The today on Steam released Update 1.2.0 for Quern - Undying Thoughts (a spiritual successor to Myst) fixes the problems with controllers on Linux and adds Steam Cloud saves among other things:

Quern 1.2.0 is here! This patch focuses on making Quern run better and look nicer. We also added Steam Cloud function to the game. This means your saved files are now stored in the cloud so you can play from a different computer and continue where you left off. We made some improvements to the user interface to work better with different screen resolutions.

Simplified Chinese and Polish languages added.
New graphical options are available to tweak both performance and quality.
We decreased the lowest and increased the highest possible graphics settings.
We fixed an issue that prevented loading between the game’s scenes on weaker systems.
Cloud save function is now available.
Fixed a bug that caused the controller bindings to be off on Linux systems.
Subtitles can be disabled from now on.
We optimized the user interface for any resolution.
Many minor and several major bugfixes.