$HOME, not so sweet $HOME
This post is a detailed discussion into user profiles, their directories, and how they are-to put it bluntly-in total disarray on Windows and Linux (I haven't used a Mac in ages, but I assume the situation is very similar there, too). Applications treat the user profile as a dumping ground, and any user with a reasonably wide list of installed software will find their user profile very difficult to traverse after some time in use. There are platform conventions and attempts to standardise things on more open-source platforms, but a lot of developers resolutely refuse to change the behaviour of their software for a variety of reasons (some less valid than others).
The first part is a deep dive into user profiles on Linux and Windows, and the conventions that have been established on these platforms over the years. The second section details how they are broken on each platform, and why they are broken.
This happens to be one of my pet peeves" as well. One the left, my home directory. On the right, my home directory but with all the garbage unhidden. This is bananas.
First, it's been my long-standing conviction that if you, as a developer, need to actively hide things from the user in this way, you're doing it wrong and and you're writing bad code. If you're an operating system developer, don't use hidden directories and files to hide stuff from the user - use clear directory names, encourage the use of human-readable file names and contents, and put them in places that make sense.
Second, if you're an application developer, follow the damn guidelines of the operating system you're coding for. More often than not, these guidelines aren't that hard to understand, they're not onerous, and they're certainly not going to be worse than whatever nonsense you yourself can come up with. Having a hidden .paradoxlauncher directory in my home directory displays just such an utter disrespect for me as a user, and tells me that you just don't care, whether that's you, the developer, personally, or whatever manager is instructing you to do the wrong thing.
At the same time, aside from excessive symlinking, there's really no solution to any of this. As users, we just have to deal with the results of incompetence and ridiculous crunch culture in software and game development.