In the AppCafe, on my fresh reinstall, there are dozens of packages flagged as orphaned. Things like "Lumina", "dhcpcd", "xorg-drivers". I inadvertently cleaned all of these and had to reinstall into a new book environment. I'm pretty sure this is a bug.
It looks like this issue was brought up in December, but still seems to be an issue. https://discourse.trueos.org/t/appcafe-auto-clean-packages/364