Most Linux distributions have a set of default folders, such as Downloads, Documents, Music, Pictures, etc., in the home directory.
If you just delete them, they will automatically reappear. Here is how to remove the permanently.
1. Edit user-dirs File
In the following file
~/.config/user-dirs.dirs
outcomment all the lines corresponding to the unwanted folders.
2. Update user-dirs
Execute:
xdg-user-dirs-udpdate
3. Delete the Folders
Delete the unwanted folders and all their content:
rm -rf ~/Documents ~/Downloads ~/Music # etc.
Now they should never reappear again.