1) In yEd, "folder" node is just another name for a closed group node.
2) Do not use GML, use GraphML. GML is a legacy format that does not support all the features yEd offers.
That said, we do not provide help on file format specifications. If you want to create GraphML files yourself, either reverse-engineer GraphML (create a diagram in yEd, save as GraphML, inspect file in a text editor) or license the commercial yFiles diagramming library and use its GraphML framework.