Considered opinion from decades of desktop computer usage:
Trying to use paths to meaningfully separate data by type is a fool's errand and no one will ever get it "right". It is the primary thing UNIX systems got extremely wrong that not only holds them back in the personal desktop space, but through cultural cross pollination has been ruining other desktop OSs too.
Original single-user desktop OSs had the best solution: keep everything related to the application functionality with the application. The application (in AppDir/file with resource fork/whatever form) itself can be wherever the user feels like putting it, and saved documents go wherever the hell the user feels like putting them. The only exception should be cache and temp data, which should go somewhere global.
This has the benefit of being clear and obvious to the user.
The obvious objections:
> but multiuser!
Is a use case that basically doesn't exist in personal desktop space. To the extent it was ever a useful concept it was during a time when a desktop computer was the only way to access the internet and they were too expensive and bulky to justify more than one in a home. Even then, we managed fine without OS level multiuser support.
To the extent that anything like a multiuser desktop exists it is certainly a niche, and therefore we should handle its problems with virtualization, containerization, filesystem overlay hackery, etc.
> but ease of backup!
Depends entirely on what cross section of things you care about backing up. As it is you already have to search dozens of places for including what you want and have rules for excluding what you don't and no standard is ever going to fix that. Applying those same things to the "everything with the application" model is, at worst, not any worse than things already are.
> but if I copy the application, it also copies the config.
That's a decent point, but I would argue this is the obvious thing and also perhaps what is intended. Solution is to have a standardized mechanism of clearing out the config and other state from the application directory, such that it can be done with a right-click context menu. A factory reset of the application if you will.
> but I never use a mouse and only use the GUI as a really fancy tmux
That's fine, nothing about this model makes your life conceptually any harder. Keep all the applications in directories in your PATH. Factory reset of the application can be just as easily done with a command as a context menu entry. You can still put applications in repos and even overengineer a package manager for them if you really want to.