Back when I started with Unix (a long time ago), programs had a simple approach to where to look for or put little files that they needed; they went into your $HOME as dotfiles, or if the program was going to have a bunch of them it might create a dot-directory for itself. This started with shells (eg $HOME/.profile) and spread steadily from there, especially for early open source programs. When I started writing shell scripts, setup scripts for my X environment, and other bits and pieces that needed configuration files or state files, the natural, automatic thing to do was to imitate this and put my own dotfiles and dot-directories in my $HOME. The entirely unsurprising outcome of this is that my home directories have a lot of dotfiles (some of them very old, which can cause problems). How many is a lot? Well, in my oldest actively used $HOME, I have 380 of them.

(Because dotfiles are normally invisible, it's really easy for them to build up and build up to absurd levels. Not that my $HOME is neat in general, but I have many fewer non-dotfiles cluttering it up.)

Recently it slowly dawned on me that my automatic reflex to put things in $HOME as dotfiles is both not necessary and not really a good idea. It's not necessary because I can make my own code look wherever I want it to, and it's not a good idea because $HOME's dotfiles are a jumbled mess where it's very hard to keep track of things or even to see them. Instead I'm better off if I put my own files in non-dotfile directory hierarchies somewhere else, with sensible names and sensible separation into different subdirectories and all of that.

(I'm not quite sure when and why this started to crystalize for me, but it might have been when I was revising my X resources and X setup stuff on my laptop and realized that there was no particular reason to put them in _$HOME/.X<something> the way I had on my regular machines.)

I'm probably not going to rip apart my current $HOME and its collection of dotfiles. Although the idea of a scorched earth campaign is vaguely attractive, it'd be a lot of hassle for no visible change. Instead, I've decided that any time I need to make any substantial change to things that are currently dotfiles, I'll take the opportunity to move them out of $HOME.

(The first thing I did this with was my X resources, which had to change on my home machine due to a new and rather different monitor. Since I was basically gutting them to start with, I decided it made no sense to do it in place in $HOME.)

PS: Modern Unix (mostly Linux) has the XDG Base Directory Specification, which tries to move a lot of things under $HOME/.config, $HOME/.local/share, and $HOME/.cache. In theory I could move my own things under there too. In practice I'm not particularly interested in hiding them away that way; I'd rather put them somewhere more obvious, such as $HOME/share/X11/resources.