When you are in the package editor, package files, you can right click on most folders to add a file.
You cannot right click to add a folder.
I found I can work around this by adding the file elsewhere, and then right-click the file and select move to edit the path where I want it to be.
It would be better to be able to add the folder. Bonus points for remembering that adding to the VFS folder should probably be "special", and it would be great if that one gave a list of the variablized names that are allowed to select from!