But that's the whole point of wanting folder support, so you can have multiple levels.
Perhaps you could create collections with the full path as a name?
So for the example above you would get 3 collections (or even 4) collections.
collectionname1 with book1.pdf, book11.epub, book12.lrf
collectionname1\collectionname11 with book11.epub, book12.lrf
collectionname2 with book2.epub, book3.txt
collectionname11 with book11.epub, book12.lrf (this last option would/could be useful if collectionname2 were two have a subfolder also named collectionname11)