diff --git a/wp-admin/includes/class-wp-filesystem-base.php b/wp-admin/includes/class-wp-filesystem-base.php
index 2569a8674a..6b0d098169 100644
--- a/wp-admin/includes/class-wp-filesystem-base.php
+++ b/wp-admin/includes/class-wp-filesystem-base.php
@@ -210,7 +210,7 @@ class WP_Filesystem_Base {
 			return trailingslashit($base . $last_path);
 		}
 		if ( $loop )
-			return false;//Prevent tihs function looping again.
+			return false; //Prevent tihs function looping again.
 		//As an extra last resort, Change back to / if the folder wasnt found. This comes into effect when the CWD is /home/user/ but WP is at /var/www/.... mainly dedicated setups.
 		return $this->search_for_folder($folder, '/', true);
 
@@ -242,7 +242,7 @@ class WP_Filesystem_Base {
 			$info = 'd';
 		elseif (($perms & 0x2000) == 0x2000) // Character special
 			$info = 'c';
-		elseif (($perms & 0x1000) == 0x1000)// FIFO pipe
+		elseif (($perms & 0x1000) == 0x1000) // FIFO pipe
 			$info = 'p';
 		else // Unknown
 			$info = 'u';
diff --git a/wp-admin/includes/class-wp-filesystem-direct.php b/wp-admin/includes/class-wp-filesystem-direct.php
index 03a797734c..d60c3659cf 100644
--- a/wp-admin/includes/class-wp-filesystem-direct.php
+++ b/wp-admin/includes/class-wp-filesystem-direct.php
@@ -15,38 +15,84 @@
  * @uses WP_Filesystem_Base Extends class
  */
 class WP_Filesystem_Direct extends WP_Filesystem_Base {
-	var $permission = null;
 	var $errors = null;
+	/**
+	 * constructor
+	 * 
+	 * @param $arg mixed ingored argument
+	 */
 	function WP_Filesystem_Direct($arg) {
 		$this->method = 'direct';
 		$this->errors = new WP_Error();
 	}
+	/**
+	 * connect filesystem.
+	 * 
+	 * @return bool Returns true on success or false on failure (always true for WP_Filesystem_Direct).
+	 */
 	function connect() {
 		return true;
 	}
-	function setDefaultPermissions($perm) {
-		$this->permission = $perm;
-	}
+	/**
+	 * Reads entire file into a string
+	 * 
+	 * @param $file string Name of the file to read.
+	 * @return string|bool The function returns the read data or false on failure. 
+	 */
 	function get_contents($file) {
 		return @file_get_contents($file);
 	}
+	/**
+	 * Reads entire file into an array
+	 * 
+	 * @param $file string Path to the file. 
+	 * @return array|bool the file contents in an array or false on failure. 
+	 */
 	function get_contents_array($file) {
 		return @file($file);
 	}
+	/**
+	 * Write a string to a file
+	 * 
+	 * @param $file string Path to the file where to write the data. 
+	 * @param $contents string The data to write.
+	 * @param $mode int (optional) The file permissions as octal number, usually 0644.
+	 * @param $type string (optional) Specifies additional type of access you require to the file.
+	 * @return bool False upon failure.
+	 */
 	function put_contents($file, $contents, $mode = false, $type = '') {
 		if ( ! ($fp = @fopen($file, 'w' . $type)) )
 			return false;
 		@fwrite($fp, $contents);
 		@fclose($fp);
-		$this->chmod($file,$mode);
+		$this->chmod($file, $mode);
 		return true;
 	}
+	/**
+	 * Gets the current working directory
+	 * 
+	 * @return string|bool the current working directory on success, or false on failure. 
+	 */
 	function cwd() {
 		return @getcwd();
 	}
+	/**
+	 * Change directory
+	 *
+	 * @param $dir string The new current directory. 
+	 * @return bool Returns true on success or false on failure.
+	 */
 	function chdir($dir) {
 		return @chdir($dir);
 	}
+	/**
+	 * Changes file group
+	 * 
+	 * @param $file string Path to the file. 
+	 * @param $group mixed A group name or number.
+	 * @param $recursive bool (optional) If set True changes file group recursivly. Defaults to False. 
+	 * @return bool Returns true on success or false on failure.
+	 */
 	function chgrp($file, $group, $recursive = false) {
 		if ( ! $this->exists($file) )
 			return false;
@@ -62,14 +108,20 @@ class WP_Filesystem_Direct extends WP_Filesystem_Base {
 
 		return true;
 	}
+	/**
+	 * Changes filesystem permissions
+	 * 
+	 * @param $file string Path to the file.
+	 * @param $mode int (optional) The permissions as octal number, usually 0644 for files, 0755 for dirs.
+	 * @param $recursive bool (optional) If set True changes file group recursivly. Defaults to False. 
+	 * @return bool Returns true on success or false on failure.
+	 */
 	function chmod($file, $mode = false, $recursive = false) {
 		if ( ! $this->exists($file) )
 			return false;
 
 		if ( ! $mode ) {
-			if ( $this->permission )
-				$mode = $this->permission;
-			elseif ( $this->is_file($file) )
+			if ( $this->is_file($file) )
 				$mode = FS_CHMOD_FILE;
 			elseif ( $this->is_dir($file) )
 				$mode = FS_CHMOD_DIR;
@@ -89,6 +141,14 @@ class WP_Filesystem_Direct extends WP_Filesystem_Base {
 
 		return true;
 	}
+	/**
+	 * Changes file owner
+	 * 
+	 * @param $file string Path to the file. 
+	 * @param $owner mixed A user name or number.
+	 * @param $recursive bool (optional) If set True changes file owner recursivly. Defaults to False. 
+	 * @return bool Returns true on success or false on failure.
+	 */
 	function chown($file, $owner, $recursive = false) {
 		if ( ! $this->exists($file) )
 			return false;
@@ -98,11 +158,17 @@ class WP_Filesystem_Direct extends WP_Filesystem_Base {
 			return @chown($file, $owner);
 		//Is a directory, and we want recursive
 		$filelist = $this->dirlist($file);
-		foreach ($filelist as $filename){
+		foreach ($filelist as $filename) {
 			$this->chown($file . '/' . $filename, $owner, $recursive);
 		}
 		return true;
 	}
+	/**
+	 * Gets file owner
+	 * 
+	 * @param $file string Path to the file. 
+	 * @return string Username of the user.
+	 */
 	function owner($file) {
 		$owneruid = @fileowner($file);
 		if ( ! $owneruid )
@@ -112,6 +178,14 @@ class WP_Filesystem_Direct extends WP_Filesystem_Base {
 		$ownerarray = posix_getpwuid($owneruid);
 		return $ownerarray['name'];
 	}
+	/**
+	 * Gets file permissions
+	 * 
+	 * FIXME does not handle errors in fileperms()
+	 * 
+	 * @param $file string Path to the file. 
+	 * @return string Mode of the file (last 4 digits).
+	 */
 	function getchmod($file) {
 		return substr(decoct(@fileperms($file)),3);
 	}
@@ -133,7 +207,7 @@ class WP_Filesystem_Direct extends WP_Filesystem_Base {
 
 	function move($source, $destination, $overwrite = false) {
 		//Possible to use rename()?
-		if ( $this->copy($source, $destination, $overwrite) && $this->exists($destination) ){
+		if ( $this->copy($source, $destination, $overwrite) && $this->exists($destination) ) {
 			$this->delete($source);
 			return true;
 		} else {
@@ -197,7 +271,7 @@ class WP_Filesystem_Direct extends WP_Filesystem_Base {
 		return @filesize($file);
 	}
 
-	function touch($file, $time = 0, $atime = 0){
+	function touch($file, $time = 0, $atime = 0) {
 		if ($time == 0)
 			$time = time();
 		if ($atime == 0)
@@ -205,7 +279,10 @@ class WP_Filesystem_Direct extends WP_Filesystem_Base {
 		return @touch($file, $time, $atime);
 	}
 
-	function mkdir($path, $chmod = false, $chown = false, $chgrp = false){
+	function mkdir($path, $chmod = false, $chown = false, $chgrp = false) {
+		if ( ! $chmod )
+			$chmod = FS_CHMOD_DIR;
+
 		if ( ! @mkdir($path) )
 			return false;
 		$this->chmod($path, $chmod);
diff --git a/wp-admin/includes/class-wp-filesystem-ftpext.php b/wp-admin/includes/class-wp-filesystem-ftpext.php
index db9e307d79..a03f11b20b 100644
--- a/wp-admin/includes/class-wp-filesystem-ftpext.php
+++ b/wp-admin/includes/class-wp-filesystem-ftpext.php
@@ -19,8 +19,6 @@ class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 	var $errors = null;
 	var $options = array();
 
-	var $permission = null;
-
 	function WP_Filesystem_FTPext($opt='') {
 		$this->method = 'ftpext';
 		$this->errors = new WP_Error();
@@ -90,19 +88,15 @@ class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 		return true;
 	}
 
-	function setDefaultPermissions($perm) {
-		$this->permission = $perm;
-	}
-
-	function get_contents($file, $type = '', $resumepos = 0 ){
-		if( empty($type) )
+	function get_contents($file, $type = '', $resumepos = 0 ) {
+		if ( empty($type) )
 			$type = FTP_BINARY;
 
 		$temp = tmpfile();
 		if ( ! $temp )
 			return false;
 
-		if( ! @ftp_fget($this->link, $temp, $file, $type, $resumepos) )
+		if ( ! @ftp_fget($this->link, $temp, $file, $type, $resumepos) )
 			return false;
 
 		fseek($temp, 0); //Skip back to the start of the file being written to
@@ -118,7 +112,7 @@ class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 		return explode("\n", $this->get_contents($file));
 	}
 	function put_contents($file, $contents, $type = '' ) {
-		if( empty($type) )
+		if ( empty($type) )
 			$type = $this->is_binary($contents) ? FTP_BINARY : FTP_ASCII;
 
 		$temp = tmpfile();
@@ -135,7 +129,7 @@ class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 	}
 	function cwd() {
 		$cwd = @ftp_pwd($this->link);
-		if( $cwd )
+		if ( $cwd )
 			$cwd = trailingslashit($cwd);
 		return $cwd;
 	}
@@ -146,12 +140,18 @@ class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 		return false;
 	}
 	function chmod($file, $mode = false, $recursive = false) {
-		if( ! $mode )
-			$mode = $this->permission;
-		if( ! $mode )
-			return false;
 		if ( ! $this->exists($file) && ! $this->is_dir($file) )
 			return false;
+
+		if ( ! $mode ) {
+			if ( $this->is_file($file) )
+				$mode = FS_CHMOD_FILE;
+			elseif ( $this->is_dir($file) )
+				$mode = FS_CHMOD_DIR;
+			else
+				return false;	
+		}
+
 		if ( ! $recursive || ! $this->is_dir($file) ) {
 			if ( ! function_exists('ftp_chmod') )
 				return @ftp_site($this->link, sprintf('CHMOD %o %s', $mode, $file));
@@ -159,7 +159,7 @@ class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 		}
 		//Is a directory, and we want recursive
 		$filelist = $this->dirlist($file);
-		foreach($filelist as $filename){
+		foreach ( $filelist as $filename ) {
 			$this->chmod($file . '/' . $filename, $mode, $recursive);
 		}
 		return true;
@@ -180,10 +180,10 @@ class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 		return $dir[$file]['group'];
 	}
 	function copy($source, $destination, $overwrite = false ) {
-		if( ! $overwrite && $this->exists($destination) )
+		if ( ! $overwrite && $this->exists($destination) )
 			return false;
 		$content = $this->get_contents($source);
-		if( false === $content)
+		if ( false === $content)
 			return false;
 		return $this->put_contents($destination, $content);
 	}
@@ -216,7 +216,7 @@ class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 	function is_dir($path) {
 		$cwd = $this->cwd();
 		$result = @ftp_chdir($this->link, trailingslashit($path) );
-		if( $result && $path == $this->cwd() || $this->cwd() != $cwd ) {
+		if ( $result && $path == $this->cwd() || $this->cwd() != $cwd ) {
 			@ftp_chdir($this->link, $cwd);
 			return true;
 		}
@@ -243,13 +243,14 @@ class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 		return false;
 	}
 	function mkdir($path, $chmod = false, $chown = false, $chgrp = false) {
-		if( !ftp_mkdir($this->link, $path) )
+		if  ( !ftp_mkdir($this->link, $path) )
 			return false;
-		if( $chmod )
-			$this->chmod($path, $chmod);
-		if( $chown )
+		if ( ! $chmod )
+			$chmod = FS_CHMOD_DIR;
+		$this->chmod($path, $chmod);
+		if ( $chown )
 			$this->chown($path, $chown);
-		if( $chgrp )
+		if ( $chgrp )
 			$this->chgrp($path, $chgrp);
 		return true;
 	}
@@ -262,9 +263,9 @@ class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 		if ( is_null($is_windows) )
 			$is_windows = strpos( strtolower(ftp_systype($this->link)), 'win') !== false;
 
-		if ($is_windows && preg_match("/([0-9]{2})-([0-9]{2})-([0-9]{2}) +([0-9]{2}):([0-9]{2})(AM|PM) +([0-9]+|<DIR>) +(.+)/", $line, $lucifer)) {
+		if ( $is_windows && preg_match("/([0-9]{2})-([0-9]{2})-([0-9]{2}) +([0-9]{2}):([0-9]{2})(AM|PM) +([0-9]+|<DIR>) +(.+)/", $line, $lucifer) ) {
 			$b = array();
-			if ($lucifer[3]<70) { $lucifer[3] +=2000; } else { $lucifer[3]+=1900; } // 4digit year fix
+			if ( $lucifer[3] < 70 ) { $lucifer[3] +=2000; } else { $lucifer[3] += 1900; } // 4digit year fix
 			$b['isdir'] = ($lucifer[7]=="<DIR>");
 			if ( $b['isdir'] )
 				$b['type'] = 'd';
@@ -323,7 +324,7 @@ class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 	}
 
 	function dirlist($path = '.', $incdot = false, $recursive = false) {
-		if( $this->is_file($path) ) {
+		if ( $this->is_file($path) ) {
 			$limitFile = basename($path);
 			$path = dirname($path) . '/';
 		} else {
@@ -358,9 +359,9 @@ class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 			if ( 'd' == $struc['type'] ) {
 				$struc['files'] = array();
 
-				if ( $incdot ){
+				if ( $incdot ) {
 					//We're including the doted starts
-					if( '.' != $struc['name'] && '..' != $struc['name'] ){ //Ok, It isnt a special folder
+					if ( '.' != $struc['name'] && '..' != $struc['name'] ) { //Ok, It isnt a special folder
 						if ($recursive)
 							$struc['files'] = $this->dirlist($path . '/' . $struc['name'], $incdot, $recursive);
 					}
@@ -375,8 +376,8 @@ class WP_Filesystem_FTPext extends WP_Filesystem_Base {
 		return $ret;
 	}
 
-	function __destruct(){
-		if( $this->link )
+	function __destruct() {
+		if ( $this->link )
 			ftp_close($this->link);
 	}
 }
diff --git a/wp-admin/includes/class-wp-filesystem-ftpsockets.php b/wp-admin/includes/class-wp-filesystem-ftpsockets.php
index 3f0b74fd55..101b741e8e 100644
--- a/wp-admin/includes/class-wp-filesystem-ftpsockets.php
+++ b/wp-admin/includes/class-wp-filesystem-ftpsockets.php
@@ -19,14 +19,12 @@ class WP_Filesystem_ftpsockets extends WP_Filesystem_Base {
 	var $errors = null;
 	var $options = array();
 
-	var $permission = null;
-
 	function WP_Filesystem_ftpsockets($opt = '') {
 		$this->method = 'ftpsockets';
 		$this->errors = new WP_Error();
 
 		//Check if possible to use ftp functions.
-		if( ! @include_once ABSPATH . 'wp-admin/includes/class-ftp.php' )
+		if ( ! @include_once ABSPATH . 'wp-admin/includes/class-ftp.php' )
 				return false;
 		$this->ftp = new ftp();
 
@@ -83,15 +81,11 @@ class WP_Filesystem_ftpsockets extends WP_Filesystem_Base {
 		return true;
 	}
 
-	function setDefaultPermissions($perm) {
-		$this->permission = $perm;
-	}
-
 	function get_contents($file, $type = '', $resumepos = 0) {
-		if( ! $this->exists($file) )
+		if ( ! $this->exists($file) )
 			return false;
 
-		if( empty($type) )
+		if ( empty($type) )
 			$type = FTP_AUTOASCII;
 		$this->ftp->SetType($type);
 
@@ -122,7 +116,7 @@ class WP_Filesystem_ftpsockets extends WP_Filesystem_Base {
 	}
 
 	function put_contents($file, $contents, $type = '' ) {
-		if( empty($type) )
+		if ( empty($type) )
 			$type = $this->is_binary($contents) ? FTP_BINARY : FTP_ASCII;
 
 		$this->ftp->SetType($type);
@@ -145,7 +139,7 @@ class WP_Filesystem_ftpsockets extends WP_Filesystem_Base {
 
 	function cwd() {
 		$cwd = $this->ftp->pwd();
-		if( $cwd )
+		if ( $cwd )
 			$cwd = trailingslashit($cwd);
 		return $cwd;
 	}
@@ -159,14 +153,18 @@ class WP_Filesystem_ftpsockets extends WP_Filesystem_Base {
 	}
 
 	function chmod($file, $mode = false, $recursive = false ) {
-		if( ! $mode )
-			$mode = $this->permission;
-		if( ! $mode )
-			return false;
-		//if( ! $this->exists($file) )
-		//	return false;
-		if( ! $recursive || ! $this->is_dir($file) ) {
-			return $this->ftp->chmod($file,$mode);
+
+		if ( ! $mode ) {
+			if ( $this->is_file($file) )
+				$mode = FS_CHMOD_FILE;
+			elseif ( $this->is_dir($file) )
+				$mode = FS_CHMOD_DIR;
+			else
+				return false;	
+		}
+
+		if ( ! $recursive || ! $this->is_dir($file) ) {
+			return $this->ftp->chmod($file, $mode);
 		}
 		//Is a directory, and we want recursive
 		$filelist = $this->dirlist($file);
@@ -196,7 +194,7 @@ class WP_Filesystem_ftpsockets extends WP_Filesystem_Base {
 	}
 
 	function copy($source, $destination, $overwrite = false ) {
-		if( ! $overwrite && $this->exists($destination) )
+		if ( ! $overwrite && $this->exists($destination) )
 			return false;
 
 		$content = $this->get_contents($source);
@@ -265,26 +263,27 @@ class WP_Filesystem_ftpsockets extends WP_Filesystem_Base {
 	}
 
 	function mkdir($path, $chmod = false, $chown = false, $chgrp = false ) {
-		if( ! $this->ftp->mkdir($path) )
+		if ( ! $this->ftp->mkdir($path) )
 			return false;
-		if( $chmod )
-			$this->chmod($path, $chmod);
-		if( $chown )
+		if ( ! $chmod )
+			$chmod = FS_CHMOD_DIR;
+		$this->chmod($path, $chmod);
+		if ( $chown )
 			$this->chown($path, $chown);
-		if( $chgrp )
+		if ( $chgrp )
 			$this->chgrp($path, $chgrp);
 		return true;
 	}
 
 	function rmdir($path, $recursive = false ) {
-		if( ! $recursive )
+		if ( ! $recursive )
 			return $this->ftp->rmdir($path);
 
 		return $this->ftp->mdel($path);
 	}
 
 	function dirlist($path = '.', $incdot = false, $recursive = false ) {
-		if( $this->is_file($path) ) {
+		if ( $this->is_file($path) ) {
 			$limitFile = basename($path);
 			$path = dirname($path) . '/';
 		} else {
@@ -292,9 +291,9 @@ class WP_Filesystem_ftpsockets extends WP_Filesystem_Base {
 		}
 
 		$list = $this->ftp->dirlist($path);
-		if( ! $list )
+		if ( ! $list )
 			return false;
-		if( empty($list) )
+		if ( empty($list) )
 			return array();
 
 		$ret = array();
@@ -305,7 +304,7 @@ class WP_Filesystem_ftpsockets extends WP_Filesystem_Base {
 
 				if ( $incdot ){
 					//We're including the doted starts
-					if( '.' != $struc['name'] && '..' != $struc['name'] ){ //Ok, It isnt a special folder
+					if ( '.' != $struc['name'] && '..' != $struc['name'] ){ //Ok, It isnt a special folder
 						if ($recursive)
 							$struc['files'] = $this->dirlist($path . '/' . $struc['name'], $incdot, $recursive);
 					}
diff --git a/wp-admin/includes/class-wp-filesystem-ssh2.php b/wp-admin/includes/class-wp-filesystem-ssh2.php
index d406106b50..a9f8dbd652 100644
--- a/wp-admin/includes/class-wp-filesystem-ssh2.php
+++ b/wp-admin/includes/class-wp-filesystem-ssh2.php
@@ -48,8 +48,6 @@ class WP_Filesystem_SSH2 extends WP_Filesystem_Base {
 	var $errors = array();
 	var $options = array();
 
-	var $permission = 0644;
-
 	function WP_Filesystem_SSH2($opt='') {
 		$this->method = 'ssh2';
 		$this->errors = new WP_Error();
@@ -152,12 +150,6 @@ class WP_Filesystem_SSH2 extends WP_Filesystem_Base {
 		return false;
 	}
 
-	function setDefaultPermissions($perm) {
-		$this->debug("setDefaultPermissions();");
-		if ( $perm )
-			$this->permission = $perm;
-	}
-
 	function get_contents($file, $type = '', $resumepos = 0 ) {
 		$file = ltrim($file, '/');
 		return file_get_contents('ssh2.sftp://' . $this->sftp_link . '/' . $file);
@@ -193,12 +185,18 @@ class WP_Filesystem_SSH2 extends WP_Filesystem_Base {
 	}
 
 	function chmod($file, $mode = false, $recursive = false) {
-		if( ! $mode )
-			$mode = $this->permission;
-		if( ! $mode )
-			return false;
 		if ( ! $this->exists($file) )
 			return false;
+
+		if ( ! $mode ) {
+			if ( $this->is_file($file) )
+				$mode = FS_CHMOD_FILE;
+			elseif ( $this->is_dir($file) )
+				$mode = FS_CHMOD_DIR;
+			else
+				return false;	
+		}
+
 		if ( ! $recursive || ! $this->is_dir($file) )
 			return $this->run_command(sprintf('chmod %o %s', $mode, escapeshellarg($file)), true);
 		return $this->run_command(sprintf('chmod -R %o %s', $mode, escapeshellarg($file)), true);
@@ -307,9 +305,10 @@ class WP_Filesystem_SSH2 extends WP_Filesystem_Base {
 		//Not implmented.
 	}
 
-	function mkdir($path, $chmod = null, $chown = false, $chgrp = false) {
+	function mkdir($path, $chmod = false, $chown = false, $chgrp = false) {
 		$path = untrailingslashit($path);
-		$chmod = !empty($chmod) ? $chmod : $this->permission;
+		if ( ! $chmod )
+			$chmod = FS_CHMOD_DIR;
 		if ( ! ssh2_sftp_mkdir($this->sftp_link, $path, $chmod, true) )
 			return false;
 		if ( $chown )