I upgraded the distro to Karaf 4.0.8 last night - I just noticed that this breaks the apt upgrade right now.
So please refrain from upgrading through apt until further notice!
UPDATE: @Benjy was so kind to provide a fix - with this, you are not asked anymore whether you want to overwrite certain files and thus you cannot give the wrong answer anymore
All should be fine again.
Karaf 4.0.8 now allows a highly optimized way of installing add-ons, which is now used by openHAB. This should especially speed up the installation process after a first startup or upgrade.