We use Drush to update our Drupal installation and plugins.
Drush discharges all files that aren't in a standard Drupal installation, so after an update, use git checkout to restore previous version of our files:
After the update of the core, tag the commit with number of the release, and push also the tag
Do a separate commit for every plugin.
Every plugin is in a subfolder of sites/all/modules
Enter in the root of the www-test repo and use: