At the moment I can find no way to (manually or otherwise) add an entire folder to the package / bundle using pathing that's relative to the project directory using AIR 13.0.0.111 and Flash CC. The "Add Folder" icon invokes some custom Adobe file browser that does not have an address bar or any means of text entry, and there is no option to use the standard windows dialog instead.
If there's a workaround, I'd like to hear it. If not, I'd love to get this request to the AIR / Flash team and have it addressed in a forthcoming update. Where's the right place to do that?