I accidentially copied my whole home directory into one of my subdirectories, causing me to exceed my disk quota on a server.
Or does anyone know how to undo a command in general?
When it comes to the shell, you are the undo. The opposite of copying is deleting (rm), so delete the copies.
I recommend installing the trash-cli package, and then setting these Bash aliases:
alias rrm='rm -i'
Of course, in your case, since you're out of disk space, you probably don't want to trash the files first. Even so, it's a good practice to use the trash.