My experience with directories in Spine and TexturePacker(smart directories). Spine will keep the folder path shown in the Hierarchy. TexturePacker however will only retain the subfolders during export if it finds duplicate file names. i.e. hero/head and monster/head
Otherwise TexturePacker drops the folders in favor of just file names in the libGDX export
Trick solution, duplicate at least one small asset into a sibling folder, while also having "Enable auto alias" On. This will cause the folders to be exported with out using any extra pixel space in the image.
