org.yuzu_emu.yuzu VS net.pcsx2.PCSX2

Running at anywhere from 10-20fps. Using official joycons as controllers (because of course why not?). CPU and GPU overclocked to 2.091GHz and 921Mhz respectively. There is more info at this github issue on how this came about: https://github.com/flathub/org.yuzu_emu.yuzu/issues/911

Bottles app, yuzu emulator

Yuzu does not request the host filesystem.

Looks like you're using flatpak. I've never heard of a program called "Yuzu"; this is the only one with that name on flathub, so I'll assume that that's what you're using. According to the manifest file it doesn't have any access to your files by default, except via portals. And according to this bug report Yuzu does support portals, but the SDL2 version doesn't. So if you are using the SDL2 version, you could try using another one (I'm assuming that there is another one, otherwise that bug report doesn't make sense). Or you could try giving it direct access to your data. You can use flatseal for that.

Same same way you look at diffs for anything else on GitHub because that's where Flathub's source data is hosted.

For PS2 games, PCSX2.

PCSX2 does request the host filesystem.

According to Flathub, which is the designated packing system for Steam Deck, it was updated April 24nd 2022, https://flathub.org/apps/details/net.pcsx2.PCSX2

Flatpaks: - Dolphin - mGBA - MelonDS - PCSX2 - Citra - PPSSPP

I think this manifest file from PCSX2 is a good example for you, it has everything, pulls in lots of external modules, bundle's some dependencies as submodules, that's pretty much the options you have for your dependencies.