diff --git a/includes/bootstrap.inc b/includes/bootstrap.inc
index 30ab874..d9f5aa1 100644
--- a/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -1747,37 +1747,22 @@ function watchdog($type, $message, $variables = array(), $severity = WATCHDOG_NO
 }
 
 /**
- * Sets a message to display to the user.
+ * Sets a message which reflects the status of the performed operation.
  *
- * Messages are stored in a session variable and displayed in page.tpl.php via
- * the $messages theme variable.
+ * If the function is called with no arguments, this function returns all set
+ * messages without clearing them.
  *
- * Example usage:
- * @code
- * drupal_set_message(t('An error occurred and processing did not complete.'), 'error');
- * @endcode
- *
- * @param string $message
- *   (optional) The translated message to be displayed to the user. For
- *   consistency with other messages, it should begin with a capital letter and
- *   end with a period.
- * @param string $type
- *   (optional) The message's type. Defaults to 'status'. These values are
- *   supported:
+ * @param $message
+ *   The message to be displayed to the user. For consistency with other
+ *   messages, it should begin with a capital letter and end with a period.
+ * @param $type
+ *   The type of the message. One of the following values are possible:
  *   - 'status'
  *   - 'warning'
  *   - 'error'
- * @param bool $repeat
- *   (optional) If this is FALSE and the message is already set, then the
- *   message won't be repeated. Defaults to TRUE.
- *
- * @return array|null
- *   A multidimensional array with keys corresponding to the set message types.
- *   The indexed array values of each contain the set messages for that type.
- *   Or, if there are no messages set, the function returns NULL.
- *
- * @see drupal_get_messages()
- * @see theme_status_messages()
+ * @param $repeat
+ *   If this is FALSE and the message is already set, then the message won't
+ *   be repeated.
  */
 function drupal_set_message($message = NULL, $type = 'status', $repeat = TRUE) {
   if ($message) {
diff --git a/includes/filetransfer/filetransfer.inc b/includes/filetransfer/filetransfer.inc
index 230c0c5..ee12bcb 100644
--- a/includes/filetransfer/filetransfer.inc
+++ b/includes/filetransfer/filetransfer.inc
@@ -1,12 +1,12 @@
 <?php
 
-/*
+/**
  * @file
  * Defines a base file transfer class and associated classes.
  */
 
-/*
- * Defines a base file transer class.
+/**
+ * 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
@@ -47,8 +47,6 @@ abstract class FileTransfer {
   /**
    * Constructs a FileTransfer object.
    *
-   * This method is also called from the classes that extend this class and
-   * override this method.
    *
    * @param $jail
    *   The full path where all file operations performed by this object will
@@ -73,6 +71,8 @@ abstract class FileTransfer {
    *   An array of connection settings for the FileTransfer subclass. If the
    *   getSettingsForm() method uses any nested settings, the same structure
    *   will be assumed here.
+   * @return object
+   *   New instance of the appropriate FileTransfer subclass.
    *
    * @throws FileTransferException
    */
@@ -81,7 +81,7 @@ abstract class FileTransfer {
   }
 
   /**
-   * Implements the magic __get() method.
+   * Implements PHP 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
@@ -126,12 +126,12 @@ abstract class FileTransfer {
   }
 
   /**
-   * Changes the permissions of the file / directory specified.
+   * Changes the permissions of the file or directory specified.
    *
    * @param string $path
    *   The file / directory to change the permissions of.
    * @param long $mode
-   *   @see http://php.net/chmod
+   *   See the $mode argument from http://php.net/chmod.
    * @param bool $recursive
    *   Pass TRUE to recursively chmod the entire directory specified in $path.
    *
@@ -220,9 +220,8 @@ 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.
@@ -249,7 +248,7 @@ abstract class FileTransfer {
   * @param string $path
   *   The path to modify.
   *
-  * @return string
+  * @return string $path
   *   The modified path.
   */
   function sanitizePath($path) {
@@ -325,6 +324,8 @@ abstract class FileTransfer {
    *
    * @param $path
    *   The path to check.
+   *
+   * @return bool
    */
   abstract public function isDirectory($path);
 
@@ -333,6 +334,8 @@ abstract class FileTransfer {
    *
    * @param $path
    *   The path to check.
+   *
+   * @return bool
    */
   abstract public function isFile($path);
 
@@ -384,7 +387,7 @@ abstract class FileTransfer {
    * specific information they need, or override it entirely.
    *
    * @return
-   *   Array containing a form definition.
+   *   An array containing a form definition.
    */
   public function getSettingsForm() {
     $form['username'] = array(
@@ -452,7 +455,7 @@ class FileTransferException extends Exception {
 interface FileTransferChmodInterface {
 
   /**
-   * Changes the permissions of the file / directory specified in $path
+   * Changes the permissions of the file or directory specified in $path
    *
    * @param string $path
    *   Path to change permissions of.
diff --git a/includes/filetransfer/ftp.inc b/includes/filetransfer/ftp.inc
index 2591c72..b2c7d0a 100644
--- a/includes/filetransfer/ftp.inc
+++ b/includes/filetransfer/ftp.inc
@@ -24,10 +24,6 @@ abstract class FileTransferFTP extends FileTransfer {
   /**
    * Overrides FileTransfer::factory().
    *
-   * @return FileTransferFTP
-   *   The appropriate FileTransferFTP subclass based on the available
-   *   options. If the FTP PHP extension is available, use it.
-   *
    * @throws FileTransferException
    */
   static function factory($jail, $settings) {
@@ -190,9 +186,6 @@ 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, $filename));
diff --git a/includes/filetransfer/local.inc b/includes/filetransfer/local.inc
index 2c80a58..2da6a05 100644
--- a/includes/filetransfer/local.inc
+++ b/includes/filetransfer/local.inc
@@ -21,7 +21,7 @@ class FileTransferLocal extends FileTransfer implements FileTransferChmodInterfa
    * Overrides FileTransfer::factory().
    *
    * @return FileTransferLocal
-   *   Returns a FileTransferLocal object
+   *   Returns a FileTransferLocal object.
    */
   static function factory($jail, $settings) {
     return new FileTransferLocal($jail);
diff --git a/includes/filetransfer/ssh.inc b/includes/filetransfer/ssh.inc
index 8d44bb0..7bafd89 100644
--- a/includes/filetransfer/ssh.inc
+++ b/includes/filetransfer/ssh.inc
@@ -40,7 +40,7 @@ class FileTransferSSH extends FileTransfer implements FileTransferChmodInterface
    * Overrides FileTransfer::factory().
    *
    * @return FileTransferSSH
-   *   Returns a FileTransferSSH object
+   *   Returns a FileTransferSSH object.
    */
   static function factory($jail, $settings) {
     $username = empty($settings['username']) ? '' : $settings['username'];
@@ -114,6 +114,8 @@ class FileTransferSSH extends FileTransfer implements FileTransferChmodInterface
    *   TRUE if $path is a directory, FALSE if not.
    *
    * @throws FileTransferException
+   *
+   * @todo Need to test functionality of this.
    */
   public function isDirectory($path) {
     $directory = escapeshellarg($path);
diff --git a/modules/forum/forums.tpl.php b/modules/forum/forums.tpl.php
index 6a0e02e..01919ab 100644
--- a/modules/forum/forums.tpl.php
+++ b/modules/forum/forums.tpl.php
@@ -12,6 +12,7 @@
  * - $forums_defined: A flag to indicate that the forums are configured.
  *
  * @see template_preprocess_forums()
+ * @see theme_forums()
  *
  * @ingroup themeable
  */