Using the package explorer, you can add import files/folder from your file system.
To import folders from the file system: In (windows) explorer, select the file(s)/folder(s) you want into the NSF, and copy them (CTRL+C or right click/copy). Then in Package Explorer, select the WebContent folder, and paste (CTRL+V or right click/paste).
It's as simple as that :)
If you're wondering what I needed this for, it's to create/maintain CKEditor plugins locally in an NSF. You can import "external" plugins using CKEDITOR.plugins.addExternal.
The imported files are noticed by the Design task, so this also works with templates.