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protonfixes
A module for applying fixes at runtime to unsupported games with Steam Proton without changing game installation files (by GloriousEggroll)
That wouldn't help with your issue. You're talking about this: https://github.com/ValveSoftware/Proton/issues/2691
It's the second line of the readme
With Btrfs or XFS you can easily deduplicate the data with tools like duperemove, potentially saving a lot of space if you've installed many small games.
Valve says it's okay to do with their Proton; precisely because this containerization is already handled by them. And, officially supported in Steam. https://github.com/ValveSoftware/steam-for-linux/issues/5677
Prefix deduplication has massive space savings potential. I made a script that you can run periodically that handles running duperemove on installed Proton versions and the compatdata folder for BTRFS filesystems: vacuum-steamplay
I suppose save game detection and folder merging could be done on a per-game basis with something like protonfixes.
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