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If you aren't Linux savvy I'd recommend sticking to the KDE Discover appstore, it uses flatpacks which are installed in a separate folder without trying to change system files/directories. PCSX2 is there and it gets updated with the dev build once every week.
imo, its bad advice to suggest using flatpack in arch based os like manjaro or steam os: it consumes additional space you dont want to waste, and usually its considered a last resource if you were unable to install or use a program through other methods, including AppImage, which is safer and more reliable and versatile (you can place the file-program in a different disk, saving space and avoiding issueas related to missing dependencies).
btw, maybe op can try luck with this version of the program
https://github.com/ferion11/PCSX2_Appimage
https://www.youtube.com/watch?v=bXZma0t0PKE
If you want something which is not on steam, flathub is your only option.
Or simply said. You can only get apps from the discover app store
As others said, your best option are flatpaks or trying to find a way to install it to a directory that is writeable.
If the application you wish is not avaliable on Flathub, try using toolbx[containertoolbx.org] or distrobox[distrobox.privatedns.org].
If the Steam OS uses ostree, you can try to do something with the ostree command and pacman's -r switch, which should let you install it into a writeable directory, see https://ostreedev.github.io/ostree/introduction/
OSTree is a complicated piece of software, so I'd recommend understanding it all before running any commands. I'd also use it only as a last resort since it requires you to reboot your computer every time you install something.
You could also just run "pacman blahblahblah -r ~/folder_you_created", find the executable created and hope that the Steam deck has all the dependencies installed. This is very likely not to work.
Appimages should work but flatpaks are the official way to get software on the Deck, so it should be supported pretty well.
https://www.youtube.com/watch?v=pnCObNCg0Ic
And if you have a PS4/5 and want to stream gameplay, Bryant has you covered:
https://youtu.be/D_HXLn0DmYw
It will have /sysroot and /ostree directories on the root filesystem if it uses OSTree.
Also according to the video, there should be some sort of "developer mode" option that enables a read-write tree.
Discover currently only has support for Flatpaks, firmware updates, PackageKit, snaps and rpm-ostree. Since SteamOS does not use rpm-ostree, if you can get system updates via Discover, they must give you the source code on how they did it. Maybe this will help understand how its immutable filesystem works (that is, if it is not OSTree).
Also the "System" settings section calls the OS Version as "snapshot" and shows the date of the "OS Build" - changing to a beta branch pushes the date forward. Too bad the beta branch doesn't have a unique changelog...
Use flatpack.
It does not matter what other people say. It is the only one.
You could risk unlocking the OS and installing anything in any way you want but you will risk losing all of that in an OS update.
https://help.steampowered.com/en/faqs/view/671A-4453-E8D2-323C
They say that pacman's packages 'may' be wiped when the OS upgrades. That is not very specific.