If you haven’t tried OpenShift yet, you should!
Anyway I have a WordPress installation there. When upgrading WordPress to a new version, files are changed on the server but they would be overwritten if I push the repository. So I created a script to download a snapshot of the OpenShift app, extract the changes in the php directory where WordPress resides, and add them to repository.
It is fully automated except for the crucial git push.
The script is called update-repo-from-snapshot.sh and is meant to be commited to the root of each repository.