Linux

https://wiki.archlinux.org/title/XDG_Base_Directory#Support, the situation is crap tbh and alot of devs refuse to even give you the option of switching to XDG standards for some reason. I started using flatpaks for most of my programs just to escape this.

I do know XDG standards are messy for devs to implement but at least have everything in .config or .local instead of spewing it across my home folder

No. Some applications won't change even if you'd make the PR for them, simply because they don't want to change legacy features.

For instance, the bash maintainers have refused to put .bashrc into .config/ and to even allow the option to move it.

xdg ninja can help move some stuff out of your home dir tho

There this program call xdg-ninja which tells you how to change the settings of various packages that live in $HOME.

Is not a perfect though because you'll have to do all changes manually but its the best I can think about. Hope its helps!

$XDG_CONFIG_HOME not every application respects it, but a lot do

From my experience there's no simple way to do it. It's something you'll have to handle on a per-app basis as there's no standard that is followed universally. Here's a website with links to resources on various methods people use.

Might be worth looking into immutable distros (nix, guix) and their home management systems, or containerised apps (flatpak, where you can inject config). A lot of tools are hardcoded to non standard locations so it's kind of a losing battle by default. A similar strategy would be to use permissions or mount certain folders as read only.

the existing comments point out excellent solutions, but no one has mentioned boxxy (https://github.com/queer/boxxy) yet

One option might be to run certain of your apps in Docker. There are ways to go about running even graphical apps in Docker. And with Docker, you can tell it to mount /home//.config/someapp on the host to /home//.someapp in the container.

This tool can help you with certain programs that requires some extra steps to use .config/

Xdg-ninja that was mentioned by other people is probably the best for the main issue.
For the git stuff, look into bare git repos. Iirc distrotube has a good video explaining the concept

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