Loading git_deploy in update.php to properly check version dependencies.

This hack resolves these issues for us:
  http://drupal.org/node/1905736
  http://drupal.org/node/1013302

update.php is quite explicit in ONLY loading the system module and nothing
else, so there seems to be no way for a module to modify its dependency
checking behavior.
The profiles directory is now just stock as we are not customizing them currently.