Also, I know that this community and dot-files in general are Unix based, but this holds true for Windows development as well. You should be putting app files in the users' %APPDATA% directory, not their user folder. It's probably even more important since Windows doesn't autohide dot files.
I absolutely despise the following directories: Documents, Music, Pictures, Public, Templates, Videos. Why? Because applications randomly dump stuff into these directories and fill them with junk files. I don't want any application putting anything into directories I actually use, unless I explicitly tell them to. It is not possible to keep your files organized if applications randomly dump trash files into them.
They may not want their configuration stored in $HOME, for example:
they’re on a machine that isn’t under their physical control and ~/.config is mounted over the network from their personal machine;
That sounds like it's a bad way to handle configuration, since among many other problems, it won't work with the many programs that do have dotfiles in home directory, but even if that happened, you could just symlink it.
they prefer to version control their configuration files using git, with a configuration directory managed over different branches;
I do that. I symlink that config into a git-controlled directory. If OP plans to put his entire ~/.config in git, he is doing things wrong, because some of that needs to be machine-local.
the user simply wants to have a clean and consistent $HOME directory and filesystem
If whatever program you are using to view your home directory cannot hide those files, it is broken, as it does not work with a whole lot of existing software.
less secure,
If your home directory is "not secure", you're probably in trouble already.
Like, there are reasons you may not want to put dotfiles in a homedir, but none of the arguments in the article are them.
EDIT: I will ask developers to stop dumping directories and files that don't start with a dot in people's home directories, though. I gave up over twenty years ago and put my actual stuff under ~/m just to keep it from being polluted with all the other things that dump non-dotfiles/-dotdirs in a home directory. Looking at my current system, I have:
A number of directories containing video game saves and configuration. I am pretty sure that these are mostly bad Windows ports or possibly Windows programs under WINE that just dump stuff into a user's home directory there (not even good on Windows). Some are Windows Steam games.
WINE apparently has decided that it's a good idea to default to sticking the Windows home directory and all of its directories in there.
Apparently some webcam software that I used at one point.
The rust library mentioned there doesn’t support system install paths for windows or macOS, it only uses XDG. I recommend the directories crate which properly supports Linux, Mac, and Windows.
You might wanna backup your dotfiles somewhere remote too. I literally lost dotfiles that I'd been building up for years because I couldn't remember the password to my Linux machine after coming back from vacation. Funny enough though, a couple hours after nuking my OS I magically remember my password.
Tangentially related: I recently learned that there are tools for handling dotfiles such as chezmoi and yadm. I would suppose that after spending some time on backing up the dotfiles that matter one can purge the remainders without much issue. I also remember some tool that was made for the purpose of cleaning $HOME, but can not recall its name (if anyone knows please let me know).
I hate it when an application puts its configuration data in its own dotfile under $HOME instead in ~/.config. Also hate it when caches are stored in ~/.config, because then I have to manually tag those subdirectories for exclusion before doing a backup.
Is there any good gui application for mange these but also edit them in a user friendly way like getting a dropdown for a settings like: Yes/No, Country Sweden. Number size range etc. So include validation.
Even nix os does not have that.