing_apps.html b/user_guide/general/managing_apps.html
index babed5f..9f23de4 100644
--- a/user_guide/general/managing_apps.html
+++ b/user_guide/general/managing_apps.html
@@ -58,7 +58,7 @@
 <h1>Managing your Applications</h1>
 
 <p>By default it is assumed that you only intend to use CodeIgniter to manage one application, which you will build in your
-<dfn>system/application/</dfn> directory.  It is possible, however, to have multiple sets of applications that share a single
+<dfn>application/</dfn> directory.  It is possible, however, to have multiple sets of applications that share a single
 CodeIgniter installation, or even to rename or relocate your <dfn>application</dfn> folder.</p>
 
 <h2>Renaming the Application Folder</h2>
@@ -83,29 +83,29 @@
 put all of the directories located inside your <kbd>application</kbd> folder into their
 own sub-folder.</p>
 
-<p>For example, let's say you want to create two applications, "foo" and "bar".  You will structure your
-application folder like this:</p>
+<p>For example, let's say you want to create two applications, "foo" and "bar".  You could structure your
+application folders like this:</p>
 
-<code>system/application/<var>foo</var>/<br />
-system/application/<var>foo</var>/config/<br />
-system/application/<var>foo</var>/controllers/<br />
-system/application/<var>foo</var>/errors/<br />
-system/application/<var>foo</var>/libraries/<br />
-system/application/<var>foo</var>/models/<br />
-system/application/<var>foo</var>/views/<br />
-system/application/<samp>bar</samp>/<br />
-system/application/<samp>bar</samp>/config/<br />
-system/application/<samp>bar</samp>/controllers/<br />
-system/application/<samp>bar</samp>/errors/<br />
-system/application/<samp>bar</samp>/libraries/<br />
-system/application/<samp>bar</samp>/models/<br />
-system/application/<samp>bar</samp>/views/</code>
+<code>applications/<var>foo</var>/<br />
+applications/<var>foo</var>/config/<br />
+applications/<var>foo</var>/controllers/<br />
+applications/<var>foo</var>/errors/<br />
+applications/<var>foo</var>/libraries/<br />
+applications/<var>foo</var>/models/<br />
+applications/<var>foo</var>/views/<br />
+applications/<samp>bar</samp>/<br />
+applications/<samp>bar</samp>/config/<br />
+applications/<samp>bar</samp>/controllers/<br />
+applications/<samp>bar</samp>/errors/<br />
+applications/<samp>bar</samp>/libraries/<br />
+applications/<samp>bar</samp>/models/<br />
+applications/<samp>bar</samp>/views/</code>
 
 
 <p>To select a particular application for use requires that you open your main <kbd>index.php</kbd> file and set the <dfn>$application_folder</dfn>
 variable.  For example, to select the "foo" application for use you would do this:</p>
 
-<code>$application_folder = "application/foo";</code>
+<code>$application_folder = "applications/foo";</code>
 
 <p class="important"><strong>Note:</strong>&nbsp; Each of your applications will need its own <dfn>index.php</dfn> file which 
 calls the desired application.  The index.php file can be named anything you want.</p>
diff --git a/user_guide/general/profiling.html b/user_guide/general/profiling.html
index 8622ede..f865031 100644
--- a/user_guide/general/profiling.html
+++ b/user_guide/general/profiling.html
@@ -87,7 +87,7 @@
 
 <h2>Enabling and Disabling Profiler Sections</h2>
 
-	<p>Each section of Profiler data can be enabled or disabled by setting a corresponding config variable to <var>TRUE</var> or <var>FALSE</var>.  This can be done one of two ways.  First, you can set application wide defaults with the <dfn>system/application/config/profiler.php</dfn> config file.</p>
+	<p>Each section of Profiler data can be enabled or disabled by setting a corresponding config variable to <var>TRUE</var> or <var>FALSE</var>.  This can be done one of two ways.  First, you can set application wide defaults with the <dfn>application/config/profiler.php</dfn> config file.</p>
 
 	<code>$config['config']&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;= FALSE;<br />
 	$config['queries']&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;= FALSE;<br /></code>
diff --git a/user_guide/helpers/text_helper.html b/user_guide/helpers/text_helper.html
index 9e8f8f5..0e075b9 100644
--- a/user_guide/helpers/text_helper.html
+++ b/user_guide/helpers/text_helper.html
@@ -121,7 +121,7 @@
 
 <code>$string = convert_accented_characters($string);</code>
 	
-<p>This function uses a companion config file <dfn>system/application/config/foreign_chars.php</dfn> to define the to and from array for transliteration.</p>
+<p>This function uses a companion config file <dfn>application/config/foreign_chars.php</dfn> to define the to and from array for transliteration.</p>
 
 <h2>word_censor()</h2>
 
diff --git a/user_guide/installation/upgrade_154.html b/user_guide/installation/upgrade_154.html
index 5e44686..b1bc8bb 100644
--- a/user_guide/installation/upgrade_154.html
+++ b/user_guide/installation/upgrade_154.html
@@ -67,7 +67,7 @@
 
 <ul>
 
-<li><dfn>system/application/config/mimes.php</dfn></li>
+<li><dfn>application/config/mimes.php</dfn></li>
 <li><dfn>system/codeigniter</dfn></li>
 <li><dfn>system/database</dfn></li>
 <li><dfn>system/helpers</dfn></li>
@@ -78,7 +78,7 @@
 <p class="important"><strong>Note:</strong> If you have any custom developed files in these folders please make copies of them first.</p>
 
 <h2>Step 2: Add charset to your config.php </h2>
-<p>Add the following to system/application/config/config.php</p>
+<p>Add the following to application/config/config.php</p>
 <code>/*<br />
 	|--------------------------------------------------------------------------<br />
 	| Default Character Set<br />
@@ -91,7 +91,7 @@
 	$config['charset'] = &quot;UTF-8&quot;;</code>
 
 <h2>Step 3: Autoloading language files </h2>
-<p>If you want to autoload any language files, add this line to system/application/config/autoload.php</p>
+<p>If you want to autoload any language files, add this line to application/config/autoload.php</p>
 <code>$autoload['language'] = array();</code>
 
 <h2>Step 4: Update your user guide</h2>
diff --git a/user_guide/installation/upgrade_160.html b/user_guide/installation/upgrade_160.html
index e817e24..5568f8c 100644
--- a/user_guide/installation/upgrade_160.html
+++ b/user_guide/installation/upgrade_160.html
@@ -78,10 +78,10 @@
 <p class="important"><strong>Note:</strong> If you have any custom developed files in these folders please make copies of them first.</p>
 
 <h2>Step 2: Add time_to_update to your config.php </h2>
-<p>Add the following to system/application/config/config.php with the other session configuration options</p>
+<p>Add the following to application/config/config.php with the other session configuration options</p>
 <p><code>$config['sess_time_to_update'] 		= 300;</code></p>
 <h2>Step 3: Add $autoload['model']</h2>
-<p>Add the following to system/application/config/autoload.php</p>
+<p>Add the following to application/config/autoload.php</p>
 <p><code> /*<br />
 	| -------------------------------------------------------------------<br />
 	|  Auto-load Model files<br />
@@ -94,7 +94,7 @@
 	<br />
 	$autoload['model'] = array();</code></p>
 <h2>Step 4: Add  to your database.php </h2>
-<p>Make the following changes to your system/application/config/database.php file:</p>
+<p>Make the following changes to your application/config/database.php file:</p>
 <p>Add the following variable above the database configuration options, with <dfn>$active_group</dfn></p>
 <p><code>$active_record = TRUE;</code></p>
 <p>Remove the following from your database configuration options</p>
diff --git a/user_guide/installation/upgrade_162.html b/user_guide/installation/upgrade_162.html
index fd34ab0..c9eb2bf 100644
--- a/user_guide/installation/upgrade_162.html
+++ b/user_guide/installation/upgrade_162.html
@@ -78,12 +78,12 @@
 
 
 <h2>Step 2: Encryption Key</h2>
-<p>If you are using sessions, open up system/application/config/config.php and verify you've set an encryption key.</p>
+<p>If you are using sessions, open up application/config/config.php and verify you've set an encryption key.</p>
 
 <h2>Step 3: Constants File</h2>
-<p>Copy /system/application/config/constants.php to your installation, and modify if necessary.</p>
+<p>Copy /application/config/constants.php to your installation, and modify if necessary.</p>
 <h2>Step 4: Mimes File</h2>
-<p>Replace /system/application/config/mimes.php with the dowloaded version. If you've added custom mime types, you'll need to re-add them.</p>
+<p>Replace /application/config/mimes.php with the dowloaded version. If you've added custom mime types, you'll need to re-add them.</p>
 <h2>Step 5: Update your user guide</h2>
 <p>Please also replace your local copy of the user guide with the new version.</p>
 
diff --git a/user_guide/libraries/javascript.html b/user_guide/libraries/javascript.html
index 08982fd..ac0af84 100644
--- a/user_guide/libraries/javascript.html
+++ b/user_guide/libraries/javascript.html
@@ -79,7 +79,7 @@
 </code></p>
 <p>$library_src, is where the actual library file will be loaded, as well as any subsequent plugin script calls; $script_head is where specific events, functions and other commands will be rendered.</p>
 <h3>Set the path to the librarys with config items</h3>
-<p>There are some configuration items in javascript library. These can either be set in system/application/config.php, within its own confg/javascript.php file, or within any controller usings the set_item() function. </p>
+<p>There are some configuration items in javascript library. These can either be set in application/config.php, within its own confg/javascript.php file, or within any controller usings the set_item() function. </p>
 <p>An image to be used as an &quot;ajax loader&quot;, or progress indicator. Without one, the simple text message of &quot;loading&quot; will appear when Ajax calls need to be made.</p>
 <p><code>$config['javascript_location'] = 'http://localhost/codeigniter/themes/js/jquery/');<br />
 		$config['javascript_ajax_img'] = 'images/ajax-loader.gif';</code></p>
diff --git a/user_guide/libraries/jquery.html b/user_guide/libraries/jquery.html
index 98c9a9c..69b8389 100644
--- a/user_guide/libraries/jquery.html
+++ b/user_guide/libraries/jquery.html
@@ -81,7 +81,7 @@
 <p><code>&lt;?php echo $jquery_script;?&gt;<br />
 &lt;?php echo $script_head;?&gt;</code></p>
 
-<p>There are 2 configuration items in jQuery library. These can either be set in system/application/config.php, or within any controller. The first is the path from the root of your site to the jquery library ('js' is the default) and the second is an image to be used as an &quot;ajax loader&quot;, or progress indicator. Without one, the simple text message of &quot;loading&quot; will appear when Ajax calls need to be made.</p>
+<p>There are 2 configuration items in jQuery library. These can either be set in application/config.php, or within any controller. The first is the path from the root of your site to the jquery library ('js' is the default) and the second is an image to be used as an &quot;ajax loader&quot;, or progress indicator. Without one, the simple text message of &quot;loading&quot; will appear when Ajax calls need to be made.</p>
 
 <p><code>$config['javascript_folder'] = 'js';<br />
 	$config['javascript_ajax_img'] = 'images/ajax-loader.gif';</code></p>
diff --git a/user_guide/libraries/language.html b/user_guide/libraries/language.html
index 9e50901..ee78c76 100644
--- a/user_guide/libraries/language.html
+++ b/user_guide/libraries/language.html
@@ -64,7 +64,7 @@
 your own language files as needed in order to display error and other messages in other languages.</p>
 
 <p>Language files are typically stored in your <dfn>system/language</dfn> directory.  Alternately you can create a folder called <kbd>language</kbd> inside
-your <kbd>application</kbd> folder and store them there.  CodeIgniter will look first in your <dfn>system/application/language</dfn>
+your <kbd>application</kbd> folder and store them there.  CodeIgniter will look first in your <dfn>application/language</dfn>
 directory.  If the directory does not exist or the specified language is not located there CI will instead look in your global
 <dfn>system/language</dfn> folder.</p>
 
diff --git a/user_guide/libraries/loader.html b/user_guide/libraries/loader.html
index ce693e0..98520e7 100644
--- a/user_guide/libraries/loader.html
+++ b/user_guide/libraries/loader.html
@@ -187,14 +187,14 @@
 
 <h2>Application "Packages"</h2>
 
-<p>An application package allows for the easy distribution of complete sets of resources in a single directory, complete with its own libraries, models, helpers, config, and language files.  It is recommended that these packages be placed in the <dfn>system/application/third_party</dfn> folder.  Below is a sample map of an package directory</p>
+<p>An application package allows for the easy distribution of complete sets of resources in a single directory, complete with its own libraries, models, helpers, config, and language files.  It is recommended that these packages be placed in the <dfn>application/third_party</dfn> folder.  Below is a sample map of an package directory</p>
 
 
 <h2>Sample Package "Foo Bar" Directory Map</h2>
 
 <p>The following is an example of a directory for an application package named "Foo Bar".</p>
 
-<code>/system/application/third_party/foo_bar<br />
+<code>/application/third_party/foo_bar<br />
 <br />
 config/<br />
 helpers/<br />