Not really software but, personally I think the FHS could do with replacing. It feels like its got a lot of historical baggage tacked on that it could really do with shedding.
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Are there any things in Linux that need to be started over from scratch?
Yes, Linux itself! (ie the kernel). It would've been awesome if Linux were a microkernel, there's so many advantages to it like security, modularity and resilience.
Got that in performant?
dmesg
/jk
Wayland could already do with a replacement.
It is so much better than X
Seriously, I'm not a heavy software developer that partakes in projects of that scale nor complexity but just seeing it from the outside makes me hurt. All these protocols left-right and center, surely just an actual program would be cleaner? Like they just rewrite X from scratch implementing and supporting all modern technology and using a monolithic model.
Then small projects could still survive since making a compositor would almost be trivial, no need to rewrite Wayland from scratch cause we got "Waykit" (fictional name I just thought of for this X rewrite), just import that into your project and use the API.
I agree in the sense that Wayland adoption would have definitely gone quicker if that was the case, however in the long run this approach does make sense (otherwise you will eventually just run into the same sorts of issues X11 had).
Btw what you're describing is not that far off from the normal way of using Wayland protocols in development - you use wayland-scanner to generate C source files from the protocols, and you include those to actually "use" the protocols in your programs. Admittedly all my Wayland development experience has been "client-side", so I really don't know how complex it is to build a compositor, but dwl (minimalist Wayland compositor) is only around 3k lines of code (only slightly more than dwm (minimalist X wm)).