Merge branch 'develop' into feature/unit-tests

Conflicts:
	.hgignore

16 files changed, 669 insertions, 184 deletions

diff --git a/system/core/Benchmark.php b/system/core/Benchmark.php
index 3686c2d73..a200727ab 100644..100755
--- a/system/core/Benchmark.php
+++ b/system/core/Benchmark.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -19,7 +19,7 @@
  * CodeIgniter Benchmark Class
  *
  * This class enables you to mark points and calculate the time difference
- * between them. Memory consumption can also be displayed.
+ * between them.  Memory consumption can also be displayed.
  *
  * @package		CodeIgniter
  * @subpackage	Libraries
@@ -29,6 +29,11 @@
  */
 class CI_Benchmark {
 
+	/**
+	 * List of all benchmark markers and when they were added
+	 *
+	 * @var array
+	 */
 	var $marker = array();
 
 	// --------------------------------------------------------------------
diff --git a/system/core/CodeIgniter.php b/system/core/CodeIgniter.php
index b6f5e872c..0a1391d18 100644..100755
--- a/system/core/CodeIgniter.php
+++ b/system/core/CodeIgniter.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -27,30 +27,44 @@
  * @link		http://codeigniter.com/user_guide/
  */
 
-/*
- * ------------------------------------------------------
- * Define the CodeIgniter Version
- * ------------------------------------------------------
+/**
+ * CodeIgniter Version
+ *
+ * @var string
+ *
  */
+	/**
+	 * CodeIgniter Version
+	 *
+	 * @var string
+	 *
+	 */
 	define('CI_VERSION', '2.0.2');
 
-/*
- * ------------------------------------------------------
- * Define the CodeIgniter Branch (Core = TRUE, Reactor = FALSE)
- * ------------------------------------------------------
+/**
+ * CodeIgniter Branch (Core = TRUE, Reactor = FALSE)
+ *
+ * @var boolean
+ *
  */
+	/**
+	 * CodeIgniter Branch (Core = TRUE, Reactor = FALSE)
+	 *
+	 * @var string
+	 *
+	 */
 	define('CI_CORE', FALSE);
 
 /*
  * ------------------------------------------------------
- * Load the global functions
+ *  Load the global functions
  * ------------------------------------------------------
  */
 	require(BASEPATH.'core/Common.php');
 
 /*
  * ------------------------------------------------------
- * Load the framework constants
+ *  Load the framework constants
  * ------------------------------------------------------
  */
 	if (defined('ENVIRONMENT') AND file_exists(APPPATH.'config/'.ENVIRONMENT.'/constants.php'))
@@ -64,7 +78,7 @@
 
 /*
  * ------------------------------------------------------
- * Define a custom error handler so we can log PHP errors
+ *  Define a custom error handler so we can log PHP errors
  * ------------------------------------------------------
  */
 	set_error_handler('_exception_handler');
@@ -76,7 +90,7 @@
 
 /*
  * ------------------------------------------------------
- * Set the subclass_prefix
+ *  Set the subclass_prefix
  * ------------------------------------------------------
  *
  * Normally the "subclass_prefix" is set in the config file.
@@ -85,7 +99,7 @@
  * "libraries" folder. Since CI allows config items to be
  * overriden via data set in the main index. php file,
  * before proceeding we need to know if a subclass_prefix
- * override exists. If so, we will set this value now,
+ * override exists.  If so, we will set this value now,
  * before any classes are loaded
  * Note: Since the config file data is cached it doesn't
  * hurt to load it here.
@@ -97,7 +111,7 @@
 
 /*
  * ------------------------------------------------------
- * Set a liberal script execution time limit
+ *  Set a liberal script execution time limit
  * ------------------------------------------------------
  */
 	if (function_exists("set_time_limit") == TRUE AND @ini_get("safe_mode") == 0)
@@ -107,7 +121,7 @@
 
 /*
  * ------------------------------------------------------
- * Start the timer... tick tock tick tock...
+ *  Start the timer... tick tock tick tock...
  * ------------------------------------------------------
  */
 	$BM =& load_class('Benchmark', 'core');
@@ -116,21 +130,21 @@
 
 /*
  * ------------------------------------------------------
- * Instantiate the hooks class
+ *  Instantiate the hooks class
  * ------------------------------------------------------
  */
 	$EXT =& load_class('Hooks', 'core');
 
 /*
  * ------------------------------------------------------
- * Is there a "pre_system" hook?
+ *  Is there a "pre_system" hook?
  * ------------------------------------------------------
  */
 	$EXT->_call_hook('pre_system');
 
 /*
  * ------------------------------------------------------
- * Instantiate the config class
+ *  Instantiate the config class
  * ------------------------------------------------------
  */
 	$CFG =& load_class('Config', 'core');
@@ -143,7 +157,7 @@
 
 /*
  * ------------------------------------------------------
- * Instantiate the UTF-8 class
+ *  Instantiate the UTF-8 class
  * ------------------------------------------------------
  *
  * Note: Order here is rather important as the UTF-8
@@ -157,14 +171,14 @@
 
 /*
  * ------------------------------------------------------
- * Instantiate the URI class
+ *  Instantiate the URI class
  * ------------------------------------------------------
  */
 	$URI =& load_class('URI', 'core');
 
 /*
  * ------------------------------------------------------
- * Instantiate the routing class and set the routing
+ *  Instantiate the routing class and set the routing
  * ------------------------------------------------------
  */
 	$RTR =& load_class('Router', 'core');
@@ -178,14 +192,14 @@
 
 /*
  * ------------------------------------------------------
- * Instantiate the output class
+ *  Instantiate the output class
  * ------------------------------------------------------
  */
 	$OUT =& load_class('Output', 'core');
 
 /*
  * ------------------------------------------------------
- *	Is there a valid cache file? If so, we're done...
+ *	Is there a valid cache file?  If so, we're done...
  * ------------------------------------------------------
  */
 	if ($EXT->_call_hook('cache_override') === FALSE)
@@ -205,21 +219,21 @@
 
 /*
  * ------------------------------------------------------
- * Load the Input class and sanitize globals
+ *  Load the Input class and sanitize globals
  * ------------------------------------------------------
  */
 	$IN	=& load_class('Input', 'core');
 
 /*
  * ------------------------------------------------------
- * Load the Language class
+ *  Load the Language class
  * ------------------------------------------------------
  */
 	$LANG =& load_class('Lang', 'core');
 
 /*
  * ------------------------------------------------------
- * Load the app controller and local controller
+ *  Load the app controller and local controller
  * ------------------------------------------------------
  *
  */
@@ -252,14 +266,14 @@
 
 /*
  * ------------------------------------------------------
- * Security check
+ *  Security check
  * ------------------------------------------------------
  *
- * None of the functions in the app controller or the
- * loader class can be called via the URI, nor can
- * controller functions that begin with an underscore
+ *  None of the functions in the app controller or the
+ *  loader class can be called via the URI, nor can
+ *  controller functions that begin with an underscore
  */
-	$class = $RTR->fetch_class();
+	$class  = $RTR->fetch_class();
 	$method = $RTR->fetch_method();
 
 	if ( ! class_exists($class)
@@ -267,19 +281,37 @@
 		OR in_array(strtolower($method), array_map('strtolower', get_class_methods('CI_Controller')))
 		)
 	{
-		show_404("{$class}/{$method}");
+		if ( ! empty($RTR->routes['404_override']))
+		{
+			$x = explode('/', $RTR->routes['404_override']);
+			$class = $x[0];
+			$method = (isset($x[1]) ? $x[1] : 'index');
+			if ( ! class_exists($class))
+			{
+				if ( ! file_exists(APPPATH.'controllers/'.$class.'.php'))
+				{
+					show_404("{$class}/{$method}");
+				}
+
+				include_once(APPPATH.'controllers/'.$class.'.php');
+			}
+		}
+		else
+		{
+			show_404("{$class}/{$method}");
+		}
 	}
 
 /*
  * ------------------------------------------------------
- * Is there a "pre_controller" hook?
+ *  Is there a "pre_controller" hook?
  * ------------------------------------------------------
  */
 	$EXT->_call_hook('pre_controller');
 
 /*
  * ------------------------------------------------------
- * Instantiate the requested controller
+ *  Instantiate the requested controller
  * ------------------------------------------------------
  */
 	// Mark a start point so we can benchmark the controller
@@ -289,14 +321,14 @@
 
 /*
  * ------------------------------------------------------
- * Is there a "post_controller_constructor" hook?
+ *  Is there a "post_controller_constructor" hook?
  * ------------------------------------------------------
  */
 	$EXT->_call_hook('post_controller_constructor');
 
 /*
  * ------------------------------------------------------
- * Call the requested method
+ *  Call the requested method
  * ------------------------------------------------------
  */
 	// Is there a "remap" function? If so, we call it instead
@@ -345,14 +377,14 @@
 
 /*
  * ------------------------------------------------------
- * Is there a "post_controller" hook?
+ *  Is there a "post_controller" hook?
  * ------------------------------------------------------
  */
 	$EXT->_call_hook('post_controller');
 
 /*
  * ------------------------------------------------------
- * Send the final rendered output to the browser
+ *  Send the final rendered output to the browser
  * ------------------------------------------------------
  */
 	if ($EXT->_call_hook('display_override') === FALSE)
@@ -362,14 +394,14 @@
 
 /*
  * ------------------------------------------------------
- * Is there a "post_system" hook?
+ *  Is there a "post_system" hook?
  * ------------------------------------------------------
  */
 	$EXT->_call_hook('post_system');
 
 /*
  * ------------------------------------------------------
- * Close the DB connection if one exists
+ *  Close the DB connection if one exists
  * ------------------------------------------------------
  */
 	if (class_exists('CI_DB') AND isset($CI->db))
diff --git a/system/core/Common.php b/system/core/Common.php
index eb9e14425..db9fbeb9f 100644
--- a/system/core/Common.php
+++ b/system/core/Common.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -39,6 +39,8 @@
 * @param	string
 * @return	bool	TRUE if the current version is $version or higher
 */
+if ( ! function_exists('is_php'))
+{
 	function is_php($version = '5.0.0')
 	{
 		static $_is_php;
@@ -51,6 +53,7 @@
 
 		return $_is_php[$version];
 	}
+}
 
 // ------------------------------------------------------------------------
 
@@ -58,12 +61,14 @@
  * Tests for file writability
  *
  * is_writable() returns TRUE on Windows servers when you really can't write to
- * the file, based on the read-only attribute. is_writable() is also unreliable
+ * the file, based on the read-only attribute.  is_writable() is also unreliable
  * on Unix servers if safe_mode is on.
  *
  * @access	private
  * @return	void
  */
+if ( ! function_exists('is_really_writable'))
+{
 	function is_really_writable($file)
 	{
 		// If we're on a Unix server with safe_mode off we call is_writable
@@ -73,7 +78,7 @@
 		}
 
 		// For windows servers and safe_mode "on" installations we'll actually
-		// write a file then read it. Bah...
+		// write a file then read it.  Bah...
 		if (is_dir($file))
 		{
 			$file = rtrim($file, '/').'/'.md5(mt_rand(1,100).mt_rand(1,100));
@@ -96,14 +101,15 @@
 		fclose($fp);
 		return TRUE;
 	}
+}
 
 // ------------------------------------------------------------------------
 
 /**
 * Class registry
 *
-* This function acts as a singleton. If the requested class does not
-* exist it is instantiated and set to a static variable. If it has
+* This function acts as a singleton.  If the requested class does not
+* exist it is instantiated and set to a static variable.  If it has
 * previously been instantiated the variable is returned.
 *
 * @access	public
@@ -112,11 +118,13 @@
 * @param	string	the class name prefix
 * @return	object
 */
+if ( ! function_exists('load_class'))
+{
 	function &load_class($class, $directory = 'libraries', $prefix = 'CI_')
 	{
 		static $_classes = array();
 
-		// Does the class exist? If so, we're done...
+		// Does the class exist?  If so, we're done...
 		if (isset($_classes[$class]))
 		{
 			return $_classes[$class];
@@ -141,7 +149,7 @@
 			}
 		}
 
-		// Is the request a class extension? If so we load it too
+		// Is the request a class extension?  If so we load it too
 		if (file_exists(APPPATH.$directory.'/'.config_item('subclass_prefix').$class.'.php'))
 		{
 			$name = config_item('subclass_prefix').$class;
@@ -166,16 +174,19 @@
 		$_classes[$class] = new $name();
 		return $_classes[$class];
 	}
+}
 
 // --------------------------------------------------------------------
 
 /**
-* Keeps track of which libraries have been loaded. This function is
+* Keeps track of which libraries have been loaded.  This function is
 * called by the load_class() function above
 *
 * @access	public
 * @return	array
 */
+if ( ! function_exists('is_loaded'))
+{
 	function is_loaded($class = '')
 	{
 		static $_is_loaded = array();
@@ -187,6 +198,7 @@
 
 		return $_is_loaded;
 	}
+}
 
 // ------------------------------------------------------------------------
 
@@ -199,6 +211,8 @@
 * @access	private
 * @return	array
 */
+if ( ! function_exists('get_config'))
+{
 	function &get_config($replace = array())
 	{
 		static $_config;
@@ -242,6 +256,7 @@
 
 		return $_config[0] =& $config;
 	}
+}
 
 // ------------------------------------------------------------------------
 
@@ -251,6 +266,8 @@
 * @access	public
 * @return	mixed
 */
+if ( ! function_exists('config_item'))
+{
 	function config_item($item)
 	{
 		static $_config_item = array();
@@ -268,6 +285,7 @@
 
 		return $_config_item[$item];
 	}
+}
 
 // ------------------------------------------------------------------------
 
@@ -283,12 +301,15 @@
 * @access	public
 * @return	void
 */
+if ( ! function_exists('show_error'))
+{
 	function show_error($message, $status_code = 500, $heading = 'An Error Was Encountered')
 	{
 		$_error =& load_class('Exceptions', 'core');
 		echo $_error->show_error($heading, $message, 'error_general', $status_code);
 		exit;
 	}
+}
 
 // ------------------------------------------------------------------------
 
@@ -302,12 +323,15 @@
 * @access	public
 * @return	void
 */
+if ( ! function_exists('show_404'))
+{
 	function show_404($page = '', $log_error = TRUE)
 	{
 		$_error =& load_class('Exceptions', 'core');
 		$_error->show_404($page, $log_error);
 		exit;
 	}
+}
 
 // ------------------------------------------------------------------------
 
@@ -320,6 +344,8 @@
 * @access	public
 * @return	void
 */
+if ( ! function_exists('log_message'))
+{
 	function log_message($level = 'error', $message, $php_error = FALSE)
 	{
 		static $_log;
@@ -332,6 +358,7 @@
 		$_log =& load_class('Log');
 		$_log->write_log($level, $message, $php_error);
 	}
+}
 
 // ------------------------------------------------------------------------
 
@@ -343,6 +370,8 @@
  * @param	string
  * @return	void
  */
+if ( ! function_exists('set_status_header'))
+{
 	function set_status_header($code = 200, $text = '')
 	{
 		$stati = array(
@@ -399,7 +428,7 @@
 
 		if ($text == '')
 		{
-			show_error('No status text available. Please check your status code number or supply your own message text.', 500);
+			show_error('No status text available.  Please check your status code number or supply your own message text.', 500);
 		}
 
 		$server_protocol = (isset($_SERVER['SERVER_PROTOCOL'])) ? $_SERVER['SERVER_PROTOCOL'] : FALSE;
@@ -417,6 +446,7 @@
 			header("HTTP/1.1 {$code} {$text}", TRUE, $code);
 		}
 	}
+}
 
 // --------------------------------------------------------------------
 
@@ -424,7 +454,7 @@
 * Exception Handler
 *
 * This is the custom exception handler that is declaired at the top
-* of Codeigniter.php. The main reason we use this is to permit
+* of Codeigniter.php.  The main reason we use this is to permit
 * PHP errors to be logged in our own log files since the user may
 * not have access to server logs. Since this function
 * effectively intercepts PHP errors, however, we also need
@@ -434,6 +464,8 @@
 * @access	private
 * @return	void
 */
+if ( ! function_exists('_exception_handler'))
+{
 	function _exception_handler($severity, $message, $filepath, $line)
 	{
 		 // We don't bother with "strict" notices since they tend to fill up
@@ -455,7 +487,7 @@
 			$_error->show_php_error($severity, $message, $filepath, $line);
 		}
 
-		// Should we log the error? No? We're done...
+		// Should we log the error?  No?  We're done...
 		if (config_item('log_threshold') == 0)
 		{
 			return;
@@ -463,32 +495,35 @@
 
 		$_error->log_exception($severity, $message, $filepath, $line);
 	}
+}
 
-	// --------------------------------------------------------------------
-
-	/**
-	 * Remove Invisible Characters
-	 *
-	 * This prevents sandwiching null characters
-	 * between ascii characters, like Java\0script.
-	 *
-	 * @access	public
-	 * @param	string
-	 * @return	string
-	 */
+// --------------------------------------------------------------------
+
+/**
+ * Remove Invisible Characters
+ *
+ * This prevents sandwiching null characters
+ * between ascii characters, like Java\0script.
+ *
+ * @access	public
+ * @param	string
+ * @return	string
+ */
+if ( ! function_exists('remove_invisible_characters'))
+{
 	function remove_invisible_characters($str, $url_encoded = TRUE)
 	{
 		$non_displayables = array();
-
+		
 		// every control character except newline (dec 10)
 		// carriage return (dec 13), and horizontal tab (dec 09)
-
+		
 		if ($url_encoded)
 		{
 			$non_displayables[] = '/%0[0-8bcef]/';	// url encoded 00-08, 11, 12, 14, 15
 			$non_displayables[] = '/%1[0-9a-f]/';	// url encoded 16-31
 		}
-
+		
 		$non_displayables[] = '/[\x00-\x08\x0B\x0C\x0E-\x1F\x7F]+/S';	// 00-08, 11, 12, 14-31, 127
 
 		do
@@ -499,7 +534,7 @@
 
 		return $str;
 	}
-
+}
 
 /* End of file Common.php */
 /* Location: ./system/core/Common.php */
\ No newline at end of file
diff --git a/system/core/Config.php b/system/core/Config.php
index 55c623b3c..9c5e22fb2 100644..100755
--- a/system/core/Config.php
+++ b/system/core/Config.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -28,8 +28,23 @@
  */
 class CI_Config {
 
+	/**
+	 * List of all loaded config values
+	 *
+	 * @var array
+	 */
 	var $config = array();
+	/**
+	 * List of all loaded config files
+	 *
+	 * @var array
+	 */
 	var $is_loaded = array();
+	/**
+	 * List of paths to search when trying to load a config file
+	 *
+	 * @var array
+	 */
 	var $_config_paths = array(APPPATH);
 
 	/**
@@ -37,11 +52,11 @@ class CI_Config {
 	 *
 	 * Sets the $config data from the primary config.php file as a class variable
 	 *
-	 * @access  public
-	 * @param  string	the config file name
-	 * @param  boolean if configuration values should be loaded into their own section
-	 * @param  boolean true if errors should just return false, false if an error message should be displayed
-	 * @return boolean if the file was successfully loaded or not
+	 * @access   public
+	 * @param   string	the config file name
+	 * @param   boolean  if configuration values should be loaded into their own section
+	 * @param   boolean  true if errors should just return false, false if an error message should be displayed
+	 * @return  boolean  if the file was successfully loaded or not
 	 */
 	function __construct()
 	{
@@ -74,8 +89,8 @@ class CI_Config {
 	 *
 	 * @access	public
 	 * @param	string	the config file name
-	 * @param  boolean if configuration values should be loaded into their own section
-	 * @param  boolean true if errors should just return false, false if an error message should be displayed
+	 * @param   boolean  if configuration values should be loaded into their own section
+	 * @param   boolean  true if errors should just return false, false if an error message should be displayed
 	 * @return	boolean	if the file was loaded correctly
 	 */
 	function load($file = '', $use_sections = FALSE, $fail_gracefully = FALSE)
@@ -203,10 +218,7 @@ class CI_Config {
 	// --------------------------------------------------------------------
 
 	/**
-	 * Fetch a config file item - adds slash after item
-	 *
-	 * The second parameter allows a slash to be added to the end of
-	 * the item, in the case of a path.
+	 * Fetch a config file item - adds slash after item (if item is not empty)
 	 *
 	 * @access	public
 	 * @param	string	the config item name
@@ -219,6 +231,10 @@ class CI_Config {
 		{
 			return FALSE;
 		}
+		if( trim($this->config[$item]) == '')
+		{
+			return '';
+		}
 
 		return rtrim($this->config[$item], '/').'/';
 	}
@@ -227,6 +243,7 @@ class CI_Config {
 
 	/**
 	 * Site URL
+	 * Returns base_url . index_page [. uri_string]
 	 *
 	 * @access	public
 	 * @param	string	the URI string
@@ -241,14 +258,48 @@ class CI_Config {
 
 		if ($this->item('enable_query_strings') == FALSE)
 		{
+			$suffix = ($this->item('url_suffix') == FALSE) ? '' : $this->item('url_suffix');
+			return $this->slash_item('base_url').$this->slash_item('index_page').$this->_uri_string($uri).$suffix;
+		}
+		else
+		{
+			return $this->slash_item('base_url').$this->item('index_page').'?'.$this->_uri_string($uri);
+		}
+	}
+
+	// -------------------------------------------------------------
+
+	/**
+	 * Base URL
+	 * Returns base_url [. uri_string]
+	 *
+	 * @access public
+	 * @param string $uri
+	 * @return string
+	 */
+	function base_url($uri = '')
+	{
+		return $this->slash_item('base_url').ltrim($this->_uri_string($uri),'/');
+	}
+
+	// -------------------------------------------------------------
+
+	/**
+	 * Build URI string for use in Config::site_url() and Config::base_url()
+	 *
+	 * @access protected
+	 * @param  $uri
+	 * @return string
+	 */
+	protected function _uri_string($uri)
+	{
+		if ($this->item('enable_query_strings') == FALSE)
+		{
 			if (is_array($uri))
 			{
 				$uri = implode('/', $uri);
 			}
-
-			$index = $this->item('index_page') == '' ? '' : $this->slash_item('index_page');
-			$suffix = ($this->item('url_suffix') == FALSE) ? '' : $this->item('url_suffix');
-			return $this->slash_item('base_url').$index.trim($uri, '/').$suffix;
+			$uri = trim($uri, '/');
 		}
 		else
 		{
@@ -262,12 +313,10 @@ class CI_Config {
 					$str .= $prefix.$key.'='.$val;
 					$i++;
 				}
-
 				$uri = $str;
 			}
-
-			return $this->slash_item('base_url').$this->item('index_page').'?'.$uri;
 		}
+	    return $uri;
 	}
 
 	// --------------------------------------------------------------------
@@ -305,7 +354,7 @@ class CI_Config {
 	 * Assign to Config
 	 *
 	 * This function is called by the front controller (CodeIgniter.php)
-	 * after the Config class is instantiated. It permits config items
+	 * after the Config class is instantiated.  It permits config items
 	 * to be assigned or overriden by variables contained in the index.php file
 	 *
 	 * @access	private
diff --git a/system/core/Controller.php b/system/core/Controller.php
index 107d3f346..fddb81e19 100644
--- a/system/core/Controller.php
+++ b/system/core/Controller.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -37,7 +37,7 @@ class CI_Controller {
 	public function __construct()
 	{
 		self::$instance =& $this;
-
+		
 		// Assign all the class objects that were instantiated by the
 		// bootstrap file (CodeIgniter.php) to local class variables
 		// so that CI can run as one big super object.
@@ -48,8 +48,8 @@ class CI_Controller {
 
 		$this->load =& load_class('Loader', 'core');
 
-		$this->load->set_base_classes()->ci_autoloader();
-
+		$this->load->initialize();
+		
 		log_message('debug', "Controller Class Initialized");
 	}
 
diff --git a/system/core/Exceptions.php b/system/core/Exceptions.php
index 2503c907f..869739a5a 100644..100755
--- a/system/core/Exceptions.php
+++ b/system/core/Exceptions.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -30,8 +30,21 @@ class CI_Exceptions {
 	var $message;
 	var $filename;
 	var $line;
+
+	/**
+	 * Nesting level of the output buffering mechanism
+	 *
+	 * @var int
+	 * @access public
+	 */
 	var $ob_level;
 
+	/**
+	 * List if available error levels
+	 *
+	 * @var array
+	 * @access public
+	 */
 	var $levels = array(
 						E_ERROR				=>	'Error',
 						E_WARNING			=>	'Warning',
@@ -54,7 +67,7 @@ class CI_Exceptions {
 	public function __construct()
 	{
 		$this->ob_level = ob_get_level();
-		// Note: Do not log messages from this constructor.
+		// Note:  Do not log messages from this constructor.
 	}
 
 	// --------------------------------------------------------------------
@@ -75,7 +88,7 @@ class CI_Exceptions {
 	{
 		$severity = ( ! isset($this->levels[$severity])) ? $severity : $this->levels[$severity];
 
-		log_message('error', 'Severity: '.$severity.' --> '.$message. ' '.$filepath.' '.$line, TRUE);
+		log_message('error', 'Severity: '.$severity.'  --> '.$message. ' '.$filepath.' '.$line, TRUE);
 	}
 
 	// --------------------------------------------------------------------
@@ -84,7 +97,8 @@ class CI_Exceptions {
 	 * 404 Page Not Found Handler
 	 *
 	 * @access	private
-	 * @param	string
+	 * @param	string	the page
+	 * @param 	bool	log error yes/no
 	 * @return	string
 	 */
 	function show_404($page = '', $log_error = TRUE)
@@ -115,6 +129,7 @@ class CI_Exceptions {
 	 * @param	string	the heading
 	 * @param	string	the message
 	 * @param	string	the template name
+	 * @param 	int		the status code
 	 * @return	string
 	 */
 	function show_error($heading, $message, $template = 'error_general', $status_code = 500)
diff --git a/system/core/Hooks.php b/system/core/Hooks.php
index ffb3258d8..33f1c034c 100644..100755
--- a/system/core/Hooks.php
+++ b/system/core/Hooks.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -28,8 +28,23 @@
  */
 class CI_Hooks {
 
+	/**
+	 * Determines wether hooks are enabled
+	 *
+	 * @var bool
+	 */
 	var $enabled		= FALSE;
+	/**
+	 * List of all hooks set in config/hooks.php
+	 *
+	 * @var array
+	 */
 	var $hooks			= array();
+	/**
+	 * Determines wether hook is in progress, used to prevent infinte loops
+	 *
+	 * @var bool
+	 */
 	var $in_progress	= FALSE;
 
 	/**
@@ -67,7 +82,7 @@ class CI_Hooks {
 
 		if (defined('ENVIRONMENT') AND is_file(APPPATH.'config/'.ENVIRONMENT.'/hooks.php'))
 		{
-		  include(APPPATH.'config/'.ENVIRONMENT.'/hooks.php');
+		    include(APPPATH.'config/'.ENVIRONMENT.'/hooks.php');
 		}
 		elseif (is_file(APPPATH.'config/hooks.php'))
 		{
diff --git a/system/core/Input.php b/system/core/Input.php
index 89eda56b0..5a033e7b8 100644..100755
--- a/system/core/Input.php
+++ b/system/core/Input.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -28,13 +28,49 @@
  */
 class CI_Input {
 
+	/**
+	 * IP address of the current user
+	 *
+	 * @var string
+	 */
 	var $ip_address				= FALSE;
+	/**
+	 * user agent (web browser) being used by the current user
+	 *
+	 * @var string
+	 */
 	var $user_agent				= FALSE;
+	/**
+	 * If FALSE, then $_GET will be set to an empty array
+	 *
+	 * @var bool
+	 */
 	var $_allow_get_array		= TRUE;
+	/**
+	 * If TRUE, then newlines are standardized
+	 *
+	 * @var bool
+	 */
 	var $_standardize_newlines	= TRUE;
-	var $_enable_xss			= FALSE; // Set automatically based on config setting
-	var $_enable_csrf			= FALSE; // Set automatically based on config setting
-
+	/**
+	 * Determines whether the XSS filter is always active when GET, POST or COOKIE data is encountered
+	 * Set automatically based on config setting
+	 *
+	 * @var bool
+	 */
+	var $_enable_xss			= FALSE;
+	/**
+	 * Enables a CSRF cookie token to be set.
+	 * Set automatically based on config setting
+	 *
+	 * @var bool
+	 */
+	var $_enable_csrf			= FALSE;
+	/**
+	 * List of all HTTP request headers
+	 *
+	 * @var array
+	 */
 	protected $headers			= array();
 
 
@@ -201,7 +237,7 @@ class CI_Input {
 	* @param	mixed
 	* @param	string	the value of the cookie
 	* @param	string	the number of seconds until expiration
-	* @param	string	the cookie domain. Usually: .yourdomain.com
+	* @param	string	the cookie domain.  Usually:  .yourdomain.com
 	* @param	string	the cookie path
 	* @param	string	the cookie prefix
 	* @param	bool	true makes the cookie secure
@@ -582,6 +618,8 @@ class CI_Input {
 	 * In Apache, you can simply call apache_request_headers(), however for
 	 * people running other webservers the function is undefined.
 	 *
+	 * @param	bool XSS cleaning
+	 *
 	 * @return array
 	 */
 	public function request_headers($xss_clean = FALSE)
@@ -672,7 +710,7 @@ class CI_Input {
 	 */
 	public function is_cli_request()
 	{
-		return (bool) defined('STDIN');
+		return (php_sapi_name() == 'cli') or defined('STDIN');
 	}
 
 }
diff --git a/system/core/Lang.php b/system/core/Lang.php
index 79eb443a0..5ac671838 100644..100755
--- a/system/core/Lang.php
+++ b/system/core/Lang.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -26,7 +26,17 @@
  */
 class CI_Lang {
 
+	/**
+	 * List of translations
+	 *
+	 * @var array
+	 */
 	var $language	= array();
+	/**
+	 * List of loaded language files
+	 *
+	 * @var array
+	 */
 	var $is_loaded	= array();
 
 	/**
@@ -47,6 +57,9 @@ class CI_Lang {
 	 * @access	public
 	 * @param	mixed	the name of the language file to be loaded. Can be an array
 	 * @param	string	the language (english, etc.)
+	 * @param	bool	return loaded array of translations
+	 * @param 	bool	add suffix to $langfile
+	 * @param 	string	alternative path to look for language file
 	 * @return	mixed
 	 */
 	function load($langfile = '', $idiom = '', $return = FALSE, $add_suffix = TRUE, $alt_path = '')
diff --git a/system/core/Loader.php b/system/core/Loader.php
index 87f05d86e..e7fa3d3f6 100644..100755
--- a/system/core/Loader.php
+++ b/system/core/Loader.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -29,17 +29,90 @@
 class CI_Loader {
 
 	// All these are set automatically. Don't mess with them.
+	/**
+	 * Nesting level of the output buffering mechanism
+	 *
+	 * @var int
+	 * @access protected
+	 */
 	protected $_ci_ob_level;
+	/**
+	 * List of paths to load views from
+	 *
+	 * @var array
+	 * @access protected
+	 */
 	protected $_ci_view_paths		= array();
+	/**
+	 * List of paths to load libraries from
+	 *
+	 * @var array
+	 * @access protected
+	 */
 	protected $_ci_library_paths	= array();
+	/**
+	 * List of paths to load models from
+	 *
+	 * @var array
+	 * @access protected
+	 */
 	protected $_ci_model_paths		= array();
+	/**
+	 * List of paths to load helpers from
+	 *
+	 * @var array
+	 * @access protected
+	 */
 	protected $_ci_helper_paths		= array();
+	/**
+	 * List of loaded base classes
+	 * Set by the controller class
+	 *
+	 * @var array
+	 * @access protected
+	 */
 	protected $_base_classes		= array(); // Set by the controller class
+	/**
+	 * List of cached variables
+	 *
+	 * @var array
+	 * @access protected
+	 */
 	protected $_ci_cached_vars		= array();
+	/**
+	 * List of loaded classes
+	 *
+	 * @var array
+	 * @access protected
+	 */
 	protected $_ci_classes			= array();
+	/**
+	 * List of loaded files
+	 *
+	 * @var array
+	 * @access protected
+	 */
 	protected $_ci_loaded_files		= array();
+	/**
+	 * List of loaded models
+	 *
+	 * @var array
+	 * @access protected
+	 */
 	protected $_ci_models			= array();
+	/**
+	 * List of loaded helpers
+	 *
+	 * @var array
+	 * @access protected
+	 */
 	protected $_ci_helpers			= array();
+	/**
+	 * List of class name mappings
+	 *
+	 * @var array
+	 * @access protected
+	 */
 	protected $_ci_varmap			= array('unit_test' => 'unit',
 											'user_agent' => 'agent');
 
@@ -50,7 +123,7 @@ class CI_Loader {
 	 */
 	public function __construct()
 	{
-		$this->_ci_ob_level = ob_get_level();
+		$this->_ci_ob_level  = ob_get_level();
 		$this->_ci_library_paths = array(APPPATH, BASEPATH);
 		$this->_ci_helper_paths = array(APPPATH, BASEPATH);
 		$this->_ci_model_paths = array(APPPATH);
@@ -62,17 +135,22 @@ class CI_Loader {
 	// --------------------------------------------------------------------
 
 	/**
-	 * Set _base_classes variable
+	 * Initialize the Loader
 	 *
 	 * This method is called once in CI_Controller.
 	 *
 	 * @param 	array
 	 * @return 	object
 	 */
-	public function set_base_classes()
+	public function initialize()
 	{
+		$this->_ci_classes = array();
+		$this->_ci_loaded_files = array();
+		$this->_ci_models = array();
 		$this->_base_classes =& is_loaded();
 
+		$this->_ci_autoloader();
+
 		return $this;
 	}
 
@@ -260,7 +338,7 @@ class CI_Loader {
 			return DB($params, $active_record);
 		}
 
-		// Initialize the db variable. Needed to prevent
+		// Initialize the db variable.  Needed to prevent
 		// reference errors with some configurations
 		$CI->db = '';
 
@@ -323,11 +401,11 @@ class CI_Loader {
 	/**
 	 * Load View
 	 *
-	 * This function is used to load a "view" file. It has three parameters:
+	 * This function is used to load a "view" file.  It has three parameters:
 	 *
 	 * 1. The name of the "view" file to be included.
 	 * 2. An associative array of data to be extracted for use in the view.
-	 * 3. TRUE/FALSE - whether to return the data or load it. In
+	 * 3. TRUE/FALSE - whether to return the data or load it.  In
 	 * some cases it's advantageous to be able to return data so that
 	 * a developer can process it in some way.
 	 *
@@ -366,6 +444,7 @@ class CI_Loader {
 	 * the controller class and its "view" files.
 	 *
 	 * @param	array
+	 * @param 	string
 	 * @return	void
 	 */
 	public function vars($vars = array(), $val = '')
@@ -389,6 +468,21 @@ class CI_Loader {
 	// --------------------------------------------------------------------
 
 	/**
+	 * Get Variable
+	 *
+	 * Check if a variable is set and retrieve it.
+	 *
+	 * @param	array
+	 * @return	void
+	 */
+	public function get_var($key)
+	{
+		return isset($this->_ci_cached_vars[$key]) ? $this->_ci_cached_vars[$key] : NULL;
+	}
+
+	// --------------------------------------------------------------------
+
+	/**
 	 * Load Helper
 	 *
 	 * This function loads the specified helper file.
@@ -492,6 +586,8 @@ class CI_Loader {
 	 * Loads a config file
 	 *
 	 * @param	string
+	 * @param	bool
+	 * @param 	bool
 	 * @return	void
 	 */
 	public function config($file = '', $use_sections = FALSE, $fail_gracefully = FALSE)
@@ -580,6 +676,7 @@ class CI_Loader {
 	 * If no path is provided, the most recently added path is removed.
 	 *
 	 * @param	type
+	 * @param 	bool
 	 * @return	type
 	 */
 	public function remove_package_path($path = '', $remove_config_path = TRUE)
@@ -710,9 +807,9 @@ class CI_Loader {
 		 * We buffer the output for two reasons:
 		 * 1. Speed. You get a significant speed boost.
 		 * 2. So that the final rendered template can be
-		 * post-processed by the output class. Why do we
-		 * need post processing? For one thing, in order to
-		 * show the elapsed page load time. Unless we
+		 * post-processed by the output class.  Why do we
+		 * need post processing?  For one thing, in order to
+		 * show the elapsed page load time.  Unless we
 		 * can intercept the content right before it's sent to
 		 * the browser and then stop the timer it won't be accurate.
 		 */
@@ -809,11 +906,11 @@ class CI_Loader {
 					show_error("Unable to load the requested class: ".$class);
 				}
 
-				// Safety: Was the class already loaded by a previous call?
+				// Safety:  Was the class already loaded by a previous call?
 				if (in_array($subclass, $this->_ci_loaded_files))
 				{
 					// Before we deem this to be a duplicate request, let's see
-					// if a custom object name is being supplied. If so, we'll
+					// if a custom object name is being supplied.  If so, we'll
 					// return a new instance of the object
 					if ( ! is_null($object_name))
 					{
@@ -842,17 +939,17 @@ class CI_Loader {
 			{
 				$filepath = $path.'libraries/'.$subdir.$class.'.php';
 
-				// Does the file exist? No? Bummer...
+				// Does the file exist?  No?  Bummer...
 				if ( ! file_exists($filepath))
 				{
 					continue;
 				}
 
-				// Safety: Was the class already loaded by a previous call?
+				// Safety:  Was the class already loaded by a previous call?
 				if (in_array($filepath, $this->_ci_loaded_files))
 				{
 					// Before we deem this to be a duplicate request, let's see
-					// if a custom object name is being supplied. If so, we'll
+					// if a custom object name is being supplied.  If so, we'll
 					// return a new instance of the object
 					if ( ! is_null($object_name))
 					{
@@ -875,7 +972,7 @@ class CI_Loader {
 
 		} // END FOREACH
 
-		// One last attempt. Maybe the library is in a subdirectory, but it wasn't specified?
+		// One last attempt.  Maybe the library is in a subdirectory, but it wasn't specified?
 		if ($subdir == '')
 		{
 			$path = strtolower($class).'/'.$class;
@@ -898,12 +995,13 @@ class CI_Loader {
 	 *
 	 * @param	string
 	 * @param	string
+	 * @param	bool
 	 * @param	string	an optional object name
 	 * @return	null
 	 */
 	protected function _ci_init_class($class, $prefix = '', $config = FALSE, $object_name = NULL)
 	{
-		// Is there an associated config file for this class? Note: these should always be lowercase
+		// Is there an associated config file for this class?  Note: these should always be lowercase
 		if ($config === NULL)
 		{
 			// Fetch the config paths containing any package paths
@@ -920,22 +1018,22 @@ class CI_Loader {
 					// first, global next
 					if (defined('ENVIRONMENT') AND file_exists($path .'config/'.ENVIRONMENT.'/'.strtolower($class).'.php'))
 					{
-						include_once($path .'config/'.ENVIRONMENT.'/'.strtolower($class).'.php');
+						include($path .'config/'.ENVIRONMENT.'/'.strtolower($class).'.php');
 						break;
 					}
 					elseif (defined('ENVIRONMENT') AND file_exists($path .'config/'.ENVIRONMENT.'/'.ucfirst(strtolower($class)).'.php'))
 					{
-						include_once($path .'config/'.ENVIRONMENT.'/'.ucfirst(strtolower($class)).'.php');
+						include($path .'config/'.ENVIRONMENT.'/'.ucfirst(strtolower($class)).'.php');
 						break;
 					}
 					elseif (file_exists($path .'config/'.strtolower($class).'.php'))
 					{
-						include_once($path .'config/'.strtolower($class).'.php');
+						include($path .'config/'.strtolower($class).'.php');
 						break;
 					}
 					elseif (file_exists($path .'config/'.ucfirst(strtolower($class)).'.php'))
 					{
-						include_once($path .'config/'.ucfirst(strtolower($class)).'.php');
+						include($path .'config/'.ucfirst(strtolower($class)).'.php');
 						break;
 					}
 				}
@@ -970,7 +1068,7 @@ class CI_Loader {
 		}
 
 		// Set the variable name we will assign the class to
-		// Was a custom class name supplied? If so we'll use it
+		// Was a custom class name supplied?  If so we'll use it
 		$class = strtolower($class);
 
 		if (is_null($object_name))
@@ -1005,24 +1103,20 @@ class CI_Loader {
 	 * The config/autoload.php file contains an array that permits sub-systems,
 	 * libraries, and helpers to be loaded automatically.
 	 *
-	 * This function is public, as it's used in the CI_Controller class.
-	 * However, there is no reason you should ever needs to use it.
-	 *
 	 * @param	array
 	 * @return	void
 	 */
-	public function ci_autoloader()
+	private function _ci_autoloader()
 	{
 		if (defined('ENVIRONMENT') AND file_exists(APPPATH.'config/'.ENVIRONMENT.'/autoload.php'))
 		{
-			include_once(APPPATH.'config/'.ENVIRONMENT.'/autoload.php');
+			include(APPPATH.'config/'.ENVIRONMENT.'/autoload.php');
 		}
 		else
 		{
-			include_once(APPPATH.'config/autoload.php');
+			include(APPPATH.'config/autoload.php');
 		}
 
-
 		if ( ! isset($autoload))
 		{
 			return FALSE;
@@ -1107,6 +1201,7 @@ class CI_Loader {
 	/**
 	 * Get a reference to a specific library or model
 	 *
+	 * @param 	string
 	 * @return	bool
 	 */
 	protected function &_ci_get_component($component)
@@ -1123,6 +1218,7 @@ class CI_Loader {
 	 * This function preps the name of various items to make loading them more reliable.
 	 *
 	 * @param	mixed
+	 * @param 	string
 	 * @return	array
 	 */
 	protected function _ci_prep_filename($filename, $extension)
diff --git a/system/core/Model.php b/system/core/Model.php
index 61c71b672..e15ffbebc 100644..100755
--- a/system/core/Model.php
+++ b/system/core/Model.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -42,6 +42,7 @@ class CI_Model {
 	 * Allows models to access CI's loaded classes using the same
 	 * syntax as controllers.
 	 *
+	 * @param	string
 	 * @access private
 	 */
 	function __get($key)
diff --git a/system/core/Output.php b/system/core/Output.php
index 562dbb86b..ccecafd2b 100644..100755
--- a/system/core/Output.php
+++ b/system/core/Output.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -28,15 +28,67 @@
  */
 class CI_Output {
 
+	/**
+	 * Current output string
+	 *
+	 * @var string
+	 * @access 	protected
+	 */
 	protected $final_output;
+	/**
+	 * Cache expiration time
+	 *
+	 * @var int
+	 * @access 	protected
+	 */
 	protected $cache_expiration	= 0;
+	/**
+	 * List of server headers
+	 *
+	 * @var array
+	 * @access 	protected
+	 */
 	protected $headers			= array();
-	protected $mime_types			= array();
+	/**
+	 * List of mime types
+	 *
+	 * @var array
+	 * @access 	protected
+	 */
+	protected $mime_types		= array();
+	/**
+	 * Determines wether profiler is enabled
+	 *
+	 * @var book
+	 * @access 	protected
+	 */
 	protected $enable_profiler	= FALSE;
+	/**
+	 * Determines if output compression is enabled
+	 *
+	 * @var bool
+	 * @access 	protected
+	 */
 	protected $_zlib_oc			= FALSE;
+	/**
+	 * List of profiler sections
+	 *
+	 * @var array
+	 * @access 	protected
+	 */
 	protected $_profiler_sections = array();
-	protected $parse_exec_vars	= TRUE;	// whether or not to parse variables like {elapsed_time} and {memory_usage}
+	/**
+	 * Whether or not to parse variables like {elapsed_time} and {memory_usage}
+	 *
+	 * @var bool
+	 * @access 	protected
+	 */
+	protected $parse_exec_vars	= TRUE;
 
+	/**
+	 * Constructor
+	 *
+	 */
 	function __construct()
 	{
 		$this->_zlib_oc = @ini_get('zlib.output_compression');
@@ -44,7 +96,7 @@ class CI_Output {
 		// Get mime types for later
 		if (defined('ENVIRONMENT') AND file_exists(APPPATH.'config/'.ENVIRONMENT.'/mimes.php'))
 		{
-		  include APPPATH.'config/'.ENVIRONMENT.'/mimes.php';
+		    include APPPATH.'config/'.ENVIRONMENT.'/mimes.php';
 		}
 		else
 		{
@@ -122,11 +174,12 @@ class CI_Output {
 	 *
 	 * Lets you set a server header which will be outputted with the final display.
 	 *
-	 * Note: If a file is cached, headers will not be sent. We need to figure out
+	 * Note:  If a file is cached, headers will not be sent.  We need to figure out
 	 * how to permit header data to be saved with the cache data...
 	 *
 	 * @access	public
 	 * @param	string
+	 * @param 	bool
 	 * @return	void
 	 */
 	function set_header($header, $replace = TRUE)
@@ -261,15 +314,16 @@ class CI_Output {
 	 * $this->final_output
 	 *
 	 * This function sends the finalized output data to the browser along
-	 * with any server headers and profile data. It also stops the
+	 * with any server headers and profile data.  It also stops the
 	 * benchmark timer so the page rendering speed and memory usage can be shown.
 	 *
 	 * @access	public
+	 * @param 	string
 	 * @return	mixed
 	 */
 	function _display($output = '')
 	{
-		// Note: We use globals because we can't use $CI =& get_instance()
+		// Note:  We use globals because we can't use $CI =& get_instance()
 		// since this function is sometimes called by the caching mechanism,
 		// which happens before the CI super object is available.
 		global $BM, $CFG;
@@ -290,7 +344,7 @@ class CI_Output {
 
 		// --------------------------------------------------------------------
 
-		// Do we need to write a cache file? Only if the controller does not have its
+		// Do we need to write a cache file?  Only if the controller does not have its
 		// own _output() method and we are not dealing with a cache file, which we
 		// can determine by the existence of the $CI object above
 		if ($this->cache_expiration > 0 && isset($CI) && ! method_exists($CI, '_output'))
@@ -368,7 +422,7 @@ class CI_Output {
 			// we will remove them and add them back after we insert the profile data
 			if (preg_match("|</body>.*?</html>|is", $output))
 			{
-				$output = preg_replace("|</body>.*?</html>|is", '', $output);
+				$output  = preg_replace("|</body>.*?</html>|is", '', $output);
 				$output .= $CI->profiler->run();
 				$output .= '</body></html>';
 			}
@@ -381,14 +435,14 @@ class CI_Output {
 		// --------------------------------------------------------------------
 
 		// Does the controller contain a function named _output()?
-		// If so send the output there. Otherwise, echo it.
+		// If so send the output there.  Otherwise, echo it.
 		if (method_exists($CI, '_output'))
 		{
 			$CI->_output($output);
 		}
 		else
 		{
-			echo $output; // Send it to the browser!
+			echo $output;  // Send it to the browser!
 		}
 
 		log_message('debug', "Final output sent to browser");
@@ -401,6 +455,7 @@ class CI_Output {
 	 * Write a Cache File
 	 *
 	 * @access	public
+	 * @param 	string
 	 * @return	void
 	 */
 	function _write_cache($output)
@@ -452,13 +507,15 @@ class CI_Output {
 	 * Update/serve a cached file
 	 *
 	 * @access	public
+	 * @param 	object	config class
+	 * @param 	object	uri class
 	 * @return	void
 	 */
 	function _display_cache(&$CFG, &$URI)
 	{
 		$cache_path = ($CFG->item('cache_path') == '') ? APPPATH.'cache/' : $CFG->item('cache_path');
 
-		// Build the file path. The file name is an MD5 hash of the full URI
+		// Build the file path.  The file name is an MD5 hash of the full URI
 		$uri =	$CFG->item('base_url').
 				$CFG->item('index_page').
 				$URI->uri_string;
diff --git a/system/core/Router.php b/system/core/Router.php
index a76a7bd0a..6da667472 100644..100755
--- a/system/core/Router.php
+++ b/system/core/Router.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -28,12 +28,54 @@
  */
 class CI_Router {
 
+	/**
+	 * Config class
+	 *
+	 * @var object
+	 * @access public
+	 */
 	var $config;
+	/**
+	 * List of routes
+	 *
+	 * @var array
+	 * @access public
+	 */
 	var $routes			= array();
+	/**
+	 * List of error routes
+	 *
+	 * @var array
+	 * @access public
+	 */
 	var $error_routes	= array();
+	/**
+	 * Current class name
+	 *
+	 * @var string
+	 * @access public
+	 */
 	var $class			= '';
+	/**
+	 * Current method name
+	 *
+	 * @var string
+	 * @access public
+	 */
 	var $method			= 'index';
+	/**
+	 * Sub-directory that contains the requested controller class
+	 *
+	 * @var string
+	 * @access public
+	 */
 	var $directory		= '';
+	/**
+	 * Default controller (and method if specific)
+	 *
+	 * @var string
+	 * @access public
+	 */
 	var $default_controller;
 
 	/**
@@ -61,7 +103,7 @@ class CI_Router {
 	 */
 	function _set_routing()
 	{
-		// Are query strings enabled in the config file? Normally CI doesn't utilize query strings
+		// Are query strings enabled in the config file?  Normally CI doesn't utilize query strings
 		// since URI segments are more search-engine friendly, but they can optionally be used.
 		// If this feature is enabled, we will gather the directory/class/method a little differently
 		$segments = array();
@@ -103,7 +145,7 @@ class CI_Router {
 		// the URI doesn't correlated to a valid controller.
 		$this->default_controller = ( ! isset($this->routes['default_controller']) OR $this->routes['default_controller'] == '') ? FALSE : strtolower($this->routes['default_controller']);
 
-		// Were there any query string segments? If so, we'll validate them and bail out since we're done.
+		// Were there any query string segments?  If so, we'll validate them and bail out since we're done.
 		if (count($segments) > 0)
 		{
 			return $this->_validate_request($segments);
@@ -212,7 +254,7 @@ class CI_Router {
 	// --------------------------------------------------------------------
 
 	/**
-	 * Validates the supplied segments. Attempts to determine the path to
+	 * Validates the supplied segments.  Attempts to determine the path to
 	 * the controller.
 	 *
 	 * @access	private
@@ -244,7 +286,20 @@ class CI_Router {
 				// Does the requested controller exist in the sub-folder?
 				if ( ! file_exists(APPPATH.'controllers/'.$this->fetch_directory().$segments[0].'.php'))
 				{
-					show_404($this->fetch_directory().$segments[0]);
+					if ( ! empty($this->routes['404_override']))
+					{
+						$x = explode('/', $this->routes['404_override']);
+
+						$this->set_directory('');
+						$this->set_class($x[0]);
+						$this->set_method(isset($x[1]) ? $x[1] : 'index');
+
+						return $x;
+					}
+					else
+					{
+						show_404($this->fetch_directory().$segments[0]);
+					}
 				}
 			}
 			else
@@ -277,7 +332,7 @@ class CI_Router {
 
 
 		// If we've gotten this far it means that the URI does not correlate to a valid
-		// controller class. We will now see if there is an override
+		// controller class.  We will now see if there is an override
 		if ( ! empty($this->routes['404_override']))
 		{
 			$x = explode('/', $this->routes['404_override']);
@@ -296,7 +351,7 @@ class CI_Router {
 	// --------------------------------------------------------------------
 
 	/**
-	 * Parse Routes
+	 *  Parse Routes
 	 *
 	 * This function matches any routes that may exist in
 	 * the config/routes.php file against the URI to
@@ -310,7 +365,7 @@ class CI_Router {
 		// Turn the segment array into a URI string
 		$uri = implode('/', $this->uri->segments);
 
-		// Is there a literal match? If so we're done
+		// Is there a literal match?  If so we're done
 		if (isset($this->routes[$uri]))
 		{
 			return $this->_set_request(explode('/', $this->routes[$uri]));
@@ -370,7 +425,7 @@ class CI_Router {
 	// --------------------------------------------------------------------
 
 	/**
-	 * Set the method name
+	 *  Set the method name
 	 *
 	 * @access	public
 	 * @param	string
@@ -384,7 +439,7 @@ class CI_Router {
 	// --------------------------------------------------------------------
 
 	/**
-	 * Fetch the current method
+	 *  Fetch the current method
 	 *
 	 * @access	public
 	 * @return	string
@@ -402,7 +457,7 @@ class CI_Router {
 	// --------------------------------------------------------------------
 
 	/**
-	 * Set the directory name
+	 *  Set the directory name
 	 *
 	 * @access	public
 	 * @param	string
@@ -416,7 +471,7 @@ class CI_Router {
 	// --------------------------------------------------------------------
 
 	/**
-	 * Fetch the sub-directory (if any) that contains the requested controller class
+	 *  Fetch the sub-directory (if any) that contains the requested controller class
 	 *
 	 * @access	public
 	 * @return	string
@@ -429,7 +484,7 @@ class CI_Router {
 	// --------------------------------------------------------------------
 
 	/**
-	 * Set the controller overrides
+	 *  Set the controller overrides
 	 *
 	 * @access	public
 	 * @param	array
diff --git a/system/core/Security.php b/system/core/Security.php
index f5bfafd9b..dcc680a11 100644..100755
--- a/system/core/Security.php
+++ b/system/core/Security.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -26,13 +26,48 @@
  */
 class CI_Security {
 
+	/**
+	 * Random Hash for protecting URLs
+	 *
+	 * @var string
+	 * @access protected
+	 */
 	protected $_xss_hash			= '';
+	/**
+	 * Random Hash for Cross Site Request Forgery Protection Cookie
+	 *
+	 * @var string
+	 * @access protected
+	 */
 	protected $_csrf_hash			= '';
-	protected $_csrf_expire			= 7200; // Two hours (in seconds)
+	/**
+	 * Expiration time for Cross Site Request Forgery Protection Cookie
+	 * Defaults to two hours (in seconds)
+	 *
+	 * @var int
+	 * @access protected
+	 */
+	protected $_csrf_expire			= 7200;
+	/**
+	 * Token name for Cross Site Request Forgery Protection Cookie
+	 *
+	 * @var string
+	 * @access protected
+	 */
 	protected $_csrf_token_name		= 'ci_csrf_token';
+	/**
+	 * Cookie name for Cross Site Request Forgery Protection Cookie
+	 *
+	 * @var string
+	 * @access protected
+	 */
 	protected $_csrf_cookie_name	= 'ci_csrf_token';
-
-	/* never allowed, string replacement */
+	/**
+	 * List of never allowed strings
+	 *
+	 * @var array
+	 * @access protected
+	 */
 	protected $_never_allowed_str = array(
 					'document.cookie'	=> '[removed]',
 					'document.write'	=> '[removed]',
@@ -46,6 +81,12 @@ class CI_Security {
 	);
 
 	/* never allowed, regex replacement */
+	/**
+	 * List of never allowed regex replacement
+	 *
+	 * @var array
+	 * @access protected
+	 */
 	protected $_never_allowed_regex = array(
 					"javascript\s*:"			=> '[removed]',
 					"expression\s*(\(|&\#40;)"	=> '[removed]', // CSS and IE
@@ -196,14 +237,14 @@ class CI_Security {
 	 * XSS Clean
 	 *
 	 * Sanitizes data so that Cross Site Scripting Hacks can be
-	 * prevented. This function does a fair amount of work but
+	 * prevented.  This function does a fair amount of work but
 	 * it is extremely thorough, designed to prevent even the
-	 * most obscure XSS attempts. Nothing is ever 100% foolproof,
+	 * most obscure XSS attempts.  Nothing is ever 100% foolproof,
 	 * of course, but I haven't been able to get anything passed
 	 * the filter.
 	 *
 	 * Note: This function should only be used to deal with data
-	 * upon submission. It's not something that should
+	 * upon submission.  It's not something that should
 	 * be used for general runtime processing.
 	 *
 	 * This function was based in part on some code and ideas I
@@ -215,6 +256,7 @@ class CI_Security {
 	 * http://ha.ckers.org/xss.html
 	 *
 	 * @param	mixed	string or array
+	 * @param 	bool
 	 * @return	string
 	 */
 	public function xss_clean($str, $is_image = FALSE)
@@ -311,13 +353,13 @@ class CI_Security {
 		}
 		else
 		{
-			$str = str_replace(array('<?', '?'.'>'), array('&lt;?', '?&gt;'), $str);
+			$str = str_replace(array('<?', '?'.'>'),  array('&lt;?', '?&gt;'), $str);
 		}
 
 		/*
 		 * Compact any exploded words
 		 *
-		 * This corrects words like: j a v a s c r i p t
+		 * This corrects words like:  j a v a s c r i p t
 		 * These words are compacted back to their correct state.
 		 */
 		$words = array(
@@ -388,7 +430,7 @@ class CI_Security {
 		 *
 		 * Similar to above, only instead of looking for
 		 * tags it looks for PHP and JavaScript commands
-		 * that are disallowed. Rather than removing the
+		 * that are disallowed.  Rather than removing the
 		 * code, it simply converts the parenthesis to entities
 		 * rendering the code un-executable.
 		 *
@@ -457,7 +499,7 @@ class CI_Security {
 	 *
 	 * In some versions of PHP the native function does not work
 	 * when UTF-8 is the specified character set, so this gives us
-	 * a work-around. More info here:
+	 * a work-around.  More info here:
 	 * http://bugs.php.net/bug.php?id=25670
 	 *
 	 * NOTE: html_entity_decode() has a bug in some PHP versions when UTF-8 is the
@@ -475,7 +517,7 @@ class CI_Security {
 		// The reason we are not using html_entity_decode() by itself is because
 		// while it is not technically correct to leave out the semicolon
 		// at the end of an entity most browsers will still interpret the entity
-		// correctly. html_entity_decode() does not convert entities without
+		// correctly.  html_entity_decode() does not convert entities without
 		// semicolons, so we are left with our own little solution here. Bummer.
 
 		if (function_exists('html_entity_decode') &&
@@ -505,6 +547,7 @@ class CI_Security {
 	 * Filename Security
 	 *
 	 * @param	string
+	 * @param 	bool
 	 * @return	string
 	 */
 	public function sanitize_filename($str, $relative_path = FALSE)
@@ -751,7 +794,7 @@ class CI_Security {
 		/*
 		 * Validate standard character entities
 		 *
-		 * Add a semicolon if missing. We do this to enable
+		 * Add a semicolon if missing.  We do this to enable
 		 * the conversion of entities to ASCII later.
 		 *
 		 */
diff --git a/system/core/URI.php b/system/core/URI.php
index 94fac59ac..a3ae20cc3 100644..100755
--- a/system/core/URI.php
+++ b/system/core/URI.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *
@@ -28,15 +28,40 @@
  */
 class CI_URI {
 
+	/**
+	 * List of cached uri segments
+	 *
+	 * @var array
+	 * @access public
+	 */
 	var	$keyval			= array();
+	/**
+	 * Current uri string
+	 *
+	 * @var string
+	 * @access public
+	 */
 	var $uri_string;
+	/**
+	 * List of uri segments
+	 *
+	 * @var array
+	 * @access public
+	 */
 	var $segments		= array();
+	/**
+	 * Re-indexed list of uri segments
+	 * Starts at 1 instead of 0
+	 *
+	 * @var array
+	 * @access public
+	 */
 	var $rsegments		= array();
 
 	/**
 	 * Constructor
 	 *
-	 * Simply globalizes the $RTR object. The front
+	 * Simply globalizes the $RTR object.  The front
 	 * loads the Router class early on so it's not available
 	 * normally as other classes are.
 	 *
@@ -62,7 +87,7 @@ class CI_URI {
 		if (strtoupper($this->config->item('uri_protocol')) == 'AUTO')
 		{
 			// Is the request coming from the command line?
-			if (defined('STDIN'))
+			if (php_sapi_name() == 'cli' or defined('STDIN'))
 			{
 				$this->_set_uri_string($this->_parse_cli_args());
 				return;
@@ -85,7 +110,7 @@ class CI_URI {
 			}
 
 			// No PATH_INFO?... What about QUERY_STRING?
-			$path = (isset($_SERVER['QUERY_STRING'])) ? $_SERVER['QUERY_STRING'] : @getenv('QUERY_STRING');
+			$path =  (isset($_SERVER['QUERY_STRING'])) ? $_SERVER['QUERY_STRING'] : @getenv('QUERY_STRING');
 			if (trim($path, '/') != '')
 			{
 				$this->_set_uri_string($path);
@@ -127,6 +152,7 @@ class CI_URI {
 	 * Set the URI String
 	 *
 	 * @access	public
+	 * @param 	string
 	 * @return	string
 	 */
 	function _set_uri_string($str)
@@ -251,7 +277,7 @@ class CI_URI {
 	 */
 	function _remove_url_suffix()
 	{
-		if ($this->config->item('url_suffix') != "")
+		if  ($this->config->item('url_suffix') != "")
 		{
 			$this->uri_string = preg_replace("|".preg_quote($this->config->item('url_suffix'))."$|", "", $this->uri_string);
 		}
@@ -285,7 +311,7 @@ class CI_URI {
 	 * Re-index Segments
 	 *
 	 * This function re-indexes the $this->segment array so that it
-	 * starts at 1 rather than 0. Doing so makes it simpler to
+	 * starts at 1 rather than 0.  Doing so makes it simpler to
 	 * use functions like $this->uri->segment(n) since there is
 	 * a 1:1 relationship between the segment array and the actual segments.
 	 *
@@ -323,7 +349,7 @@ class CI_URI {
 	 * Fetch a URI "routed" Segment
 	 *
 	 * This function returns the re-routed URI segment (assuming routing rules are used)
-	 * based on the number provided. If there is no routing this function returns the
+	 * based on the number provided.  If there is no routing this function returns the
 	 * same result as $this->segment()
 	 *
 	 * @access	public
@@ -366,6 +392,11 @@ class CI_URI {
 	/**
 	 * Identical to above only it uses the re-routed segment array
 	 *
+	 * @access 	public
+	 * @param 	integer	the starting segment number
+	 * @param 	array	an array of default values
+	 * @return 	array
+	 *
 	 */
 	function ruri_to_assoc($n = 3, $default = array())
 	{
@@ -425,7 +456,7 @@ class CI_URI {
 
 		$i = 0;
 		$lastval = '';
-		$retval = array();
+		$retval  = array();
 		foreach ($segments as $seg)
 		{
 			if ($i % 2)
diff --git a/system/core/Utf8.php b/system/core/Utf8.php
index 738d7e9d8..2a27d1f35 100644
--- a/system/core/Utf8.php
+++ b/system/core/Utf8.php
@@ -1,4 +1,4 @@
-<?php if ( ! defined('BASEPATH')) exit('No direct script access allowed');
+<?php  if ( ! defined('BASEPATH')) exit('No direct script access allowed');
 /**
  * CodeIgniter
  *