I don’t use Pamac, but I wanted to test it out so I installed it and realized I had quite a few orphans, which from my understanding are packages that are no longer in use, and therefore should be safe to remove. This did not seem to be the case, because as soon as I had removed them, applications started to malfunction. I rebooted, and now a significant number of applications are missing. So far I have identified Flatpak (and applications installed via Flatpak), Gedit, Thunar + volman etc, Mullvad, sxhkd and most odd of them all Pamac itself, to be missing. Odds are there are others too, and whilst reinstalling seems to work fine, I’m now quite curious how these applications were removed. None of them would have been listed in the Orphan category, and surely removing orphans would not pull these applications along with them?
Orphans are not packages that are no longer in use. They are packages that were installed as dependencies of other packages and there are no longer any packages that require them. For example, if you install plasma-meta and then remove it your system will continue to work fine. However, if you blindly remove orphans all of the plasma packages will be removed.
It is hard to say without knowing the details and your settings in pamac. Look in your pacman.log to see what happened.
That being said, removing orphans is one of those situations where you shouldn’t do it blindly. Always carefully review the final package list to be removed before saying OK.
Thanks for the information. Next time I’ll make sure to do a snapshot prior to removing them as well.