Index: admin-header.php
===================================================================
--- admin-header.php	(revision 8640)
+++ admin-header.php	(working copy)
@@ -18,6 +18,12 @@
 $the_current_page = preg_replace('|^.*/wp-admin/|i', '', $_SERVER['PHP_SELF']);
 $ie6_no_scrollbar = true;
 
+/**
+ * Append 'minwidth' to value.
+ *
+ * @param mixed $c
+ * @return string
+ */
 function add_minwidth($c) {
 	return $c . 'minwidth ';
 }
Index: import/blogger.php
===================================================================
--- import/blogger.php	(revision 8640)
+++ import/blogger.php	(working copy)
@@ -1,9 +1,46 @@
 <?php
+/**
+ * Blogger Importer
+ *
+ * @package WordPress
+ * @subpackage Importer
+ */
 
-define( 'MAX_RESULTS',        50 ); // How many records per GData query
-define( 'MAX_EXECUTION_TIME', 20 ); // How many seconds to let the script run
-define( 'STATUS_INTERVAL',     3 ); // How many seconds between status bar updates
+/**
+ * How many records per GData query
+ *
+ * @package WordPress
+ * @subpackage Blogger_Import
+ * @var int
+ * @since unknown
+ */
+define( 'MAX_RESULTS',        50 );
 
+/**
+ * How many seconds to let the script run
+ *
+ * @package WordPress
+ * @subpackage Blogger_Import
+ * @var int
+ * @since unknown
+ */
+define( 'MAX_EXECUTION_TIME', 20 );
+
+/**
+ * How many seconds between status bar updates
+ *
+ * @package WordPress
+ * @subpackage Blogger_Import
+ * @var int
+ * @since unknown
+ */
+define( 'STATUS_INTERVAL',     3 );
+
+/**
+ * Blogger Importer class
+ *
+ * @since unknown
+ */
 class Blogger_Import {
 
 	// Shows the welcome screen and the magic auth link.
@@ -1014,4 +1051,4 @@
 	}
 }
 
-?>
+?>
\ No newline at end of file
Index: import/blogware.php
===================================================================
--- import/blogware.php	(revision 8640)
+++ import/blogware.php	(working copy)
@@ -1,7 +1,20 @@
 <?php
+/**
+ * Blogware XML Importer
+ *
+ * @package WordPress
+ * @subpackage Importer
+ * @author Shayne Sweeney
+ * @link http://www.theshayne.com/
+ */
 
-/* By Shayne Sweeney - http://www.theshayne.com/ */
-
+/**
+ * Blogware XML Importer class
+ *
+ * Extract posts from Blogware XML export file into your blog.
+ *
+ * @since unknown
+ */
 class BW_Import {
 
 	var $file;
Index: import/btt.php
===================================================================
--- import/btt.php	(revision 8640)
+++ import/btt.php	(working copy)
@@ -1,5 +1,19 @@
 <?php
+/**
+ * BunnyTags Plugin Tag Importer
+ *
+ * @package WordPress
+ * @subpackage Importer
+ */
 
+/**
+ * BunnyTags Plugin tag converter
+ *
+ * This will process the BunnyTags plugin tags and convert them to the WordPress
+ * 2.3 taxonomy.
+ *
+ * @since unknown
+ */
 class BunnyTags_Import {
 
 	function header() {
Index: import/dotclear.php
===================================================================
--- import/dotclear.php	(revision 8640)
+++ import/dotclear.php	(working copy)
@@ -1,7 +1,11 @@
 <?php
-/*
- * DotClear import plugin
- * by Thomas Quinot - http://thomas.quinot.org/
+/**
+ * DotClear Importer
+ *
+ * @package WordPress
+ * @subpackage Importer
+ * @author Thomas Quinot
+ * @link http://thomas.quinot.org/
  */
 
 /**
@@ -10,6 +14,15 @@
 
 if(!function_exists('get_comment_count'))
 {
+	/**
+	 * Get the comment count for posts.
+	 *
+	 * @package WordPress
+	 * @subpackage Dotclear_Import
+	 *
+	 * @param int $post_ID Post ID
+	 * @return int
+	 */
 	function get_comment_count($post_ID)
 	{
 		global $wpdb;
@@ -19,6 +32,15 @@
 
 if(!function_exists('link_exists'))
 {
+	/**
+	 * Check whether link already exists.
+	 *
+	 * @package WordPress
+	 * @subpackage Dotclear_Import
+	 *
+	 * @param string $linkname
+	 * @return int
+	 */
 	function link_exists($linkname)
 	{
 		global $wpdb;
@@ -40,31 +62,73 @@
 //    This cries out for a C-implementation to be included in PHP core
 //
 
+/**
+ * @package WordPress
+ * @subpackage Dotclear_Import
+ *
+ * @param string $char
+ * @return string
+ */
 function valid_1byte($char) {
 	if(!is_int($char)) return false;
 		return ($char & 0x80) == 0x00;
 }
 
+/**
+ * @package WordPress
+ * @subpackage Dotclear_Import
+ *
+ * @param string $char
+ * @return string
+ */
 function valid_2byte($char) {
 	if(!is_int($char)) return false;
 		return ($char & 0xE0) == 0xC0;
 }
 
+/**
+ * @package WordPress
+ * @subpackage Dotclear_Import
+ *
+ * @param string $char
+ * @return string
+ */
 function valid_3byte($char) {
 	if(!is_int($char)) return false;
 		return ($char & 0xF0) == 0xE0;
 }
 
+/**
+ * @package WordPress
+ * @subpackage Dotclear_Import
+ *
+ * @param string $char
+ * @return string
+ */
 function valid_4byte($char) {
 	if(!is_int($char)) return false;
 		return ($char & 0xF8) == 0xF0;
 }
 
+/**
+ * @package WordPress
+ * @subpackage Dotclear_Import
+ *
+ * @param string $char
+ * @return string
+ */
 function valid_nextbyte($char) {
 	if(!is_int($char)) return false;
 		return ($char & 0xC0) == 0x80;
 }
 
+/**
+ * @package WordPress
+ * @subpackage Dotclear_Import
+ *
+ * @param string $string
+ * @return string
+ */
 function valid_utf8($string) {
 	$len = strlen($string);
 	$i = 0;
@@ -92,6 +156,13 @@
 	return true; // done
 }
 
+/**
+ * @package WordPress
+ * @subpackage Dotclear_Import
+ *
+ * @param string $s
+ * @return string
+ */
 function csc ($s) {
 	if (valid_utf8 ($s)) {
 		return $s;
@@ -100,13 +171,28 @@
 	}
 }
 
+/**
+ * @package WordPress
+ * @subpackage Dotclear_Import
+ *
+ * @param string $s
+ * @return string
+ */
 function textconv ($s) {
 	return csc (preg_replace ('|(?<!<br />)\s*\n|', ' ', $s));
 }
 
 /**
-	The Main Importer Class
-**/
+ * Dotclear Importer class
+ *
+ * Will process the WordPress eXtended RSS files that you upload from the export
+ * file.
+ *
+ * @package WordPress
+ * @subpackage Importer
+ *
+ * @since unknown
+ */
 class Dotclear_Import {
 
 	function header()
@@ -742,5 +828,7 @@
 }
 
 $dc_import = new Dotclear_Import();
+
 register_importer('dotclear', __('DotClear'), __('Import categories, users, posts, comments, and links from a DotClear blog.'), array ($dc_import, 'dispatch'));
-?>
+
+?>
\ No newline at end of file
Index: import/greymatter.php
===================================================================
--- import/greymatter.php	(revision 8640)
+++ import/greymatter.php	(working copy)
@@ -1,5 +1,19 @@
 <?php
+/**
+ * GreyMatter Importer
+ *
+ * @package WordPress
+ * @subpackage Importer
+ */
 
+/**
+ * GreyMatter Importer class
+ *
+ * Basic GreyMatter to WordPress importer, will import posts, comments, and
+ * posts karma.
+ *
+ * @since unknown
+ */
 class GM_Import {
 
 	var $gmnames = array ();
Index: import/jkw.php
===================================================================
--- import/jkw.php	(revision 8640)
+++ import/jkw.php	(working copy)
@@ -1,5 +1,18 @@
 <?php
+/**
+ * Jeromes Keyword Plugin Importer
+ *
+ * @package WordPress
+ * @subpackage Importer
+ */
 
+/**
+ * Jeromes Keyword Plugin Importer class
+ *
+ * Will convert Jeromes Keyword Plugin tags to WordPress taxonomy tags.
+ *
+ * @since 2.3
+ */
 class JeromesKeyword_Import {
 
 	function header() {
Index: import/livejournal.php
===================================================================
--- import/livejournal.php	(revision 8640)
+++ import/livejournal.php	(working copy)
@@ -1,5 +1,18 @@
 <?php
+/**
+ * LiveJournal Importer
+ *
+ * @package WordPress
+ * @subpackage Importer
+ */
 
+/**
+ * LiveJournal Importer class
+ *
+ * Imports your LiveJournal XML exported file into WordPress.
+ *
+ * @since unknown
+ */
 class LJ_Import {
 
 	var $file;
Index: import/mt.php
===================================================================
--- import/mt.php	(revision 8640)
+++ import/mt.php	(working copy)
@@ -1,5 +1,18 @@
 <?php
+/**
+ * Movable Type and Typepad Importer
+ *
+ * @package WordPress
+ * @subpackage Importer
+ */
 
+/**
+ * Moveable Type and Typepad Importer class
+ *
+ * Upload your exported Movable Type or Typepad entries into WordPress.
+ *
+ * @since unknown
+ */
 class MT_Import {
 
 	var $posts = array ();
Index: import/rss.php
===================================================================
--- import/rss.php	(revision 8640)
+++ import/rss.php	(working copy)
@@ -1,5 +1,20 @@
 <?php
+/**
+ * RSS Importer
+ *
+ * @package WordPress
+ * @subpackage Importer
+ */
 
+/**
+ * RSS Importer
+ *
+ * Will process a RSS feed for importing posts into WordPress. This is a very
+ * limited importer and should only be used as the last resort, when no other
+ * importer is available.
+ *
+ * @since unknown
+ */
 class RSS_Import {
 
 	var $posts = array ();
Index: import/stp.php
===================================================================
--- import/stp.php	(revision 8640)
+++ import/stp.php	(working copy)
@@ -1,4 +1,18 @@
 <?php
+/**
+ * Simple Tags Plugin Importer
+ *
+ * @package WordPress
+ * @subpackage Importer
+ */
+
+/**
+ * Simple Tags Plugin Tags converter class.
+ *
+ * Will convert Simple Tags Plugin tags over to the WordPress 2.3 taxonomy.
+ *
+ * @since unknown
+ */
 class STP_Import {
 	function header()  {
 		echo '<div class="wrap">';
Index: import/textpattern.php
===================================================================
--- import/textpattern.php	(revision 8640)
+++ import/textpattern.php	(working copy)
@@ -1,10 +1,22 @@
 <?php
 /**
-	Add These Functions to make our lives easier
-**/
+ * TextPattern Importer
+ *
+ * @package WordPress
+ * @subpackage Importer
+ */
 
 if(!function_exists('get_comment_count'))
 {
+	/**
+	 * Get the comment count for posts.
+	 *
+	 * @package WordPress
+	 * @subpackage Textpattern_Import
+	 *
+	 * @param int $post_ID Post ID
+	 * @return int
+	 */
 	function get_comment_count($post_ID)
 	{
 		global $wpdb;
@@ -14,6 +26,15 @@
 
 if(!function_exists('link_exists'))
 {
+	/**
+	 * Check whether link already exists.
+	 *
+	 * @package WordPress
+	 * @subpackage Textpattern_Import
+	 *
+	 * @param string $linkname
+	 * @return int
+	 */
 	function link_exists($linkname)
 	{
 		global $wpdb;
@@ -22,8 +43,10 @@
 }
 
 /**
-	The Main Importer Class
-**/
+ * TextPattern Importer Class
+ *
+ * @since unknown
+ */
 class Textpattern_Import {
 
 	function header()
@@ -670,5 +693,7 @@
 }
 
 $txp_import = new Textpattern_Import();
+
 register_importer('textpattern', __('Textpattern'), __('Import categories, users, posts, comments, and links from a Textpattern blog.'), array ($txp_import, 'dispatch'));
-?>
+
+?>
\ No newline at end of file
Index: import/utw.php
===================================================================
--- import/utw.php	(revision 8640)
+++ import/utw.php	(working copy)
@@ -1,5 +1,18 @@
 <?php
+/**
+ * The Ultimate Tag Warrior Importer.
+ *
+ * @package WordPress
+ * @subpackage Importer
+ */
 
+/**
+ * Ultimate Tag Warrior Converter to 2.3 taxonomy.
+ *
+ * This converts the Ultimate Tag Warrior tags to the 2.3 WordPress taxonomy.
+ *
+ * @since 2.3.0
+ */
 class UTW_Import {
 
 	function header()  {
Index: import/wordpress.php
===================================================================
--- import/wordpress.php	(revision 8640)
+++ import/wordpress.php	(working copy)
@@ -1,5 +1,19 @@
 <?php
+/**
+ * WordPress Importer
+ *
+ * @package WordPress
+ * @subpackage Importer
+ */
 
+/**
+ * WordPress Importer
+ *
+ * Will process the WordPress eXtended RSS files that you upload from the export
+ * file.
+ *
+ * @since unknown
+ */
 class WP_Import {
 
 	var $post_ids_processed = array ();
@@ -746,8 +760,15 @@
 	}
 }
 
+/**
+ * Register WordPress Importer
+ *
+ * @since unknown
+ * @var WP_Import
+ * @name $wp_import
+ */
 $wp_import = new WP_Import();
 
 register_importer('wordpress', 'WordPress', __('Import <strong>posts, comments, custom fields, pages, and categories</strong> from a WordPress export file.'), array ($wp_import, 'dispatch'));
 
-?>
+?>
\ No newline at end of file
Index: import/wp-cat2tag.php
===================================================================
--- import/wp-cat2tag.php	(revision 8640)
+++ import/wp-cat2tag.php	(working copy)
@@ -1,5 +1,19 @@
 <?php
+/**
+ * WordPress Categories to Tags Converter.
+ *
+ * @package WordPress
+ * @subpackage Importer
+ */
 
+/**
+ * WordPress categories to tags converter class.
+ *
+ * Will convert WordPress categories to tags, removing the category after the
+ * process is complete and updating all posts to switch to the tag.
+ *
+ * @since unknown
+ */
 class WP_Categories_to_Tags {
 	var $categories_to_convert = array();
 	var $all_categories = array();
Index: includes/class-ftp-pure.php
===================================================================
--- includes/class-ftp-pure.php	(revision 8640)
+++ includes/class-ftp-pure.php	(working copy)
@@ -11,6 +11,20 @@
  * @link http://www.phpclasses.org/browse/package/1743.html Site
  * @license LGPL License http://www.opensource.org/licenses/lgpl-license.html
  */
+
+/**
+ * FTP implementation using fsockopen to connect.
+ *
+ * @package PemFTP
+ * @subpackage Pure
+ * @since 2.5
+ *
+ * @version 1.0
+ * @copyright Alexey Dotsenko
+ * @author Alexey Dotsenko
+ * @link http://www.phpclasses.org/browse/package/1743.html Site
+ * @license LGPL License http://www.opensource.org/licenses/lgpl-license.html
+ */
 class ftp extends ftp_base {
 
 	function ftp($verb=FALSE, $le=FALSE) {
@@ -172,4 +186,5 @@
 		}
 	}
 }
-?>
+
+?>
\ No newline at end of file
Index: includes/class-ftp-sockets.php
===================================================================
--- includes/class-ftp-sockets.php	(revision 8640)
+++ includes/class-ftp-sockets.php	(working copy)
@@ -11,6 +11,20 @@
  * @link http://www.phpclasses.org/browse/package/1743.html Site
  * @license LGPL License http://www.opensource.org/licenses/lgpl-license.html
  */
+
+/**
+ * Socket Based FTP implementation
+ *
+ * @package PemFTP
+ * @subpackage Socket
+ * @since 2.5
+ *
+ * @version 1.0
+ * @copyright Alexey Dotsenko
+ * @author Alexey Dotsenko
+ * @link http://www.phpclasses.org/browse/package/1743.html Site
+ * @license LGPL License http://www.opensource.org/licenses/lgpl-license.html
+ */
 class ftp extends ftp_base {
 
 	function ftp($verb=FALSE, $le=FALSE) {
Index: includes/class-ftp.php
===================================================================
--- includes/class-ftp.php	(revision 8640)
+++ includes/class-ftp.php	(working copy)
@@ -11,15 +11,75 @@
  * @link http://www.phpclasses.org/browse/package/1743.html Site
  * @license LGPL License http://www.opensource.org/licenses/lgpl-license.html
  */
+
+/**
+ * Defines the newline characters, if not defined already.
+ *
+ * This can be redefined.
+ *
+ * @since 2.5
+ * @var string
+ */
 if(!defined('CRLF')) define('CRLF',"\r\n");
+
+/**
+ * Sets whatever to autodetect ASCII mode.
+ *
+ * This can be redefined.
+ *
+ * @since 2.5
+ * @var int
+ */
 if(!defined("FTP_AUTOASCII")) define("FTP_AUTOASCII", -1);
+
+/**
+ *
+ * This can be redefined.
+ * @since 2.5
+ * @var int
+ */
 if(!defined("FTP_BINARY")) define("FTP_BINARY", 1);
+
+/**
+ *
+ * This can be redefined.
+ * @since 2.5
+ * @var int
+ */
 if(!defined("FTP_ASCII")) define("FTP_ASCII", 0);
-if(!defined('FTP_FORCE')) define('FTP_FORCE', TRUE);
+
+/**
+ * Whether to force FTP.
+ *
+ * This can be redefined.
+ *
+ * @since 2.5
+ * @var bool
+ */
+if(!defined('FTP_FORCE')) define('FTP_FORCE', true);
+
+/**
+ * @since 2.5
+ * @var string
+ */
 define('FTP_OS_Unix','u');
+
+/**
+ * @since 2.5
+ * @var string
+ */
 define('FTP_OS_Windows','w');
+
+/**
+ * @since 2.5
+ * @var string
+ */
 define('FTP_OS_Mac','m');
 
+/**
+ * PemFTP base class
+ *
+ */
 class ftp_base {
 	/* Public variables */
 	var $LocalEcho;
@@ -838,5 +898,6 @@
 	$prefix = (PHP_SHLIB_SUFFIX == 'dll') ? 'php_' : '';
 	if(!@dl($prefix . 'sockets.' . PHP_SHLIB_SUFFIX)) $mod_sockets=FALSE;
 }
+
 require_once "class-ftp-".($mod_sockets?"sockets":"pure").".php";
-?>
+?>
\ No newline at end of file
Index: includes/class-pclzip.php
===================================================================
--- includes/class-pclzip.php	(revision 8640)
+++ includes/class-pclzip.php	(working copy)
@@ -1,51 +1,60 @@
 <?php
-// --------------------------------------------------------------------------------
-// PhpConcept Library - Zip Module 2.5
-// --------------------------------------------------------------------------------
-// License GNU/LGPL - Vincent Blavet - March 2006
-// http://www.phpconcept.net
-// --------------------------------------------------------------------------------
-//
-// Presentation :
-//   PclZip is a PHP library that manage ZIP archives.
-//   So far tests show that archives generated by PclZip are readable by
-//   WinZip application and other tools.
-//
-// Description :
-//   See readme.txt and http://www.phpconcept.net
-//
-// Warning :
-//   This library and the associated files are non commercial, non professional
-//   work.
-//   It should not have unexpected results. However if any damage is caused by
-//   this software the author can not be responsible.
-//   The use of this software is at the risk of the user.
-//
-// --------------------------------------------------------------------------------
-// $Id: pclzip.lib.php,v 1.44 2006/03/08 21:23:59 vblavet Exp $
-// --------------------------------------------------------------------------------
+/**
+ * PhpConcept Library - Zip Module 2.5
+ *
+ * Presentation :
+ *   PclZip is a PHP library that manage ZIP archives.
+ *   So far tests show that archives generated by PclZip are readable by
+ *   WinZip application and other tools.
+ *
+ * Warning :
+ *   This library and the associated files are non commercial, non professional
+ *   work.
+ *   It should not have unexpected results. However if any damage is caused by
+ *   this software the author can not be responsible.
+ *   The use of this software is at the risk of the user.
+ *
+ * @package External
+ * @subpackage PclZip
+ *
+ * @license License GNU/LGPL
+ * @copyright March 2006 Vincent Blavet
+ * @author Vincent Blavet
+ * @link http://www.phpconcept.net
+ * @version $Id: pclzip.lib.php,v 1.44 2006/03/08 21:23:59 vblavet Exp $
+ */
 
-  // ----- Constants
-  define( 'PCLZIP_READ_BLOCK_SIZE', 2048 );
+/**
+ * The read block size for reading zip files.
+ *
+ * @since 2.5
+ */
+define( 'PCLZIP_READ_BLOCK_SIZE', 2048 );
 
-  // ----- File list separator
-  // In version 1.x of PclZip, the separator for file list is a space
-  // (which is not a very smart choice, specifically for windows paths !).
-  // A better separator should be a comma (,). This constant gives you the
-  // abilty to change that.
-  // However notice that changing this value, may have impact on existing
-  // scripts, using space separated filenames.
-  // Recommanded values for compatibility with older versions :
-  //define( 'PCLZIP_SEPARATOR', ' ' );
-  // Recommanded values for smart separation of filenames.
-  define( 'PCLZIP_SEPARATOR', ',' );
+/**
+ * File list separator
+ *
+ * In version 1.x of PclZip, the separator for file list is a space(which is not
+ * a very smart choice, specifically for windows paths !). A better separator
+ * should be a comma (,). This constant gives you the abilty to change that.
+ *
+ * However notice that changing this value, may have impact on existing scripts,
+ * using space separated filenames. Recommanded values for compatibility with
+ * older versions :
+ * <code>define( 'PCLZIP_SEPARATOR', ' ' );</code>
+ * Recommanded values for smart separation of filenames.
+ */
+define( 'PCLZIP_SEPARATOR', ',' );
 
-  // ----- Error configuration
-  // 0 : PclZip Class integrated error handling
-  // 1 : PclError external library error handling. By enabling this
-  //     you must ensure that you have included PclError library.
-  // [2,...] : reserved for futur use
-  define( 'PCLZIP_ERROR_EXTERNAL', 0 );
+/**
+ * Error configuration
+ *
+ * 0 : PclZip Class integrated error handling
+ * 1 : PclError external library error handling. By enabling this you must
+ *     ensure that you have included PclError library.
+ * [2,...] : reserved for future use
+ */
+define( 'PCLZIP_ERROR_EXTERNAL', 0 );
 
   // ----- Optional static temporary directory
   //       By default temporary files are generated in the script current
@@ -137,7 +146,7 @@
   define( 'PCLZIP_CB_POST_EXTRACT', 78002 );
   define( 'PCLZIP_CB_PRE_ADD', 78003 );
   define( 'PCLZIP_CB_POST_ADD', 78004 );
-  /* For futur use
+  /* For future use
   define( 'PCLZIP_CB_PRE_LIST', 78005 );
   define( 'PCLZIP_CB_POST_LIST', 78006 );
   define( 'PCLZIP_CB_PRE_DELETE', 78007 );
Index: includes/class-wp-filesystem-base.php
===================================================================
--- includes/class-wp-filesystem-base.php	(revision 8640)
+++ includes/class-wp-filesystem-base.php	(working copy)
@@ -1,5 +1,17 @@
 <?php
-class WP_Filesystem_Base{
+/**
+ * Base WordPress Filesystem.
+ *
+ * @package WordPress
+ * @subpackage Filesystem
+ */
+
+/**
+ * Base WordPress Filesystem class for which Filesystem implementations extend
+ *
+ * @since 2.5
+ */
+class WP_Filesystem_Base {
 	var $verbose = false;
 	var $cache = array();
 
@@ -155,4 +167,5 @@
 		return $newmode;
 	}
 }
-?>
+
+?>
\ No newline at end of file
Index: includes/class-wp-filesystem-direct.php
===================================================================
--- includes/class-wp-filesystem-direct.php	(revision 8640)
+++ includes/class-wp-filesystem-direct.php	(working copy)
@@ -1,5 +1,19 @@
 <?php
+/**
+ * WordPress Direct Filesystem.
+ *
+ * @package WordPress
+ * @subpackage Filesystem
+ */
 
+/**
+ * WordPress Filesystem Class for direct PHP file and folder manipulation.
+ *
+ * @since 2.5
+ * @package WordPress
+ * @subpackage Filesystem
+ * @uses WP_Filesystem_Base Extends class
+ */
 class WP_Filesystem_Direct  extends WP_Filesystem_Base {
 	var $permission = null;
 	var $errors = array();
Index: includes/class-wp-filesystem-ftpext.php
===================================================================
--- includes/class-wp-filesystem-ftpext.php	(revision 8640)
+++ includes/class-wp-filesystem-ftpext.php	(working copy)
@@ -1,5 +1,20 @@
 <?php
-class WP_Filesystem_FTPext extends WP_Filesystem_Base{
+/**
+ * WordPress FTP Filesystem.
+ *
+ * @package WordPress
+ * @subpackage Filesystem
+ */
+
+/**
+ * WordPress Filesystem Class for implementing FTP.
+ *
+ * @since 2.5
+ * @package WordPress
+ * @subpackage Filesystem
+ * @uses WP_Filesystem_Base Extends class
+ */
+class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 	var $link;
 	var $timeout = 5;
 	var $errors = array();
Index: includes/class-wp-filesystem-ftpsockets.php
===================================================================
--- includes/class-wp-filesystem-ftpsockets.php	(revision 8640)
+++ includes/class-wp-filesystem-ftpsockets.php	(working copy)
@@ -1,4 +1,19 @@
 <?php
+/**
+ * WordPress FTP Sockets Filesystem.
+ *
+ * @package WordPress
+ * @subpackage Filesystem
+ */
+
+/**
+ * WordPress Filesystem Class for implementing FTP Sockets.
+ *
+ * @since 2.5
+ * @package WordPress
+ * @subpackage Filesystem
+ * @uses WP_Filesystem_Base Extends class
+ */
 class WP_Filesystem_ftpsockets extends WP_Filesystem_Base {
 	var $ftp = false;
 	var $timeout = 5;
@@ -22,7 +37,7 @@
 							'bmp' => FTP_BINARY
 							);
 
-	function WP_Filesystem_ftpsockets($opt='') {
+	function WP_Filesystem_ftpsockets($opt = '') {
 		$this->method = 'ftpsockets';
 		$this->errors = new WP_Error();
 
@@ -86,7 +101,7 @@
 		$this->permission = $perm;
 	}
 
-	function get_contents($file, $type = '', $resumepos = 0){
+	function get_contents($file, $type = '', $resumepos = 0) {
 		if( ! $this->exists($file) )
 			return false;
 
@@ -112,7 +127,7 @@
 		return $contents;
 	}
 
-	function get_contents_array($file){
+	function get_contents_array($file) {
 		return explode("\n", $this->get_contents($file) );
 	}
 
@@ -151,7 +166,7 @@
 		return false;
 	}
 
-	function chmod($file, $mode = false, $recursive = false ){
+	function chmod($file, $mode = false, $recursive = false ) {
 		if( ! $mode )
 			$mode = $this->permission;
 		if( ! $mode )
@@ -251,7 +266,7 @@
 		return $this->ftp->filesize($file);
 	}
 
-	function touch($file, $time = 0, $atime = 0 ){
+	function touch($file, $time = 0, $atime = 0 ) {
 		return false;
 	}
 
@@ -311,8 +326,9 @@
 		return $ret;
 	}
 
-	function __destruct(){
+	function __destruct() {
 		$this->ftp->quit();
 	}
 }
-?>
+
+?>
\ No newline at end of file
Index: includes/comment.php
===================================================================
--- includes/comment.php	(revision 8640)
+++ includes/comment.php	(working copy)
@@ -1,5 +1,15 @@
 <?php
 
+/**
+ * {@internal Missing Short Description}}
+ *
+ * @since unknown
+ * @uses $wpdb
+ *
+ * @param string $comment_author
+ * @param string $comment_date
+ * @return mixed Comment ID on success.
+ */
 function comment_exists($comment_author, $comment_date) {
 	global $wpdb;
 
@@ -7,6 +17,10 @@
 			WHERE comment_author = %s AND comment_date = %s", $comment_author, $comment_date) );
 }
 
+/**
+ * 
+ *
+ */
 function edit_comment() {
 
 	$comment_post_ID = (int) $_POST['comment_post_ID'];
Index: includes/update-core.php
===================================================================
--- includes/update-core.php	(revision 8640)
+++ includes/update-core.php	(working copy)
@@ -1,5 +1,20 @@
 <?php
+/**
+ * WordPress core upgrade functionality.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ * @since 2.7
+ */
 
+/**
+ * Stores files to be deleted.
+ *
+ * @since 2.7
+ * @global array $_old_files
+ * @var array
+ * @name $_old_files
+ */
 global $_old_files;
 
 $_old_files = array(
@@ -117,6 +132,44 @@
 'wp-content/plugins/textile1.php',
 );
 
+/**
+ * Upgrade the core of WordPress.
+ *
+ * This will create a .maintenance file at the base of the WordPress directory
+ * to ensure that people can not access the web site, when the files are being
+ * copied to their locations.
+ *
+ * The files in the {@link $_old_files} list will be removed and the new files
+ * copied from the zip file after the database is upgraded.
+ *
+ * The steps for the upgrader for after the new release is downloaded and
+ * unzipped is:
+ *   1. Test unzipped location for select files to ensure that unzipped worked.
+ *   2. Create the .maintenance file in current WordPress base.
+ *   3. Copy new WordPress directory over old WordPress files.
+ *   4. Upgrade WordPress to new version.
+ *   5. Delete new WordPress directory path.
+ *   6. Delete .maintenance file.
+ *   7. Remove old files.
+ *   8. Delete 'update_core' option.
+ *
+ * There are several areas of failure. For instance if PHP times out before step
+ * 6, then you will not be able to access any portion of your site. Also, since
+ * the upgrade will not continue where it left off, you will not be able to
+ * automatically remove old files and remove the 'update_core' option. This
+ * isn't that bad.
+ *
+ * If the copy of the new WordPress over the old fails, then the worse is that
+ * the new WordPress directory will remain.
+ *
+ * If it is assumed that every file will be copied over, including plugins and
+ * themes, then if you edit the default theme, you should rename it, so that
+ * your changes remain.
+ *
+ * @param string $from New release unzipped path.
+ * @param string $to Path to old WordPress installation.
+ * @return WP_Error|null WP_Error on failure, null on success.
+ */
 function update_core($from, $to) {
 	global $wp_filesystem, $_old_files;
 
Index: install-helper.php
===================================================================
--- install-helper.php	(revision 8640)
+++ install-helper.php	(working copy)
@@ -1,15 +1,76 @@
 <?php
+/**
+ * Plugins may load this file to gain access to special helper functions for
+ * plugin installation. This file is not included by WordPress and it is
+ * recommended, to prevent fatal errors, that this file is included using
+ * require_once().
+ *
+ * These functions are not optimized for speed, but they should only be used
+ * once in a while, so speed shouldn't be a concern. If it is and you are
+ * needing to use these functions a lot, you might experience time outs. If you
+ * do, then it is advised to just write the SQL code yourself.
+ *
+ * You can turn debugging on, by setting $debug to 1 after you include this
+ * file.
+ *
+ * <code>
+ * check_column('wp_links', 'link_description', 'mediumtext');
+ * if (check_column($wpdb->comments, 'comment_author', 'tinytext'))
+ *     echo "ok\n";
+ * 
+ * $error_count = 0;
+ * $tablename = $wpdb->links;
+ * // check the column
+ * if (!check_column($wpdb->links, 'link_description', 'varchar(255)')) {
+ *     $ddl = "ALTER TABLE $wpdb->links MODIFY COLUMN link_description varchar(255) NOT NULL DEFAULT '' ";
+ *     $q = $wpdb->query($ddl);
+ * }
+ * 
+ * if (check_column($wpdb->links, 'link_description', 'varchar(255)')) {
+ *     $res .= $tablename . ' - ok <br />';
+ * } else {
+ *     $res .= 'There was a problem with ' . $tablename . '<br />';
+ *     ++$error_count;
+ * }
+ * </code>
+ *
+ * @package WordPress
+ * @subpackage Plugins
+ */
+
+/**
+ * @global bool $wp_only_load_config
+ * @name $wp_only_load_config
+ * @var bool
+ * @since unknown
+ */
 $wp_only_load_config = true;
+
+/** Load WordPress Bootstrap */
 require_once(dirname(dirname(__FILE__)).'/wp-load.php');
+
+/**
+ * Turn debugging on or off.
+ * @global bool|int $debug
+ * @name $debug
+ * @var bool|int
+ * @since unknown
+ */
 $debug = 0;
 
+if ( ! function_exists('maybe_create_table') ) :
 /**
- ** maybe_create_table()
- ** Create db table if it doesn't exist.
- ** Returns:  true if already exists or on successful completion
- **           false on error
+ * Create database table, if it doesn't already exist.
+ *
+ * @since unknown
+ * @package WordPress
+ * @subpackage Plugins
+ * @uses $wpdb
+ *
+ * @param string $table_name Database table name.
+ * @param string $create_ddl Create database table SQL.
+ * @return bool False on error, true if already exists or success.
  */
-if ( ! function_exists('maybe_create_table') ) :
 function maybe_create_table($table_name, $create_ddl) {
 	global $wpdb;
 	foreach ($wpdb->get_col("SHOW TABLES",0) as $table ) {
@@ -29,20 +90,29 @@
 }
 endif;
 
+if ( ! function_exists('maybe_add_column') ) :
 /**
- ** maybe_add_column()
- ** Add column to db table if it doesn't exist.
- ** Returns:  true if already exists or on successful completion
- **           false on error
+ * Add column to database table, if column doesn't already exist in table.
+ *
+ * @since unknown
+ * @package WordPress
+ * @subpackage Plugins
+ * @uses $wpdb
+ * @uses $debug
+ *
+ * @param string $table_name Database table name
+ * @param string $column_name Table column name
+ * @param string $create_ddl SQL to add column to table.
+ * @return bool False on failure. True, if already exists or was successful.
  */
-if ( ! function_exists('maybe_add_column') ) :
 function maybe_add_column($table_name, $column_name, $create_ddl) {
 	global $wpdb, $debug;
 	foreach ($wpdb->get_col("DESC $table_name",0) as $column ) {
 		if ($debug) echo("checking $column == $column_name<br />");
-			if ($column == $column_name) {
-				return true;
-			}
+
+		if ($column == $column_name) {
+			return true;
+		}
 	}
 	//didn't find it try to create it.
 	$wpdb->query($create_ddl);
@@ -57,10 +127,17 @@
 endif;
 
 /**
- ** maybe_drop_column()
- ** Drop column from db table if it exists.
- ** Returns:  true if it doesn't already exist or on successful drop
- **           false on error
+ * Drop column from database table, if it exists.
+ *
+ * @since unknown
+ * @package WordPress
+ * @subpackage Plugins
+ * @uses $wpdb
+ *
+ * @param string $table_name Table name
+ * @param string $column_name Column name
+ * @param string $drop_ddl SQL statement to drop column.
+ * @return bool False on failure, true on success or doesn't exist.
  */
 function maybe_drop_column($table_name, $column_name, $drop_ddl) {
 	global $wpdb;
@@ -80,20 +157,30 @@
 	return true;
 }
 
-
 /**
- ** check_column()
- ** Check column matches passed in criteria.
- ** Pass in null to skip checking that criteria
- ** Returns:  true if it matches
- **           false otherwise
- ** (case sensitive) Column names returned from DESC table are:
- **      Field
- **      Type
- **      Null
- **      Key
- **      Default
- **      Extra
+ * Check column matches criteria.
+ *
+ * Uses the SQL DESC for retrieving the table info for the column. It will help
+ * understand the parameters, if you do more research on what column information
+ * is returned by the SQL statement. Pass in null to skip checking that
+ * criteria.
+ *
+ * Column names returned from DESC table are case sensitive and are listed:
+ *      Field
+ *      Type
+ *      Null
+ *      Key
+ *      Default
+ *      Extra
+ *
+ * @param string $table_name Table name
+ * @param string $col_name Column name
+ * @param string $col_type Column type
+ * @param bool $is_null Optional. Check is null.
+ * @param mixed $key Optional. Key info.
+ * @param mixed $default Optional. Default value.
+ * @param mixed $extra Optional. Extra value.
+ * @return bool True, if matches. False, if not matching.
  */
 function check_column($table_name, $col_name, $col_type, $is_null = null, $key = null, $default = null, $extra = null) {
 	global $wpdb, $debug;
@@ -102,55 +189,33 @@
 
 	foreach ($results as $row ) {
 		if ($debug > 1) print_r($row);
-			if ($row->Field == $col_name) {
-				// got our column, check the params
-				if ($debug) echo ("checking $row->Type against $col_type\n");
-				if (($col_type != null) && ($row->Type != $col_type)) {
-					++$diffs;
-				}
-				if (($is_null != null) && ($row->Null != $is_null)) {
-					++$diffs;
-				}
-				if (($key != null) && ($row->Key  != $key)) {
-					++$diffs;
-				}
-				if (($default != null) && ($row->Default != $default)) {
-					++$diffs;
-				}
-				if (($extra != null) && ($row->Extra != $extra)) {
-					++$diffs;
-				}
-				if ($diffs > 0) {
-					if ($debug) echo ("diffs = $diffs returning false\n");
-					return false;
-				}
-				return true;
-			} // end if found our column
+
+		if ($row->Field == $col_name) {
+			// got our column, check the params
+			if ($debug) echo ("checking $row->Type against $col_type\n");
+			if (($col_type != null) && ($row->Type != $col_type)) {
+				++$diffs;
+			}
+			if (($is_null != null) && ($row->Null != $is_null)) {
+				++$diffs;
+			}
+			if (($key != null) && ($row->Key  != $key)) {
+				++$diffs;
+			}
+			if (($default != null) && ($row->Default != $default)) {
+				++$diffs;
+			}
+			if (($extra != null) && ($row->Extra != $extra)) {
+				++$diffs;
+			}
+			if ($diffs > 0) {
+				if ($debug) echo ("diffs = $diffs returning false\n");
+				return false;
+			}
+			return true;
+		} // end if found our column
 	}
 	return false;
 }
 
-/*
-echo "<p>testing</p>";
-echo "<pre>";
-
-//check_column('wp_links', 'link_description', 'mediumtext');
-//if (check_column($wpdb->comments, 'comment_author', 'tinytext'))
-//    echo "ok\n";
-$error_count = 0;
-$tablename = $wpdb->links;
-// check the column
-if (!check_column($wpdb->links, 'link_description', 'varchar(255)'))
-{
-	$ddl = "ALTER TABLE $wpdb->links MODIFY COLUMN link_description varchar(255) NOT NULL DEFAULT '' ";
-	$q = $wpdb->query($ddl);
-}
-if (check_column($wpdb->links, 'link_description', 'varchar(255)')) {
-	$res .= $tablename . ' - ok <br />';
-} else {
-	$res .= 'There was a problem with ' . $tablename . '<br />';
-	++$error_count;
-}
-echo "</pre>";
-*/
-?>
+?>
\ No newline at end of file
Index: install.php
===================================================================
--- install.php	(revision 8640)
+++ install.php	(working copy)
@@ -1,14 +1,38 @@
 <?php
+/**
+ * WordPress Installer
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/**
+ * We are installing WordPress.
+ *
+ * @since unknown
+ * @var bool
+ */
 define('WP_INSTALLING', true);
 
+/** Load WordPress Bootstrap */
 require_once('../wp-load.php');
+
+/** Load WordPress Administration Upgrade API */
 require_once('./includes/upgrade.php');
 
 if (isset($_GET['step']))
 	$step = $_GET['step'];
 else
 	$step = 0;
-function display_header(){
+
+/**
+ * Display install header.
+ *
+ * @since unknown
+ * @package WordPress
+ * @subpackage Installer
+ */
+function display_header() {
 header( 'Content-Type: text/html; charset=utf-8' );
 ?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
Index: link-add.php
===================================================================
--- link-add.php	(revision 8640)
+++ link-add.php	(working copy)
@@ -1,4 +1,12 @@
 <?php
+/**
+ * Add Link Administration Panel.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/** Load WordPress Administration Bootstrap */
 require_once('admin.php');
 
 $title = __('Add Link');
Index: link-category.php
===================================================================
--- link-category.php	(revision 8640)
+++ link-category.php	(working copy)
@@ -1,4 +1,15 @@
 <?php
+/**
+ * Manage link category administration actions.
+ *
+ * This page is accessed by the link management pages and handles the forms and
+ * AJAX processes for category actions.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/** Load WordPress Administration Bootstrap */
 require_once('admin.php');
 
 wp_reset_vars(array('action', 'cat'));
@@ -31,7 +42,7 @@
 	$default_cat_id = get_option('default_link_category');
 
 	// Don't delete the default cats.
-    if ( $cat_ID == $default_cat_id )
+	if ( $cat_ID == $default_cat_id )
 		wp_die(sprintf(__("Can&#8217;t delete the <strong>%s</strong> category: this is the default one"), $cat_name));
 
 	wp_delete_term($cat_ID, 'link_category', array('default' => $default_cat_id));
@@ -86,4 +97,4 @@
 break;
 }
 
-?>
+?>
\ No newline at end of file
Index: link-import.php
===================================================================
--- link-import.php	(revision 8640)
+++ link-import.php	(working copy)
@@ -1,7 +1,14 @@
 <?php
-// Links
-// Copyright (C) 2002 Mike Little -- mike@zed1.com
+/**
+ * Links Import Administration Panel.
+ *
+ * @copyright 2002 Mike Little <mike@zed1.com>
+ * @author Mike Little <mike@zed1.com>
+ * @package WordPress
+ * @subpackage Administration
+ */
 
+/** Load WordPress Administration Bootstrap */
 require_once('admin.php');
 $parent_file = 'edit.php';
 $title = __('Import Blogroll');
@@ -98,6 +105,7 @@
 				$opml = file_get_contents($opml_url);
 			}
 
+			/** Load OPML Parser */
 			include_once('link-parse-opml.php');
 
 			$link_count = count($names);
Index: link-manager.php
===================================================================
--- link-manager.php	(revision 8640)
+++ link-manager.php	(working copy)
@@ -1,5 +1,12 @@
 <?php
+/**
+ * Link Management Administration Panel.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
 
+/** Load WordPress Administration Bootstrap */
 require_once ('admin.php');
 
 // Handle bulk deletes
Index: link-parse-opml.php
===================================================================
--- link-parse-opml.php	(revision 8640)
+++ link-parse-opml.php	(working copy)
@@ -1,4 +1,12 @@
 <?php
+/**
+ * Parse OPML XML files and store in globals.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/** Load WordPress Bootstrap */
 require_once('../wp-load.php');
 
 // columns we wish to find are:  link_url, link_name, link_target, link_description
@@ -15,9 +23,24 @@
 $map = $opml_map;
 
 /**
- ** startElement()
- ** Callback function. Called at the start of a new xml tag.
- **/
+ * XML callback function for the start of a new XML tag.
+ *
+ * @since unknown
+ * @access private
+ *
+ * @uses $updated_timestamp Not used inside function.
+ * @uses $all_links Not used inside function.
+ * @uses $map Stores names of attributes to use.
+ * @global array $names
+ * @global array $urls
+ * @global array $targets
+ * @global array $descriptions
+ * @global array $feeds
+ *
+ * @param mixed $parser XML Parser resource.
+ * @param string $tagName XML element name.
+ * @param array $attrs XML element attributes.
+ */
 function startElement($parser, $tagName, $attrs) {
 	global $updated_timestamp, $all_links, $map;
 	global $names, $urls, $targets, $descriptions, $feeds;
@@ -41,9 +64,16 @@
 }
 
 /**
- ** endElement()
- ** Callback function. Called at the end of an xml tag.
- **/
+ * XML callback function that is called at the end of a XML tag.
+ *
+ * @since unknown
+ * @access private
+ * @package WordPress
+ * @subpackage Dummy
+ *
+ * @param mixed $parser XML Parser resource.
+ * @param string $tagName XML tag name.
+ */
 function endElement($parser, $tagName) {
 	// nothing to do.
 }
@@ -62,4 +92,4 @@
 
 // Free up memory used by the XML parser
 xml_parser_free($xml_parser);
-?>
+?>
\ No newline at end of file
Index: link.php
===================================================================
--- link.php	(revision 8640)
+++ link.php	(working copy)
@@ -1,4 +1,15 @@
 <?php
+/**
+ * Manage link administration actions.
+ *
+ * This page is accessed by the link management pages and handles the forms and
+ * AJAX processes for link actions.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/** Load WordPress Administration Bootstrap */
 require_once ('admin.php');
 
 wp_reset_vars(array('action', 'cat_id', 'linkurl', 'name', 'image', 'description', 'visible', 'target', 'category', 'link_id', 'submit', 'order_by', 'links_show_cat_id', 'rating', 'rel', 'notes', 'linkcheck[]'));
Index: media-upload.php
===================================================================
--- media-upload.php	(revision 8640)
+++ media-upload.php	(working copy)
@@ -1,4 +1,15 @@
 <?php
+/**
+ * Manage media uploaded file.
+ *
+ * There are many filters in here for media. Plugins can extend functionality
+ * by hooking into the filters.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/** Load WordPress Administration Bootstrap */
 require_once('admin.php');
 wp_enqueue_script('swfupload');
 wp_enqueue_script('swfupload-degrade');
@@ -11,7 +22,7 @@
 	wp_die(__('You do not have permission to upload files.'));
 
 // IDs should be integers
-$ID = isset($ID)? (int) $ID : 0;
+$ID = isset($ID) ? (int) $ID : 0;
 $post_id = isset($post_id)? (int) $post_id : 0;
 
 // Require an ID for the edit screen
@@ -38,4 +49,4 @@
 else
 	do_action("media_upload_$tab");
 
-?>
+?>
\ No newline at end of file
Index: media.php
===================================================================
--- media.php	(revision 8640)
+++ media.php	(working copy)
@@ -1,5 +1,12 @@
 <?php
+/**
+ * Media management action handler.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
 
+/** Load WordPress Administration Bootstrap */
 require_once('admin.php');
 
 $parent_file = 'edit.php';
@@ -116,4 +123,4 @@
 endswitch;
 
 
-?>
+?>
\ No newline at end of file
Index: menu-header.php
===================================================================
--- menu-header.php	(revision 8640)
+++ menu-header.php	(working copy)
@@ -1,4 +1,18 @@
 <?php
+/**
+ * Displays Administration Menu.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/**
+ * The current page.
+ *
+ * @global string $self
+ * @name $self
+ * @var string
+ */
 $self = preg_replace('|^.*/wp-admin/|i', '', $_SERVER['PHP_SELF']);
 $self = preg_replace('|^.*/plugins/|i', '', $self);
 
Index: menu.php
===================================================================
--- menu.php	(revision 8640)
+++ menu.php	(working copy)
@@ -1,9 +1,23 @@
 <?php
-// This array constructs the admin menu bar.
-//
-// Menu item name
-// The minimum level the user needs to access the item: between 0 and 10
-// The URL of the item's file
+/**
+ * Build Administration Menu.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/**
+ * Constructs the admin menu bar.
+ *
+ * The elements in the array are :
+ *     0: Menu item name
+ *     1: Minimum level or capability required.
+ *     2: The URL of the item's file
+ *
+ * @global array $menu
+ * @name $menu
+ * @var array
+ */
 $menu[0] = array(__('Dashboard'), 'read', 'index.php');
 
 if (strpos($_SERVER['REQUEST_URI'], 'edit-pages.php') !== false)
Index: moderation.php
===================================================================
--- moderation.php	(revision 8640)
+++ moderation.php	(working copy)
@@ -1,4 +1,12 @@
 <?php
+/**
+ * Comment Moderation Administration Panel.
+ *
+ * Redirects to edit-comments.php?comment_status=moderated.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
 require_once('../wp-load.php');
 wp_redirect('edit-comments.php?comment_status=moderated');
 ?>
Index: options-head.php
===================================================================
--- options-head.php	(revision 8640)
+++ options-head.php	(working copy)
@@ -1,5 +1,17 @@
-<?php wp_reset_vars(array('action', 'standalone', 'option_group_id')); ?>
+<?php
+/**
+ * WordPress Options Header.
+ *
+ * Resets variables: 'action', 'standalone', and 'option_group_id'. Displays
+ * updated message, if updated variable is part of the URL query.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
 
+wp_reset_vars(array('action', 'standalone', 'option_group_id'));
+?>
+
 <?php if (isset($_GET['updated'])) : ?>
 <div id="message" class="updated fade"><p><strong><?php _e('Settings saved.') ?></strong></p></div>
 <?php endif; ?>
\ No newline at end of file
Index: options-privacy.php
===================================================================
--- options-privacy.php	(revision 8640)
+++ options-privacy.php	(working copy)
@@ -1,4 +1,12 @@
 <?php
+/**
+ * Privacy Options Settings Administration Panel.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/** Load WordPress Administration Bootstrap */
 require_once('./admin.php');
 
 $title = __('Privacy Settings');
Index: post-new.php
===================================================================
--- post-new.php	(revision 8640)
+++ post-new.php	(working copy)
@@ -1,4 +1,12 @@
 <?php
+/**
+ * New Post Administration Panel.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/** Load WordPress Administration Bootstrap */
 require_once('admin.php');
 $title = __('Create New Post');
 $parent_file = 'post-new.php';
Index: profile.php
===================================================================
--- profile.php	(revision 8640)
+++ profile.php	(working copy)
@@ -1,4 +1,19 @@
 <?php
+/**
+ * User Profile Administration Panel.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/**
+ * This is a profile page.
+ *
+ * @since unknown
+ * @var bool
+ */
 define('IS_PROFILE_PAGE', true);
+
+/** Load User Editing Page */
 require_once('user-edit.php');
-?>
+?>
\ No newline at end of file
Index: setup-config.php
===================================================================
--- setup-config.php	(revision 8640)
+++ setup-config.php	(working copy)
@@ -1,4 +1,20 @@
 <?php
+/**
+ * Retrieves and creates the wp-config.php file.
+ *
+ * The permissions for the base directory must allow for writing files in order
+ * for the wp-config.php to be created using this page.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/**
+ * We are installing.
+ *
+ * @since unknown
+ * @package WordPress
+ */
 define('WP_INSTALLING', true);
 //These three defines are required to allow us to use require_wp_db() to load the database class while being wp-content/wp-db.php aware
 define('ABSPATH', dirname(dirname(__FILE__)).'/');
@@ -30,7 +46,14 @@
 else
 	$step = 0;
 
-function display_header(){
+/**
+ * Display setup wp-config.php file header.
+ *
+ * @since unknown
+ * @package WordPress
+ * @subpackage Installer_WP_Config
+ */
+function display_header() {
 	header( 'Content-Type: text/html; charset=utf-8' );
 ?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
Index: update-links.php
===================================================================
--- update-links.php	(revision 8640)
+++ update-links.php	(working copy)
@@ -1,5 +1,21 @@
 <?php
+/**
+ * Send blog links to pingomatic.com to update.
+ *
+ * You can disable this feature by deleting the option 'use_linksupdate' or
+ * setting the option to false. If no links exist, then no links are sent.
+ *
+ * Snoopy is included, but is not used. Fsockopen() is used instead to send link
+ * URLs.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/** Load WordPress Bootstrap */
 require_once('../wp-load.php');
+
+/** Load Snoopy HTTP Client class */
 require_once( ABSPATH . 'wp-includes/class-snoopy.php');
 
 if ( !get_option('use_linksupdate') )
@@ -41,4 +57,4 @@
 		$wpdb->query( $wpdb->prepare("UPDATE $wpdb->links SET link_updated = %s WHERE link_url = %s", $time, $uri) );
 	endforeach;
 }
-?>
+?>
\ No newline at end of file
Index: upgrade-functions.php
===================================================================
--- upgrade-functions.php	(revision 8640)
+++ upgrade-functions.php	(working copy)
@@ -1,5 +1,13 @@
 <?php
-// Deprecated.  Use includes/upgrade.php.
+/**
+ * WordPress Upgrade Functions. Old file, must not be used. Include
+ * wp-admin/includes/upgrade.php instead.
+ *
+ * @deprecated 2.5
+ * @package WordPress
+ * @subpackage Administration
+ */
+
 _deprecated_file( basename(__FILE__), '2.5', 'wp-admin/includes/upgrade.php' );
 require_once(ABSPATH . 'wp-admin/includes/upgrade.php');
-?>
+?>
\ No newline at end of file
Index: upgrade.php
===================================================================
--- upgrade.php	(revision 8640)
+++ upgrade.php	(working copy)
@@ -1,7 +1,22 @@
 <?php
+/**
+ * Upgrade WordPress Page.
+ *
+ * @package WordPress
+ * @subpackage Administration
+ */
+
+/**
+ * We are upgrading WordPress.
+ *
+ * @since unknown
+ * @var bool
+ */
 define('WP_INSTALLING', true);
 
+/** Load WordPress Bootstrap */
 require('../wp-load.php');
+
 timer_start();
 require_once(ABSPATH . 'wp-admin/includes/upgrade.php');