Please no. This article is literally "Dotfile madness", don't make it worse!

I have to deal already with these on file shares, specifically for Apple: .DS_Store, .Trashes and .AppleDouble, or for Windows: Thumbs.db, $RECYCLE.BIN (for some reason Windows sometimes ignores the fact I've disabled the recycle bin on a share and creates this instead) and desktop.ini. Please don't drop crap around directories where there exist a multitude of tidier alternatives.

How do you have to “deal with” them? What are the portable tidier alternatives?

Because when you have multiple OSs accessing the same shared folder, they all create their own crap, which is then visible to the other OSs, and fills up directories with stuff that confuses normal users.

I don't run multiple OSes, but I do use USB sticks and SD cards on other people's computers and vice versa. I'm pretty sure that is "normal user" behaviour.

It gets annoying real quickly because you see the "crap" files of all the OSes you're not using. And you delete them, you only have to insert the stick and they're back. This happens in different ways for all of Mac, Windows, Android and certain Linuxes.

Some users however access our file shares from their Macs, or their Windows PCs, or even some from their Linux machines. That's fairly normal.

A daemon with a CLI and a programmatic interface, backed by a SQLite store, hooked into Linux audit and perhaps an LD_PRELOAD?

For me, mostly exclude them from select all, or perhaps scroll past them to see meaningful files.

Sidecar files for storing file tags make querying the tag system a huge chore; it totally kills performance. I understand the conceptual appeal but it's just not the way to go.

This is what Mac does to track download locations, if I remember correctly (._file).