100% agree with you OP.

To still sorta replicate that, I just set up a script at /usr/local/bin/update for it:

#!/usr/bin/env bash

sudo emaint sync -a &&
sudo emerge -utDU @world &&
sudo emerge -c;
flatpak --user update;
doom upgrade &&
doom sync &&
doom purge

I'm using MX Linux and don't use any flatpak or snaps, only good old debs

What a weird question, also that was never the case in the first place. You can still accomplish this with a simple bash script too.

Is it possible to bring back that experience? A unified, reliable CLI solution to make sure EVERYTHING is up to date?

Yes. Use a Linux distro that doesn't use flatpacks and you're good to go.

flatpaks are all updated at once, just like distro packages, so yeah you might need to commands, but that's still very different to having each application update itself (and the security hell implied by that)

Also I think pkcon can manage your updates across various backends (unless you are on Arch, where I think there are both technical & ideological objections to having a simple tool that just works)

I use very minimal software and usually don't care about Flatpak

I think a script with apt/pacman/dnf etc., flatpak update can do the job as well?

IMO its against the unix vision to extend apt to manage flatpak as well.

Fedora updates flatpaks automatically, system updates too, but you need to reboot. Which Fedora version do you use?

emerge -uDN @world

...and head to bed for me.

I use fedora as well and I just update through the GUI. It's more stable that way and waiting until I turn off my computer for them to apply is not a big deal.

I use one command to upgrade the whole system: paru one one system and yay on the other laptop.

Yeah, flatpaks are a pain in the ass. So glad that I don't have to use them since switching to Arch.

Huh, I stopped using Linux long ago, and I hardly understand any of the issues you are facing... can someone ELI5?

yeah like other people have rec'd, I just wrote a script for installing/removing/upgrading/searching all the package managers I have. this was used as a tongue in cheek jab and has never truly been a brag.

I use BAUH as a GUI "update everything in one click" does repos, aur, flatpak, snaps, appimages. Paru is CLI option for repo, aur and flatpak. I dunno if it does snaps never checked.