It's really out of control.
The shell is probably the most used software on a developer's computer and it's a total mess.
Are there any solutions to this?
> Then every dev tool pastes some config into some of these config files.
This is why you see it to be complicated. Don't do this. The only thing you should really ever be editing is $PATH, and even then I'd argue not to. Do something else. Use direnv, source .env files, write wrapper scripts.
I don't put arbitrary shit into shell profiles or shell rc files, you're just asking for pain.
You should understand what you're doing before pasting arbitrary bits into these files.