Add repair step for updater issues

The updater as shipped with ownCloud =< 9.0.1 has several bugs leading to a not properly executed update. For example the third-party changes are not copied.

This pull request:

1. Ships the third-party files changed since ownCloud 9.0.1 in the resources folder. On update the files are replaced. (https://github.com/owncloud/updater/issues/316)
2. Adds updater/* and _oc_upgrade/* as an exemption to the code integrity checker since the updater is updating in the wrong order. (https://github.com/owncloud/updater/issues/318)