diff --git a/libraries/auth/cookie.auth.lib.php b/libraries/auth/cookie.auth.lib.php
index ffd75e09b..83f49a62a 100644
--- a/libraries/auth/cookie.auth.lib.php
+++ b/libraries/auth/cookie.auth.lib.php
@@ -13,6 +13,9 @@ if (! defined('PHPMYADMIN')) {
     exit;
 }
 
+/**
+ * Swekey authentication functions.
+ */
 require './libraries/auth/swekey/swekey.auth.lib.php';
 
 if (function_exists('mcrypt_encrypt')) {
diff --git a/libraries/auth/swekey/authentication.inc.php b/libraries/auth/swekey/authentication.inc.php
index ea23393df..1977f883e 100644
--- a/libraries/auth/swekey/authentication.inc.php
+++ b/libraries/auth/swekey/authentication.inc.php
@@ -1,3 +1,8 @@
+<?php
+/**
+ * @package Swekey
+ */
+?>
 
 <script>
 
@@ -7,32 +12,32 @@
 	// Create the swekey plugin if it does not exists
 	function Swekey_Plugin()
 	{
-		try 
-		{		
+		try
+		{
 			if (g_SwekeyPlugin != null)
 				return g_SwekeyPlugin;
-						
+
 			if (window.ActiveXObject)
 			{
     			g_SwekeyPlugin = document.getElementById("swekey_activex");
     			if (g_SwekeyPlugin == null)
-    			{	
+    			{
                     // we must create the activex that way instead of new ActiveXObject("FbAuthAx.FbAuthCtl");
-                    // ortherwise SetClientSite is not called and we can not get the url			
+                    // ortherwise SetClientSite is not called and we can not get the url
   			  		var div = document.createElement('div');
 	   				div.innerHTML='<object id="swekey_activex" style="display:none" CLASSID="CLSID:8E02E3F9-57AA-4EE1-AA68-A42DD7B0FADE"></object>';
 
     				// Never append to the body because it may still loading and it breaks IE
 	   				document.body.insertBefore(div, document.body.firstChild);
-    				g_SwekeyPlugin = document.getElementById("swekey_activex"); 
-                }				
+    				g_SwekeyPlugin = document.getElementById("swekey_activex");
+                }
 				return g_SwekeyPlugin;
 			}
 
 			g_SwekeyPlugin = document.getElementById("swekey_plugin");
 			if (g_SwekeyPlugin != null)
 				return g_SwekeyPlugin;
-				
+
 			for (i = 0; i < navigator.plugins.length; i ++)
 			{
 				try
@@ -63,25 +68,25 @@
 				}
 			}
 		}
-		catch (e) 
+		catch (e)
 		{
 			//alert("Swekey_Plugin " + e);
 			g_SwekeyPlugin = null;
 		}
 		return null;
 	}
-	
+
 	// -------------------------------------------------------------------
 	// Returns true if the swekey plugin is installed
 	function Swekey_Installed()
 	{
 		return (Swekey_Plugin() != null);
 	}
-	
+
 	// -------------------------------------------------------------------
-	// List the id of the Swekey connected to the PC 
+	// List the id of the Swekey connected to the PC
 	// Returns a string containing comma separated Swekey Ids
-    // A Swekey is a 32 char hexadecimal value.  	
+    // A Swekey is a 32 char hexadecimal value.
 	function Swekey_ListKeyIds()
 	{
 		try
@@ -94,11 +99,11 @@
 		}
 		return "";
 	}
-	
+
 	// -------------------------------------------------------------------
 	// Ask the Connected Swekey to generate an OTP
 	// id: The id of the connected Swekey (returne by Swekey_ListKeyIds())
-	// rt: A random token 	
+	// rt: A random token
 	// return: The calculated OTP encoded in a 64 chars hexadecimal value.
 	function Swekey_GetOtp(id, rt)
 	{
@@ -116,7 +121,7 @@
 	// -------------------------------------------------------------------
 	// Ask the Connected Swekey to generate a OTP linked to the current https host
 	// id: The id of the connected Swekey (returne by Swekey_ListKeyIds())
-	// rt: A random token 	
+	// rt: A random token
 	// return: The calculated OTP encoded in a 64 chars hexadecimal value.
 	// or "" if the current url does not start with https
 	function Swekey_GetLinkedOtp(id, rt)
@@ -136,13 +141,13 @@
     // Calls Swekey_GetOtp or Swekey_GetLinkedOtp depending if we are in
     // an https page or not.
 	// id: The id of the connected Swekey (returne by Swekey_ListKeyIds())
-	// rt: A random token 	
+	// rt: A random token
 	// return: The calculated OTP encoded in a 64 chars hexadecimal value.
 	function Swekey_GetSmartOtp(id, rt)
 	{
         var res = Swekey_GetLinkedOtp(id, rt);
         if (res == "")
-            res = Swekey_GetOtp(id, rt); 
+            res = Swekey_GetOtp(id, rt);
 
 		return res;
 	}
@@ -150,7 +155,7 @@
 	// -------------------------------------------------------------------
 	// Set a unplug handler (url) to the specified connected feebee
 	// id: The id of the connected Swekey (returne by Swekey_ListKeyIds())
-	// key: The key that index that url, (aplhanumeric values only) 	
+	// key: The key that index that url, (aplhanumeric values only)
 	// url: The url that will be launched ("" deletes the url)
 	function Swekey_SetUnplugUrl(id, key, url)
 	{
@@ -164,4 +169,4 @@
 		}
 	}
 
-</script>	
+</script>
diff --git a/libraries/auth/swekey/swekey.auth.lib.php b/libraries/auth/swekey/swekey.auth.lib.php
index aad555498..f53dd81c2 100644
--- a/libraries/auth/swekey/swekey.auth.lib.php
+++ b/libraries/auth/swekey/swekey.auth.lib.php
@@ -3,6 +3,9 @@
  * @package Swekey
  */
 
+/**
+ * Checks Swekey authentication.
+ */
 function Swekey_auth_check()
 {
     global $cfg;
@@ -57,6 +60,9 @@ function Swekey_auth_check()
 }
 
 
+/**
+ * Handle Swekey authentication error.
+ */
 function Swekey_auth_error()
 {
     if (! isset($_SESSION['SWEKEY']))
@@ -200,6 +206,9 @@ function Swekey_auth_error()
 }
 
 
+/**
+ * Perform login using Swekey.
+ */
 function Swekey_login($input_name, $input_go)
 {
     $swekeyErr = Swekey_auth_error();
diff --git a/libraries/dbi/mysql.dbi.lib.php b/libraries/dbi/mysql.dbi.lib.php
index 92d9424b1..e0d0de6ce 100644
--- a/libraries/dbi/mysql.dbi.lib.php
+++ b/libraries/dbi/mysql.dbi.lib.php
@@ -3,6 +3,7 @@
 /**
  * Interface to the classic MySQL extension
  *
+ * @package phpMyAdmin-DBI-MySQL
  * @version $Id$
  */
 if (! defined('PHPMYADMIN')) {
@@ -153,10 +154,10 @@ function PMA_DBI_try_query($query, $link = null, $options = 0)
             $_SESSION['debug']['queries'][$hash]['query'] = $query;
             $_SESSION['debug']['queries'][$hash]['time'] = $time;
         }
-        
+
         $trace = array();
         foreach (debug_backtrace() as $trace_step) {
-            $trace[] = PMA_Error::relPath($trace_step['file']) . '#' 
+            $trace[] = PMA_Error::relPath($trace_step['file']) . '#'
                 . $trace_step['line'] . ': '
                 . (isset($trace_step['class']) ? $trace_step['class'] : '')
                 //. (isset($trace_step['object']) ? get_class($trace_step['object']) : '')
diff --git a/libraries/dbi/mysqli.dbi.lib.php b/libraries/dbi/mysqli.dbi.lib.php
index ec47b82e7..0c973195a 100644
--- a/libraries/dbi/mysqli.dbi.lib.php
+++ b/libraries/dbi/mysqli.dbi.lib.php
@@ -3,6 +3,7 @@
 /**
  * Interface to the improved MySQL extension (MySQLi)
  *
+ * @package phpMyAdmin-DBI-MySQLi
  * @version $Id$
  */
 if (! defined('PHPMYADMIN')) {
@@ -178,7 +179,7 @@ function PMA_DBI_try_query($query, $link = null, $options = 0)
 
         $trace = array();
         foreach (debug_backtrace() as $trace_step) {
-            $trace[] = PMA_Error::relPath($trace_step['file']) . '#' 
+            $trace[] = PMA_Error::relPath($trace_step['file']) . '#'
                 . $trace_step['line'] . ': '
                 . (isset($trace_step['class']) ? $trace_step['class'] : '')
                 //. (isset($trace_step['object']) ? get_class($trace_step['object']) : '')
@@ -575,9 +576,9 @@ function PMA_DBI_field_name($result, $i)
  * @uses    MYSQLI_PRI_KEY_FLAG
  * @uses    MYSQLI_NOT_NULL_FLAG
  * @uses    MYSQLI_TYPE_BLOB
- * @uses    MYSQLI_TYPE_MEDIUM_BLOB  
- * @uses    MYSQLI_TYPE_LONG_BLOB 
- * @uses    MYSQLI_TYPE_VAR_STRING  
+ * @uses    MYSQLI_TYPE_MEDIUM_BLOB
+ * @uses    MYSQLI_TYPE_LONG_BLOB
+ * @uses    MYSQLI_TYPE_VAR_STRING
  * @uses    MYSQLI_TYPE_STRING
  * @uses    mysqli_fetch_field_direct()
  * @param   object mysqli result    $result
diff --git a/libraries/string_mb.lib.php b/libraries/string_mb.lib.php
index 641bafea4..12cc0f5e1 100644
--- a/libraries/string_mb.lib.php
+++ b/libraries/string_mb.lib.php
@@ -13,6 +13,7 @@
  * The SQL Parser code relies heavily on these functions.
  *
  * @version $Id$
+ * @package phpMyAdmin-String-MB
  */
 
 /**
diff --git a/libraries/string_native.lib.php b/libraries/string_native.lib.php
index f1c47feea..17a335d75 100644
--- a/libraries/string_native.lib.php
+++ b/libraries/string_native.lib.php
@@ -13,6 +13,7 @@
  * The SQL Parser code relies heavily on these functions.
  *
  * @version $Id$
+ * @package phpMyAdmin-String-Native
  */
 
 /**
diff --git a/libraries/string_type_ctype.lib.php b/libraries/string_type_ctype.lib.php
index 828516455..4e7a10674 100644
--- a/libraries/string_type_ctype.lib.php
+++ b/libraries/string_type_ctype.lib.php
@@ -13,6 +13,7 @@
  * The SQL Parser code relies heavily on these functions.
  *
  * @version $Id$
+ * @package phpMyAdmin-StringType-CType
  */
 
 /**
@@ -100,4 +101,4 @@ function PMA_STR_isHexDigit($c)
     return ctype_xdigit($c);
 } // end of the "PMA_STR_isHexDigit()" function
 
-?>
\ No newline at end of file
+?>
diff --git a/libraries/string_type_native.lib.php b/libraries/string_type_native.lib.php
index cad798454..337c23df7 100644
--- a/libraries/string_type_native.lib.php
+++ b/libraries/string_type_native.lib.php
@@ -13,6 +13,7 @@
  * The SQL Parser code relies heavily on these functions.
  *
  * @version $Id$
+ * @package phpMyAdmin-StringType-Native
  */
 
 /**
@@ -137,4 +138,4 @@ function PMA_STR_isHexDigit($c)
          || PMA_STR_numberInRangeInclusive($ord_c, $ord_Alower, $ord_Flower));
 } // end of the "PMA_STR_isHexDigit()" function
 
-?>
\ No newline at end of file
+?>
diff --git a/phpinfo.php b/phpinfo.php
index 56a4c9cda..e740315b1 100644
--- a/phpinfo.php
+++ b/phpinfo.php
@@ -6,9 +6,12 @@
  */
 
 /**
- * Gets core libraries and defines some variables
+ * @ignore
  */
 define('PMA_MINIMUM_COMMON', true);
+/**
+ * Gets core libraries and defines some variables
+ */
 require_once './libraries/common.inc.php';
 
 
diff --git a/webapp.php b/webapp.php
index 681e2a82e..9c21162fb 100644
--- a/webapp.php
+++ b/webapp.php
@@ -6,10 +6,16 @@
  */
 
 /**
- *
+ * @ignore
  */
 define('PMA_MINIMUM_COMMON', true);
+/**
+ * Gets core libraries and defines some variables
+ */
 require_once './libraries/common.inc.php';
+/**
+ * ZIP file handler.
+ */
 require_once './libraries/zip.lib.php';
 
 // ini file