In bug 1760 we added some basic support for migrating configuration settings when upgrading the server. It works by looking for config files that the package manager has moved out of the way because of a conflict during the upgrade¹.
One problem that needed to be solved was to ignore very old such conflict files so that we don't accidentally migrate something that wasn't current. We solved this by noting the start of the upgrade by creating the directory /opt/thinlinc/etc/.upgrade.stamp. We could then check if a conflict file was from the just performed upgrade or not.
However this file needs to be refreshed on every upgrade. It is supposed to be removed by tl-setup after it is no longer needed, so that the next upgrade can recreate it. This unfortunately often fails to happen.
There are two scenarios where this fails:
* Running tl-setup in text or automated mode
* There is nothing to migrate
These are common scenarios so it is very common that this directory is left around.
Fortunately I don't think there are any practical issues with this. Its main purpose was to handle upgrades from versions before we had this mechanism, and it still does that. Any conflict files that have been created after we added this mechanism should have been dealt with along the way. Hence there shouldn't be any conflict files lying around that could be mistaken for being part of the current upgrade.
¹ .rpmsave, .rpmnew, .dpkg-old, .dpkg-dist