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How can I get rid of the default application folders that ship with my Linux distro?

While you can delete stock folders such as Templates, Public and so on, they’ll still appear in the sidebar of your file explorer.

The good news is that they’re pretty easy to disable.

Referring to the xdg-user-dirs manual shows us that there is a configuration file of “well known” user directories that lives at $HOME/.config/user-dirs.dirs by default

Simply deleting the various entries inside might break a number of things but if you look closely, you’ll spot that changing a directory to point to your home directory will disable it

For example:

> cat $HOME/.config/user-dirs.dirs
XDG_TEMPLATES_DIR="$HOME" # templates is now disabled

This should cause the Templates folder to disappear from the sidebar of Nautilus although you might need to restart first.