Google Analytics 7.x-2.0.
LoginToboggan 7.x-1.4
Metatag 7.x-1.0-rc1

After running these update functions, you'll need to manually disable the Metatag: Facebook module if it's not needed for the current site.
Stage File Proxy 7.x-1.6

The configuration for this module is now handled via the interface, and the variables are stored in the database.

Run update.php to ensure that the current settings are copied to the database, then remove the configuration from settings.site.php manually.
Removed the settings.site.php.default file.

Since this file only contains configuration for Stage File Proxy, which isn't needed anymore, there's no reason to include a default file for these type of settings.

It's still possible to create one if needed though, as it will be included if it exists.
Improved comment.
Fixed missing newline at the end of the file.
Fixed default Drush alias for the staging environment according to the new server.
Added missing README to the sites/all/themes directory.
Drupal 7.29
Updated the patch for issue #375062.

We are now using the patch at https://www.drupal.org/node/375062#comment-8788095 instead.
Applied our patches to Drupal core.