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I started playing Silksong on my Steam Deck using the linux build. Only to discover that it maxed out at 720p (docked), and wouldn't bind right/left trigger for my controller. Enabling proton (to play the windows build) worked great. Controller worked flawlessly and the game ran smoothly at 1080p.

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Yes, and sadly this is very commonplace. At this juncture, Linux builds don't make a lot of sense anymore, especially if they are not going to receive much attention when it comes to debugging. The performance penalty of Proton is small enough that it rarely matters. The worst I have seen is perhaps -20% FPS in Helldivers 2 (with an Nvidia GPU), but normally the impact is in the 0 to 10% range, so negligible for all intents and purposes.

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