diff --git a/includes/common.inc b/includes/common.inc
index f153066..ce08390 100644
--- a/includes/common.inc
+++ b/includes/common.inc
@@ -2821,7 +2821,7 @@ function drupal_add_html_head_link($attributes, $header = FALSE) {
  *   - 'group': A number identifying the group in which to add the stylesheet.
  *     Available constants are:
  *     - CSS_SYSTEM: Any system-layer CSS.
- *     - CSS_DEFAULT: (default) Any module-layer CSS.
+ *     - CSS_DEFAULT: Any module-layer CSS.
  *     - CSS_THEME: Any theme-layer CSS.
  *     The group number serves as a weight: the markup for loading a stylesheet
  *     within a lower weight group is output to the page before the markup for
diff --git a/includes/filetransfer/filetransfer.inc b/includes/filetransfer/filetransfer.inc
index bd2057c..807b598 100644
--- a/includes/filetransfer/filetransfer.inc
+++ b/includes/filetransfer/filetransfer.inc
@@ -1,7 +1,12 @@
 <?php
 
-/*
- * Base FileTransfer class.
+/**
+ * @file
+ * Defines a base file transfer class and associated classes.
+ */
+
+/**
+ * Defines a base file transfer class.
  *
  * Classes extending this class perform file operations on directories not
  * writable by the webserver. To achieve this, the class should connect back
@@ -10,21 +15,53 @@
  * safety, all methods operate only inside a "jail", by default the Drupal root.
  */
 abstract class FileTransfer {
+
+  /**
+   * The username for this file transfer.
+   *
+   * @var string
+   */
   protected $username;
+
+  /**
+   * The password for this file transfer.
+   *
+   * @var string
+   */
   protected $password;
+
+  /**
+   * The hostname for this file transfer.
+   *
+   * @var string
+   */
   protected $hostname = 'localhost';
+
+  /**
+   * The port for this file transfer.
+   *
+   * @var int
+   */
   protected $port;
 
   /**
-   * The constructor for the UpdateConnection class. This method is also called
-   * from the classes that extend this class and override this method.
+   * Constructs a FileTransfer object.
+   *
+   *
+   * @param $jail
+   *   The full path where all file operations performed by this object will
+   *   be restricted to. This prevents the FileTransfer classes from being
+   *   able to touch other parts of the filesystem.
    */
   function __construct($jail) {
     $this->jail = $jail;
   }
 
   /**
+   * Defines a factory method for this class.
+   *
    * Classes that extend this class must override the factory() static method.
+   * They should return a new instance of the appropriate FileTransfer subclass.
    *
    * @param string $jail
    *   The full path where all file operations performed by this object will
@@ -36,17 +73,24 @@ abstract class FileTransfer {
    *   will be assumed here.
    * @return object
    *   New instance of the appropriate FileTransfer subclass.
+   * @throws FileTransferException
    */
   static function factory($jail, $settings) {
     throw new FileTransferException('FileTransfer::factory() static method not overridden by FileTransfer subclass.');
   }
 
   /**
-   * Implementation of the magic __get() method.
+   * Implements the magic __get() method.
+   *
+   * If the connection isn't set to anything, this will call the connect()
+   * method and return the result; afterwards, the connection will be returned
+   * directly without using this method.
    *
-   * If the connection isn't set to anything, this will call the connect() method
-   * and set it to and return the result; afterwards, the connection will be
-   * returned directly without using this method.
+   * @param $name
+   *   The name of the variable to return.
+   *
+   * @return
+   *   The variable specified in $name.
    */
   function __get($name) {
     if ($name == 'connection') {
@@ -81,11 +125,18 @@ abstract class FileTransfer {
   }
 
   /**
-   * @see http://php.net/chmod
+   * Changes the permissions of the file / directory specified.
    *
    * @param string $path
+   *   The file / directory to change the permissions of.
    * @param long $mode
+   *   @see http://php.net/chmod
    * @param bool $recursive
+   *   Pass TRUE to recursively chmod the entire directory specified in $path.
+   *
+   * @throws FileTransferException
+   *
+   * @see http://php.net/chmod
    */
   public final function chmod($path, $mode, $recursive = FALSE) {
     if (!in_array('FileTransferChmodInterface', class_implements(get_class($this)))) {
@@ -153,6 +204,8 @@ abstract class FileTransfer {
    *
    * @param $path
    *   A path to check against the jail.
+   *
+   * @throws FileTransferException
    */
   protected final function checkPath($path) {
     $full_jail = $this->chroot . $this->jail;
@@ -165,14 +218,17 @@ abstract class FileTransfer {
 
   /**
    * Returns a modified path suitable for passing to the server.
-   * If a path is a windows path, makes it POSIX compliant by removing the drive letter.
-   * If $this->chroot has a value, it is stripped from the path to allow for
-   * chroot'd filetransfer systems.
+   *
+   * If a path is a Windows path, makes it POSIX compliant by removing the drive
+   * letter.
    *
    * @param $path
+   *   The path to modify.
    * @param $strip_chroot
+   *   Whether to remove the path in $this->chroot.
    *
    * @return string
+   *   The modified path.
    */
   protected final function fixRemotePath($path, $strip_chroot = TRUE) {
     $path = $this->sanitizePath($path);
@@ -189,7 +245,10 @@ abstract class FileTransfer {
   * Changes backslashes to slashes, also removes a trailing slash.
   *
   * @param string $path
+  *   The path to modify.
+  *
   * @return string
+  *   The modified path.
   */
   function sanitizePath($path) {
     $path = str_replace('\\', '/', $path); // Windows path sanitization.
@@ -202,7 +261,7 @@ abstract class FileTransfer {
   /**
    * Copies a directory.
    *
-   * We need a separate method to make the $destination is in the jail.
+   * We need a separate method to make sure that $destination is in the jail.
    *
    * @param $source
    *   The source path.
@@ -260,11 +319,10 @@ abstract class FileTransfer {
   abstract protected function removeFileJailed($destination);
 
   /**
-   * Checks if a particular path is a directory
+   * Checks if a particular path is a directory.
    *
    * @param $path
-   *   The path to check
-   *
+   *   The path to check.
    * @return boolean
    */
   abstract public function isDirectory($path);
@@ -273,8 +331,7 @@ abstract class FileTransfer {
    * Checks if a particular path is a file (not a directory).
    *
    * @param $path
-   *   The path to check
-   *
+   *   The path to check.
    * @return boolean
    */
   abstract public function isFile($path);
@@ -286,7 +343,7 @@ abstract class FileTransfer {
    * it will return the chroot, otherwise FALSE.
    *
    * @return
-   *   The chroot path for this connection or FALSE.
+   *   The chroot path for this connection, or FALSE.
    */
   function findChroot() {
     // If the file exists as is, there is no chroot.
@@ -312,7 +369,7 @@ abstract class FileTransfer {
   }
 
   /**
-   * Sets the chroot and changes the jail to match the correct path scheme
+   * Sets the chroot and changes the jail to match the correct path scheme.
    *
    */
   function setChroot() {
@@ -325,6 +382,9 @@ abstract class FileTransfer {
    *
    * Implementing classes can either extend this form with fields collecting the
    * specific information they need, or override it entirely.
+   *
+   * @return
+   *   Array containing a form definition.
    */
   public function getSettingsForm() {
     $form['username'] = array(
@@ -358,11 +418,27 @@ abstract class FileTransfer {
 }
 
 /**
- * FileTransferException class.
+ * Defines an exception class for file transfers.
  */
 class FileTransferException extends Exception {
+
+  /**
+   * Arguments to be used in this exception.
+   *
+   * @var array
+   */
   public $arguments;
 
+  /**
+   * Constructs a FileTransferException object.
+   *
+   * @param $message
+   *   Exception message.
+   * @param $code
+   *   Exception code.
+   * @param $arguments
+   *   Arguments to be used in this exception.
+   */
   function __construct($message, $code = 0, $arguments = array()) {
     parent::__construct($message, $code);
     $this->arguments = $arguments;
@@ -371,7 +447,7 @@ class FileTransferException extends Exception {
 
 
 /**
- * A FileTransfer Class implementing this interface can be used to chmod files.
+ * Defines an interface to chmod files.
  */
 interface FileTransferChmodInterface {
 
@@ -382,7 +458,7 @@ interface FileTransferChmodInterface {
    *   Path to change permissions of.
    * @param long $mode
    *   @see http://php.net/chmod
-   * @param boolean $recursive
+   * @param bool $recursive
    *   Pass TRUE to recursively chmod the entire directory specified in $path.
    */
   function chmodJailed($path, $mode, $recursive);
@@ -399,7 +475,7 @@ interface FileTransferChmodInterface {
  */
 class SkipDotsRecursiveDirectoryIterator extends RecursiveDirectoryIterator {
   /**
-   * Constructs a SkipDotsRecursiveDirectoryIterator
+   * Constructs a SkipDotsRecursiveDirectoryIterator object.
    *
    * @param $path
    *   The path of the directory to be iterated over.
@@ -408,6 +484,11 @@ class SkipDotsRecursiveDirectoryIterator extends RecursiveDirectoryIterator {
     parent::__construct($path);
   }
 
+  /**
+   * Overrides RecursiveDirectoryIterator::next().
+   *
+   * Keeps calling parent::next() until a directory is found that isn't . or ..
+   */
   function next() {
     parent::next();
     while ($this->isDot()) {
diff --git a/includes/filetransfer/ftp.inc b/includes/filetransfer/ftp.inc
index 838dc7c..4c66247 100644
--- a/includes/filetransfer/ftp.inc
+++ b/includes/filetransfer/ftp.inc
@@ -1,10 +1,18 @@
 <?php
 
 /**
- * Base class for FTP implementations.
+ * @file
+ * Defines classes and functions relating to FTP file transfers.
+ */
+
+/**
+ * Defines a base class for FTP implementations.
  */
 abstract class FileTransferFTP extends FileTransfer {
 
+  /**
+   * Constructs a FileTransferFTP object.
+   */
   public function __construct($jail, $username, $password, $hostname, $port) {
     $this->username = $username;
     $this->password = $password;
@@ -14,13 +22,13 @@ abstract class FileTransferFTP extends FileTransfer {
   }
 
   /**
-   * Return an object which can implement the FTP protocol.
+   * Overrides FileTransfer::factory().
    *
-   * @param string $jail
-   * @param array $settings
    * @return FileTransferFTP
    *   The appropriate FileTransferFTP subclass based on the available
    *   options. If the FTP PHP extension is available, use it.
+   *
+   * @throws FileTransferException
    */
   static function factory($jail, $settings) {
     $username = empty($settings['username']) ? '' : $settings['username'];
@@ -39,7 +47,7 @@ abstract class FileTransferFTP extends FileTransfer {
   }
 
   /**
-   * Returns the form to configure the FileTransfer class for FTP.
+   * Overrides FileTransfer::getSettingsForm().
    */
   public function getSettingsForm() {
     $form = parent::getSettingsForm();
@@ -48,8 +56,16 @@ abstract class FileTransferFTP extends FileTransfer {
   }
 }
 
+/**
+ * Defines a file transfer class using the PHP FTP extension.
+ */
 class FileTransferFTPExtension extends FileTransferFTP implements FileTransferChmodInterface {
 
+  /**
+   * Overrides FileTransferFTP::connect().
+   *
+   * @throws FileTransferException
+   */
   public function connect() {
     $this->connection = ftp_connect($this->hostname, $this->port);
 
@@ -61,18 +77,33 @@ class FileTransferFTPExtension extends FileTransferFTP implements FileTransferCh
     }
   }
 
+  /**
+   * Overrides FileTransferFTP::copyFileJailed().
+   *
+   * @throws FileTransferException
+   */
   protected function copyFileJailed($source, $destination) {
     if (!@ftp_put($this->connection,  $destination, $source, FTP_BINARY)) {
       throw new FileTransferException("Cannot move @source to @destination", NULL, array("@source" => $source, "@destination" => $destination));
     }
   }
 
+  /**
+   * Overrides FileTransferFTP::createDirectoryJailed().
+   *
+   * @throws FileTransferException
+   */
   protected function createDirectoryJailed($directory) {
     if (!ftp_mkdir($this->connection, $directory)) {
       throw new FileTransferException("Cannot create directory @directory", NULL, array("@directory" => $directory));
     }
   }
 
+  /**
+   * Overrides FileTransferFTP::removeDirectoryJailed().
+   *
+   * @throws FileTransferException
+   */
   protected function removeDirectoryJailed($directory) {
     $pwd = ftp_pwd($this->connection);
     if (!ftp_chdir($this->connection, $directory)) {
@@ -100,12 +131,23 @@ class FileTransferFTPExtension extends FileTransferFTP implements FileTransferCh
     }
   }
 
+  /**
+   * Overrides FileTransferFTP::removeFileJailed().
+   *
+   * @throws FileTransferException
+   */
   protected function removeFileJailed($destination) {
     if (!ftp_delete($this->connection, $destination)) {
       throw new FileTransferException("Unable to remove to file @file", NULL, array('@file' => $destination));
     }
   }
 
+  /**
+   * Overrides FileTransferFTP::isDirectory().
+   *
+   * @return
+   *   TRUE if $path is a directory, FALSE if not.
+   */
   public function isDirectory($path) {
     $result = FALSE;
     $curr = ftp_pwd($this->connection);
@@ -116,10 +158,21 @@ class FileTransferFTPExtension extends FileTransferFTP implements FileTransferCh
     return $result;
   }
 
+  /**
+   * Overrides FileTransferFTP::isFile().
+   *
+   * @return
+   *   TRUE if $path is a file, FALSE if not.
+   */
   public function isFile($path) {
     return ftp_size($this->connection, $path) != -1;
   }
 
+  /**
+   * Implements FileTransferChmodInterface::chmodJailed().
+   *
+   * @throws FileTransferException
+   */
   function chmodJailed($path, $mode, $recursive) {
     if (!ftp_chmod($this->connection, $mode, $path)) {
       throw new FileTransferException("Unable to set permissions on %file", NULL, array ('%file' => $path));
@@ -137,6 +190,9 @@ class FileTransferFTPExtension extends FileTransferFTP implements FileTransferCh
   }
 }
 
+
+  // Changes the permissions of the file / directory using an FTP SITE command.
+ 
 if (!function_exists('ftp_chmod')) {
   function ftp_chmod($ftp_stream, $mode, $filename) {
     return ftp_site($ftp_stream, sprintf('CHMOD %o %s', $mode, $filename));
diff --git a/includes/filetransfer/local.inc b/includes/filetransfer/local.inc
index b125989..2da6a05 100644
--- a/includes/filetransfer/local.inc
+++ b/includes/filetransfer/local.inc
@@ -1,30 +1,59 @@
 <?php
 
 /**
- * The local connection class for copying files as the httpd user.
+ * @file
+ * Defines classes and functions relating to local file transfers.
+ */
+
+/**
+ * Defines the local connection class for copying files as the httpd user.
  */
 class FileTransferLocal extends FileTransfer implements FileTransferChmodInterface {
 
+  /**
+   * Overrides FileTransfer::connect().
+   */
   function connect() {
     // No-op
   }
 
+  /**
+   * Overrides FileTransfer::factory().
+   *
+   * @return FileTransferLocal
+   *   Returns a FileTransferLocal object.
+   */
   static function factory($jail, $settings) {
     return new FileTransferLocal($jail);
   }
 
+  /**
+   * Overrides FileTransfer::copyFileJailed().
+   *
+   * @throws FileTransferException
+   */
   protected function copyFileJailed($source, $destination) {
     if (@!copy($source, $destination)) {
       throw new FileTransferException('Cannot copy %source to %destination.', NULL, array('%source' => $source, '%destination' => $destination));
     }
   }
 
+  /**
+   * Overrides FileTransfer::createDirectoryJailed().
+   *
+   * @throws FileTransferException
+   */
   protected function createDirectoryJailed($directory) {
     if (!is_dir($directory) && @!mkdir($directory, 0777, TRUE)) {
       throw new FileTransferException('Cannot create directory %directory.', NULL, array('%directory' => $directory));
     }
   }
 
+  /**
+   * Overrides FileTransfer::removeDirectoryJailed().
+   *
+   * @throws FileTransferException
+   */
   protected function removeDirectoryJailed($directory) {
     if (!is_dir($directory)) {
       // Programmer error assertion, not something we expect users to see.
@@ -47,20 +76,42 @@ class FileTransferLocal extends FileTransfer implements FileTransferChmodInterfa
     }
   }
 
+  /**
+   * Overrides FileTransfer::removeFileJailed().
+   *
+   * @throws FileTransferException
+   */
   protected function removeFileJailed($file) {
     if (@!drupal_unlink($file)) {
       throw new FileTransferException('Cannot remove file %file.', NULL, array('%file' => $file));
     }
   }
 
+  /**
+   * Overrides FileTransfer::isDirectory().
+   *
+   * @return
+   *   TRUE if $path is a directory, FALSE if not.
+   */
   public function isDirectory($path) {
     return is_dir($path);
   }
 
+  /**
+   * Overrides FileTransfer::isFile().
+   *
+   * @return
+   *   TRUE if $path is a file, FALSE if not.
+   */
   public function isFile($path) {
     return is_file($path);
   }
 
+  /**
+   * Implements FileTransferChmodInterface::chmodJailed().
+   *
+   * @throws FileTransferException
+   */
   public function chmodJailed($path, $mode, $recursive) {
     if ($recursive && is_dir($path)) {
       foreach (new RecursiveIteratorIterator(new SkipDotsRecursiveDirectoryIterator($path), RecursiveIteratorIterator::SELF_FIRST) as $filename => $file) {
diff --git a/includes/filetransfer/ssh.inc b/includes/filetransfer/ssh.inc
index 43ec324..8d44bb0 100644
--- a/includes/filetransfer/ssh.inc
+++ b/includes/filetransfer/ssh.inc
@@ -1,10 +1,18 @@
 <?php
 
 /**
- * The SSH connection class for the update module.
+ * @file
+ * Defines classes and functions relating to SSH file transfers.
+ */
+
+/**
+ * Defines the SSH connection class for the update module.
  */
 class FileTransferSSH extends FileTransfer implements FileTransferChmodInterface {
 
+  /**
+   * Constructs a FileTransferSSH object.
+   */
   function __construct($jail, $username, $password, $hostname = "localhost", $port = 22) {
     $this->username = $username;
     $this->password = $password;
@@ -13,6 +21,11 @@ class FileTransferSSH extends FileTransfer implements FileTransferChmodInterface
     parent::__construct($jail);
   }
 
+  /**
+   * Overrides FileTransfer::connect().
+   *
+   * @throws FileTransferException
+   */
   function connect() {
     $this->connection = @ssh2_connect($this->hostname, $this->port);
     if (!$this->connection) {
@@ -23,6 +36,12 @@ class FileTransferSSH extends FileTransfer implements FileTransferChmodInterface
     }
   }
 
+  /**
+   * Overrides FileTransfer::factory().
+   *
+   * @return FileTransferSSH
+   *   Returns a FileTransferSSH object
+   */
   static function factory($jail, $settings) {
     $username = empty($settings['username']) ? '' : $settings['username'];
     $password = empty($settings['password']) ? '' : $settings['password'];
@@ -31,30 +50,55 @@ class FileTransferSSH extends FileTransfer implements FileTransferChmodInterface
     return new FileTransferSSH($jail, $username, $password, $hostname, $port);
   }
 
+  /**
+   * Overrides FileTransfer::copyFileJailed().
+   *
+   * @throws FileTransferException
+   */
   protected function copyFileJailed($source, $destination) {
     if (!@ssh2_scp_send($this->connection, $source, $destination)) {
       throw new FileTransferException('Cannot copy @source_file to @destination_file.', NULL, array('@source' => $source, '@destination' => $destination));
     }
   }
 
+  /**
+   * Overrides FileTransfer::copyDirectoryJailed().
+   *
+   * @throws FileTransferException
+   */
   protected function copyDirectoryJailed($source, $destination) {
     if (@!ssh2_exec($this->connection, 'cp -Rp ' . escapeshellarg($source) . ' ' . escapeshellarg($destination))) {
       throw new FileTransferException('Cannot copy directory @directory.', NULL, array('@directory' => $source));
     }
   }
 
+  /**
+   * Overrides FileTransfer::createDirectoryJailed().
+   *
+   * @throws FileTransferException
+   */
   protected function createDirectoryJailed($directory) {
     if (@!ssh2_exec($this->connection, 'mkdir ' . escapeshellarg($directory))) {
       throw new FileTransferException('Cannot create directory @directory.', NULL, array('@directory' => $directory));
     }
   }
 
+  /**
+   * Overrides FileTransfer::removeDirectoryJailed().
+   *
+   * @throws FileTransferException
+   */
   protected function removeDirectoryJailed($directory) {
     if (@!ssh2_exec($this->connection, 'rm -Rf ' . escapeshellarg($directory))) {
       throw new FileTransferException('Cannot remove @directory.', NULL, array('@directory' => $directory));
     }
   }
 
+  /**
+   * Overrides FileTransfer::removeFileJailed().
+   *
+   * @throws FileTransferException
+   */
   protected function removeFileJailed($destination) {
     if (!@ssh2_exec($this->connection, 'rm ' . escapeshellarg($destination))) {
       throw new FileTransferException('Cannot remove @directory.', NULL, array('@directory' => $destination));
@@ -62,7 +106,14 @@ class FileTransferSSH extends FileTransfer implements FileTransferChmodInterface
   }
 
   /**
-   * WARNING: This is untested.  It is not currently used, but should do the trick.
+   * Overrides FileTransfer::isDirectory().
+   *
+   * WARNING: This is untested. It's not currently used, but should work.
+   *
+   * @return
+   *   TRUE if $path is a directory, FALSE if not.
+   *
+   * @throws FileTransferException
    */
   public function isDirectory($path) {
     $directory = escapeshellarg($path);
@@ -77,6 +128,14 @@ class FileTransferSSH extends FileTransfer implements FileTransferChmodInterface
     }
   }
 
+  /**
+   * Overrides FileTransfer::isFile().
+   *
+   * @return
+   *   TRUE if $path is a directory, FALSE if not.
+   *
+   * @throws FileTransferException
+   */
   public function isFile($path) {
     $file = escapeshellarg($path);
     $cmd = "[ -f {$file} ] && echo 'yes'";
@@ -90,6 +149,11 @@ class FileTransferSSH extends FileTransfer implements FileTransferChmodInterface
     }
   }
 
+  /**
+   * Implements FileTransferChmodInterface::chmodJailed().
+   *
+   * @throws FileTransferException
+   */
   function chmodJailed($path, $mode, $recursive) {
     $cmd = sprintf("chmod %s%o %s", $recursive ? '-R ' : '', $mode, escapeshellarg($path));
     if (@!ssh2_exec($this->connection, $cmd)) {
@@ -98,7 +162,7 @@ class FileTransferSSH extends FileTransfer implements FileTransferChmodInterface
   }
 
   /**
-   * Returns the form to configure the FileTransfer class for SSH.
+   * Overrides FileTransfer::getSettingsForm().
    */
   public function getSettingsForm() {
     $form = parent::getSettingsForm();