Index: pathauto.admin.inc
===================================================================
RCS file: /cvs/drupal-contrib/contributions/modules/pathauto/pathauto.admin.inc,v
retrieving revision 1.5
diff -u -p -r1.5 pathauto.admin.inc
--- pathauto.admin.inc	12 May 2008 12:15:33 -0000	1.5
+++ pathauto.admin.inc	15 May 2008 21:22:55 -0000
@@ -1,9 +1,10 @@
 <?php
 // $Id: pathauto.admin.inc,v 1.5 2008/05/12 12:15:33 freso Exp $
-
 /**
  * @file
  * Functions for Pathauto's admin pages.
+ *
+ * @ingroup pathauto
  */
 
 /**
@@ -291,7 +292,13 @@ function pathauto_admin_settings() {
 /**
  * Helper function to see if they are using all -raw tokens available
  *
- * Returns a status flag if there is an error or not
+ * @param $pattern
+ *   TODO: What does this do?
+ * @param $type
+ *   A flag indicating the class of substitution tokens to use.
+ * @return
+ *   A status flag, telling whether there is an error or not.
+ * @see function token_get_list for more information on the $type parameter.
  */
 function _pathauto_check_pattern($pattern, $type) {
   // Hold items we've warned about so we only warn once per token
@@ -342,6 +349,9 @@ function _pathauto_check_pattern($patter
   return $return;
 }
 
+/**
+ * Validate Pathauto's admin settings form data.
+ */
 function pathauto_admin_settings_validate($form, &$form_state) {
   // Validate that the separator is not set to be removed per http://drupal.org/node/184119
   // This isn't really all that bad so warn, but still allow them to save the value.
Index: pathauto.inc
===================================================================
RCS file: /cvs/drupal-contrib/contributions/modules/pathauto/pathauto.inc,v
retrieving revision 1.36
diff -u -p -r1.36 pathauto.inc
--- pathauto.inc	15 May 2008 18:33:57 -0000	1.36
+++ pathauto.inc	15 May 2008 21:22:55 -0000
@@ -1,5 +1,11 @@
 <?php
 // $Id: pathauto.inc,v 1.36 2008/05/15 18:33:57 freso Exp $
+/**
+ * @file
+ * Miscellaneous functions for Pathauto
+ *
+ * @ingroup pathauto
+ */
 
 /**
  * Copied from search.module's PREG_CLASS_SEARCH_EXCLUDE
@@ -47,14 +53,16 @@ define('PREG_CLASS_ALNUM',
 
 
 /**
- * Check to see if there is already an alias pointing to a different item
+ * Check to see if there is already an alias pointing to a different item.
  *
  * @param $alias
  *   A string alias (i.e. dst).
  * @param $src
  *   A string that is the internal path.
- * @param $lang
+ * @param $language
  *   A string indicating the path's language.
+ * @return
+ *   TRUE if an alias exists, FALSE if not.
  */
 function _pathauto_alias_exists($alias, $src, $language = '') {
   $alias_pid = db_result(db_query_range("SELECT pid FROM {url_alias} WHERE dst = '%s' AND src <> '%s' AND language = '%s'", array($alias, $src, $language), 0, 1));
@@ -74,6 +82,9 @@ function _pathauto_alias_exists($alias, 
  *
  * @param string $src
  *   A string that is the internal path
+ * @return
+ *    An array with the keys "pid" and "old_alias" containing the "pid" and old
+ *    "alias", respectively, of the old alias.
  */
 function _pathauto_existing_alias_data($src) {
   $output = array(
@@ -107,6 +118,10 @@ function _pathauto_existing_alias_data($
  *
  * @param $string
  *   A string to clean.
+ * @param $clean_slash
+ *   Whether to clean slashsed from the given string.
+ * @return
+ *   The cleaned string.
  */
 function pathauto_cleanstring($string, $clean_slash = TRUE) {
   // Default words to ignore
@@ -196,7 +211,7 @@ function pathauto_cleanstring($string, $
 }
 
 /**
- * Apply patterns to create an alias
+ * Apply patterns to create an alias.
  *
  * @param $module
  *   The name of your module (e.g., 'node')
@@ -216,7 +231,7 @@ function pathauto_cleanstring($string, $
  * @param $language
  *   A string specify the path's language.
  * @return
- *   The alias that was created
+ *   The alias that was created.
  */
 function pathauto_create_alias($module, $op, $placeholders, $src, $entity_id, $type = NULL, $language = '') {
   if (($op != 'bulkupdate') and variable_get('pathauto_verbose', FALSE) && user_access('notify of path changes')) {
@@ -426,8 +441,10 @@ function pathauto_get_placeholders($type
 /**
  * Cleans tokens so they are URL friendly
  *
- * @param $values
+ * @param $full
  *   An array of token values that need to be "cleaned" for use in the URL.
+ * @return
+ *   TODO: $full->values == ?
  */
 function pathauto_clean_token_values($full) {
   foreach ($full->values as $key => $value) {
@@ -443,9 +460,15 @@ function pathauto_clean_token_values($fu
 }
 
 /**
- * Returns an array of arrays for punctuation values keyed by a name
- *   including the value and a textual description
- *   Can and should be expanded to include "all" non text punctuation values
+ * Returns an array of arrays for punctuation values.
+ * 
+ * Returns an array of arrays for punctuation values keyed by a name, including
+ * the value and a textual description.
+ * Can and should be expanded to include "all" non text punctuation values.
+ *
+ * @return
+ *   An array of arrays for punctuation values keyed by a name, including the
+ *   value and a textual description.
  */
 function pathauto_punctuation_chars() {
   $punctuation = array();
Index: pathauto.install
===================================================================
RCS file: /cvs/drupal-contrib/contributions/modules/pathauto/pathauto.install,v
retrieving revision 1.11
diff -u -p -r1.11 pathauto.install
--- pathauto.install	10 May 2008 20:27:59 -0000	1.11
+++ pathauto.install	15 May 2008 21:23:00 -0000
@@ -1,8 +1,10 @@
 <?php
 // $Id: pathauto.install,v 1.11 2008/05/10 20:27:59 freso Exp $
-
 /**
- * @file Provides install, updated, and uninstall functions for pathauto.
+ * @file
+ * Provides install, update, and uninstall functions for Pathauto.
+ *
+ * @ingroup pathauto
  */
 
 /**
Index: pathauto.module
===================================================================
RCS file: /cvs/drupal-contrib/contributions/modules/pathauto/pathauto.module,v
retrieving revision 1.107
diff -u -p -r1.107 pathauto.module
--- pathauto.module	10 May 2008 20:27:59 -0000	1.107
+++ pathauto.module	15 May 2008 21:23:00 -0000
@@ -1,8 +1,24 @@
 <?php
 // $Id: pathauto.module,v 1.107 2008/05/10 20:27:59 freso Exp $
+/**
+ * @defgroup pathauto Pathauto: Automatically generates aliases for content
+ *
+ * The Pathauto module automatically generates path aliases for various kinds of
+ * content (nodes, categories, users) without requiring the user to manually
+ * specify the path alias. This allows you to get aliases like
+ * /category/my-node-title.html instead of /node/123. The aliases are based upon
+ * a "pattern" system which the administrator can control.
+ */
 
 /**
- * Implementation of hook_help
+ * @file
+ * TODO: Describe this the main file of Pathauto.
+ *
+ * @ingroup pathauto
+ */
+
+/**
+ * Implementation of hook_help().
  */
 function pathauto_help($path, $arg) {
   switch ($path) {
@@ -26,14 +42,14 @@ function pathauto_help($path, $arg) {
 }
 
 /**
- * Implementation of hook_perm
+ * Implementation of hook_perm().
  */
 function pathauto_perm() {
   return array('administer pathauto', 'notify of path changes');
 }
 
-/*
- * Implementation of hook_menu
+/**
+ * Implementation of hook_menu().
  */
 function pathauto_menu() {
   $items['admin/build/path/pathauto'] = array(
@@ -158,6 +174,9 @@ function pathauto_token_list($type = 'al
   return $tokens;
 }
 
+/**
+ * TODO: What does this do? One-line description.
+ */
 function pathauto_path_alias_types() {
   $objects = array('user/' => t('users'), 'node/' => t('content'));
   if (module_exists('blog')) {
@@ -293,6 +312,9 @@ function pathauto_node_operations() {
 
 /**
  * Callback function for updating node aliases.
+ *
+ * @param $nodes
+ *   TODO: What exactly is this and what is being done with it?
  */
 function pathauto_node_operations_update($nodes) {
   foreach ($nodes as $nid) {
Index: pathauto_node.inc
===================================================================
RCS file: /cvs/drupal-contrib/contributions/modules/pathauto/pathauto_node.inc,v
retrieving revision 1.42
diff -u -p -r1.42 pathauto_node.inc
--- pathauto_node.inc	10 May 2008 20:27:59 -0000	1.42
+++ pathauto_node.inc	15 May 2008 21:23:00 -0000
@@ -1,8 +1,14 @@
 <?php
 // $Id: pathauto_node.inc,v 1.42 2008/05/10 20:27:59 freso Exp $
+/**
+ * @file
+ * Node hooked into Pathauto. (TODO: Better description!)
+ *
+ * @ingroup pathauto
+ */
 
-/*
- * Implementation of hook_pathauto()
+/**
+ * Implementation of hook_pathauto().
  */
 function node_pathauto($op) {
   switch ($op) {
Index: pathauto_user.inc
===================================================================
RCS file: /cvs/drupal-contrib/contributions/modules/pathauto/pathauto_user.inc,v
retrieving revision 1.26
diff -u -p -r1.26 pathauto_user.inc
--- pathauto_user.inc	10 May 2008 20:27:59 -0000	1.26
+++ pathauto_user.inc	15 May 2008 21:23:00 -0000
@@ -1,8 +1,14 @@
 <?php
 // $Id: pathauto_user.inc,v 1.26 2008/05/10 20:27:59 freso Exp $
+/**
+ * @file
+ * User hooked into Pathauto. (TODO: Better description!)
+ *
+ * @ingroup pathauto
+ */
 
 /**
- * Implementation of hook_pathauto() for user aliases
+ * Implementation of hook_pathauto() for user aliases.
  */
 function user_pathauto($op) {
   switch ($op) {
@@ -31,7 +37,7 @@ function user_pathauto($op) {
 }
 
 /**
- * Implementation of hook_pathauto() for blog aliases
+ * Implementation of hook_pathauto() for blog aliases.
  */
 function blog_pathauto($op) {
   switch ($op) {
@@ -56,7 +62,7 @@ function blog_pathauto($op) {
 }
 
 /**
- * Implementation of hook_pathauto() for user-tracker aliases
+ * Implementation of hook_pathauto() for user-tracker aliases.
  */
 function tracker_pathauto($op) {
   switch ($op) {
@@ -81,7 +87,7 @@ function tracker_pathauto($op) {
 }
 
 /**
- * Bulk generate aliases for all users without aliases
+ * Bulk generate aliases for all users without aliases.
  */
 function user_pathauto_bulkupdate() {
   $query = "SELECT uid, name, src, dst FROM {users} LEFT JOIN {url_alias} ON CONCAT('user/', CAST(uid AS CHAR)) = src WHERE uid > 0 AND src IS NULL";
@@ -104,7 +110,7 @@ function user_pathauto_bulkupdate() {
 
 
 /**
- * Bulk generate aliases for all blogs without aliases
+ * Bulk generate aliases for all blogs without aliases.
  */
 function blog_pathauto_bulkupdate() {
   $query = "SELECT uid, name, src, dst FROM {users} LEFT JOIN {url_alias} ON CONCAT('blog/', CAST(uid AS CHAR)) = src WHERE uid > 0 AND src IS NULL";
@@ -126,7 +132,7 @@ function blog_pathauto_bulkupdate() {
 }
 
 /**
- * Bulk generate aliases for user trackers without aliases
+ * Bulk generate aliases for user trackers without aliases.
  */
 function tracker_pathauto_bulkupdate() {
   // We do the double CONCAT because Pgsql8.1 doesn't support more than three arguments to CONCAT