First of all, I'm very new to open source contributing, so it's possible that I make a stupid mistake somewhere. Please bear with me.

Basically, the problem I encounter is that when upgrading or reinstalling, rua seems to mark packages as dependency when it shouldn't. I found this out because Pamac lists several of my AUR packages as orphans.

For example, Zotero. Pamac lists it as an orphan, and when I pacman -Qi zotero | grep Reason, I indeed get Install Reason : Installed as a dependency for another package. But I never marked it as such myself.

When I update or reinstall a package through rua, it does a simple pacman -U [package.tar.zst], so it doesn't explicitly tell Pacman to make it a dependency (as was the case in issue #2). And yet it somehow ends up as a dependency. When I repeat the same pacman -U command manually and add --asexplicit, the package is marked as explicitly installed again. My naive solution therefore would be to add -asexplicit to the Pacman commands when reinstalling or upgrading.

When I install a new package with rua install [package] it is marked as explicitly installed (as it should be), but as soon as I update or reinstall, the package becomes marked as a dependency.

I don't think Pamac can be interfering here, because its AUR option is disabled and I only use it to view installed packages.