Preserve modified orphan config files for even installed packages
At the moment when package is removed and it contains configuration file we keep it in database to track modified config. Problem is that we do not do the same if package is upgraded and removes configuration. We just remove modified configuration in such case.
The reason why we should not do it is to on one side preserve configuration modifications by users even if that might mean keeping around no longer used files. The second reason and more important one is that this might be just an issue in package and new version can revert to it as well as some other new package can take ownership of it. We should not reset config in such case.