Representation is not data - something that developers (and not only them) often forgot when working with different data.
Disclaimer: Yes, this is a rant. Yes, I am displeased with state of software. And yes, I can use some harsh words. You were warned. For a some time now we have Filesystem Hierarchy Standard which describes which data goes where in your *nix installation. In fact we have that for 28 years, which is almost as long as I live. This is quite some time. But for whatever reason we apply that only for the system hierarchy and we cannot have the same for something much closer to our heart - our dear $HOME.