Index: modules/comment/comment.install
===================================================================
RCS file: /cvs/drupal/drupal/modules/comment/comment.install,v
retrieving revision 1.57
diff -u -p -r1.57 comment.install
--- modules/comment/comment.install	11 Jan 2010 00:13:01 -0000	1.57
+++ modules/comment/comment.install	25 Jan 2010 07:14:30 -0000
@@ -247,6 +247,9 @@ function comment_update_7011() {
  * Create the comment_body field.
  */
 function comment_update_7012() {
+  // @todo Remove when http://drupal.org/node/211182 is fixed.
+  taxonomy_update_7002();
+
   // Create comment body field.
   $field = array(
     'field_name' => 'comment_body',
@@ -308,6 +311,13 @@ function comment_update_7013(&$sandbox) 
     db_insert($comment_body_table)
       ->from($query)
       ->execute();
+    // Update the comment body format in a similar manner as is done for other
+    // modules in filter_update_7005(), but we do this one here since we are
+    // already migrating the data.
+    db_update($comment_body_table)
+      ->fields(array('comment_body_format' => variable_get('filter_default_format', 1)))
+      ->condition('comment_body_format', 0)
+      ->execute();
 
     $sandbox['#finished'] = 1 - count($sandbox['types']) / $sandbox['total'];
   }
Index: modules/filter/filter.install
===================================================================
RCS file: /cvs/drupal/drupal/modules/filter/filter.install,v
retrieving revision 1.28
diff -u -p -r1.28 filter.install
--- modules/filter/filter.install	9 Jan 2010 22:07:56 -0000	1.28
+++ modules/filter/filter.install	25 Jan 2010 07:14:30 -0000
@@ -335,8 +335,9 @@ function filter_update_7005() {
   // using the default text format. Therefore, we have to convert all such
   // instances (in Drupal core) to explicitly use the appropriate format.
   // Note that the update of the node body field is handled separately, in
-  // node_update_7006().
-  foreach (array('block_custom', 'comment') as $table) {
+  // node_update_7006(), as is the update of the comment body field, in
+  // comment_update_7013().
+  foreach (array('block_custom') as $table) {
     if (db_table_exists($table)) {
       db_update($table)
         ->fields(array('format' => $default_format))
Index: modules/node/node.install
===================================================================
RCS file: /cvs/drupal/drupal/modules/node/node.install,v
retrieving revision 1.41
diff -u -p -r1.41 node.install
--- modules/node/node.install	24 Jan 2010 15:12:19 -0000	1.41
+++ modules/node/node.install	25 Jan 2010 07:14:30 -0000
@@ -437,6 +437,7 @@ function node_update_7005() {
  * Convert body and teaser from node properties to fields, and migrate status/comment/promote and sticky columns to the {node_revision} table.
  */
 function node_update_7006(&$context) {
+  // @todo Remove when http://drupal.org/node/211182 is fixed.
   taxonomy_update_7002();
 
   $context['#finished'] = 0;
Index: modules/system/system.install
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/system.install,v
retrieving revision 1.442
diff -u -p -r1.442 system.install
--- modules/system/system.install	13 Jan 2010 06:15:39 -0000	1.442
+++ modules/system/system.install	25 Jan 2010 07:14:30 -0000
@@ -2242,10 +2242,6 @@ function system_update_7026() {
  */
 function system_update_7027() {
   $module_list = array('text', 'number', 'list', 'options');
-  db_delete('system')
-    ->condition('type', 'module')
-    ->condition('name', $module_list)
-    ->execute();
   module_enable($module_list, FALSE);
 }