The only way I can see it getting solved is the OS sandboxing everything behind the scenes, redirecting everything the application spews in random locations to The One True Profile Folder per application. Even then it wouldn't be without challenges, off the top of my head some method if you actually wanted an application to get out of its sandbox and look at the real documents folder, another method for App1 to look at files in App2's sandbox (and detecting when this is desired), or what to do if an application is able to change how it identifies itself to the OS (new versions?).

Hence UWP, with its rampdown, the newly introduced Win32 app sandbox model for .msix distribution.

Like GNOME?

There are rules when to use what, but usually folks rather code away instead of reading documentation.

maybe if microsoft had a registryfs...

You can browse/manipulate the registry with PowerShell. There's an OOTB provider for it.

    cd HKCU:

https://learn.microsoft.com/powershell/scripting/samples/wor...

[delayed]

The registry hasn't been the recommended place for Win32 app settings for well over two decades now. The guidance is to only use it for system stuff that's already these, and have config files in the standard designated locations under %AppData% (depending on whether they are machine-specific or user-specific; ideally, apps are supposed to support both).

Also since Windows 8 it is sandboxed for Store apps actually.