Update core without moving core files out of the way.

The current implementation of updatecode drupal should work just fine with svn or bzr version control even if the core directory is not moved out of the way. The 'backup' version control could also be brought into line with code such as this:

+++ commands/pm/version_control/backup.inc	2 Apr 2010 00:23:12 -0000
@@ -10,7 +10,7 @@ class drush_pm_version_control_backup im
   /**
    * Implementation of pre_update().
    */
-  public function pre_update(&$project) {
+  public function pre_update(&$project, $items_to_test = array()) {
     $drupal_root = drush_get_context('DRUSH_DRUPAL_ROOT');
 
     // Save the date to be used in the backup directory's path name.
@@ -19,15 +19,34 @@ class drush_pm_version_control_backup im
     $backup_dir = drush_get_option('backup-dir', $drupal_root  . '/backup');
     $backup_dir = rtrim($backup_dir, '/');
     @drush_op('mkdir', $backup_dir, 0777);
-    $backup_dir .= '/modules';
-    @drush_op('mkdir', $backup_dir, 0777);
-    $backup_dir .= "/$date";
-    @drush_op('mkdir', $backup_dir, 0777);
-    $backup_target = $backup_dir . '/'. $project['name'];
-    // Save for rollback or notifications.
-    $project['backup_target'] = $backup_target;
-    if (!drush_op('rename', $project['full_project_path'], $backup_target)) {
-      return drush_set_error('DRUSH_PM_BACKUP_FAILED', dt('Failed to backup project directory !project to !backup_target', array('!project' => $project['full_project_path'], '!backup_target' => $backup_target)));
+    
+    // Special handling for updating core: move only some items to backup
+    if ($project['name'] == 'drupal') {
+      $backup_dir .= '/core';
+      @drush_op('mkdir', $backup_dir, 0777);
+      $backup_dir .= "/$date";
+      @drush_op('mkdir', $backup_dir, 0777);
+      $backup_target = $backup_dir . '/'. $project['name'];
+      @drush_op('mkdir', $backup_target, 0777);
+      // Save for rollback or notifications.
+      $project['backup_target'] = $backup_target;
+      foreach ($items_to_test as $item) {
+        if (!drush_op('rename', $project['full_project_path'] . '/' . $item, $backup_target)) {
+          return drush_set_error('DRUSH_PM_BACKUP_FAILED', dt('Failed to backup project directory !project to !backup_target', array('!project' => $project['full_project_path'], '!backup_target' => $backup_target)));
+        }
+      }
+    }
+    else {
+      $backup_dir .= '/modules';
+      @drush_op('mkdir', $backup_dir, 0777);
+      $backup_dir .= "/$date";
+      @drush_op('mkdir', $backup_dir, 0777);
+      $backup_target = $backup_dir . '/'. $project['name'];
+      // Save for rollback or notifications.
+      $project['backup_target'] = $backup_target;
+      if (!drush_op('rename', $project['full_project_path'], $backup_target)) {
+        return drush_set_error('DRUSH_PM_BACKUP_FAILED', dt('Failed to backup project directory !project to !backup_target', array('!project' => $project['full_project_path'], '!backup_target' => $backup_target)));
+      }
     }
     return TRUE;
   }
@@ -36,12 +55,24 @@ class drush_pm_version_control_backup im
    * Implementation of rollback().
    */
   public function rollback($project) {
-    if (drush_op('rename', $project['backup_target'], $project['full_project_path']) && is_dir($project['full_project_path'])) {
-      return drush_log(dt("Backups were restored successfully."), 'ok');
+    if (isset($project['backup_target'])) {
+      if ($project['name'] == 'drupal') {
+        $items_to_roll_back = drush_scan_directory($project['backup_target'], '/.*/', array('.', '..'), 0, FALSE, 'filename', 0, 0, TRUE);
+        foreach ($items_to_roll_back as $item) {
+          drush_op('rename', $project['backup_target'] . '/' . $item, $project['full_project_path']);
+        }
+        if (drush_op('rmdir', $project['backup_target'])) {
+          return drush_log(dt("Backups were restored successfully."), 'ok');
+        }
+      }
+      elseif (drush_op('rename', $project['backup_target'], $project['full_project_path']) && is_dir($project['full_project_path'])) {
+        return drush_log(dt("Backups were restored successfully."), 'ok');
+      }
+      return drush_set_error('DRUSH_PM_BACKUP_ROLLBACK_FAILED', dt('Could not restore backup and rollback from failed upgrade. You will need to resolve manually.'));
     }
-    return drush_set_error('DRUSH_PM_BACKUP_ROLLBACK_FAILED', dt('Could not restore backup and rollback from failed upgrade. You will need to resolve manually.'));
+    return TRUE;
   }

n.b. untested.

I tend to think that the current implementation works fairly well, and further improvements could wait until we're ready to refactor the pm code to fix this 'for real'. If the general consensus is that it would be an important improvement to avoid the move-out-of-the-way hack with a workaround similar to the above, then I could go ahead and see if I can make that work. Probably not too hard, but I also think there are bigger fish to fry right now...