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When it comes to gaming on Linux, there have been some dramatic strides made towards being far better than in the days of yore. Originally, consoles and PC stole Linux's lunch money, even macOS had better support for gaming for quite some time. Thanks to compatibility layers like the Wine project and Steam's Proton service, many games are now playable on Linux like they are on Windows. Open-source has made many formerly PC-exclusive titles cross-platform, and both official Linux ports and native Linux games are in vogue these days.
Unfortunately, Linux still has a serious hole in its arsenal of open-source programs across every distro in existence: there is no generalized game mod manager program that works for multiple different games native to Linux.
Some games do have specific mod managers, and some open-source engines do include a mod managing component, but these tend to be limited and highly specific to just one game. However, while Windows has multiple options for mod management, Linux oddly has nothing of any widespread renown in this regard.
Now, part of this issue is simply due to the fact it took Linux a long time to become a viable gaming platform. People were so busy working to make Linux a decent springboard for gaming in any regard for years, and it was a painful road. However, another part of this issue is a technical one, and one not easily solvable due to differences in how mod management would work on a PC platform and a POSIX-based system like Linux.
Both Windows and Linux use grossly different symbolic link layouts. Simply put, how files are linked is very important to manage how to organize where files go, and since mod managers for games are essentially dedicated to this very purpose, having a mod manager native to Linux is quite important to make sure files are properly organized for easy retrieval by games for use at runtime. Using Wine to enable Windows-specific mod managers is not an ideal solution since these programs will not easily link properly to Linux folders since the symlink structure between the two OS layouts is as different as Chinese and Greek in many respects. Further, Wine does not offer ideal performance for these programs even if they overcome the first hurdle, as they often require frequent updates that may break Wine's ability to make them play nice with Linux.
With this in mind, it's worth noting this is not an insurmountable obstacle. Linux already uses a form of mod management for installing programs called "package managers", and using a similar system would likely be quite easy to implement for game modding. Game mod sites like Nexus Mods already use a variation on this in conjunction with their Windows-oriented mod manager, and a port that would recognize the Linux symlink structure would be invaluable for those attempting to modify Linux specific games with game modification capabilities. Much of the foundational groundwork is already in existence on a programming and conceptual level, all gamers would need is for dedicated programmers to make Linux native versions of current mod management tools.
Until this happens though, Linux gamers who wish to engage in frequent game modding will certainly be frustrated with no easy alternatives in sight for this ongoing issue.