I have a fairly specific system that I've developed, mostly due to my being fairly anal about not wanting to leave random files lying around after I'm done with them and wanting to keep as little as possible in my home directory. I tend to try to keep most things in my directory that's sync'd to cloud storage (previously Dropbox, now Nextcloud since Dropbox doesn't support non-ext4 on Linux); ~/Documents and ~/Pictures are both symlinks into that folder so that I don't have to keep track of which machine something is on. I try to keep my ~/Downloads directory fairly clean, and move things to the trash liberally (through trashcli) once my initial use is finished so that I can still access them later if I need to. The only other two (non-hidden) directories I keep in my home directory are ~/dotfiles (which is a private GitHub repo that I symlink my dotfiles from) and ~/code, which has subdirectories for various categories (`forks`, `scripts`, `projects`, `scratch`, and maybe a few others I'm forgetting). Finally, I have a ~/.scratch directory where I put text files I use to take notes, short scripts I write to test something, and other files I only need for a short time.