@ondoho. I guess the OP means their file manager (Nautilus, Nemo, Dolphin, Thunar, Caja, whatever) when speaking of the desktop, not the Desktop folder specifically. Yes, capitalizing Desktop is confusing.
@OP. Even if you're the only user of this system, there are many hidden directories in $HOME that won't be shown in the file manager by default. E.g ~/.cache, ~/.config, ~/.local, etc. Try running du from inside the $HOME and see.
|