This is probably best explained with an example. The Adminer project tracks third party designs, which is now incorporating submodules as they are much simpler and more efficient than a forked repository. The theme files that are not (yet) submodules are accessible via the URLs like:
Those in submodules currently 404 if one attempts to access them by their old/expected URL like:
They are only accessible via their own repo’s URL structure like:
It would make accessing the files clean, consistent, and easy, and preserve public URLs when subdirs are later converted to submodules.
Other examples of this are collection-type repositories, such as Noah’s vim themes.