Originally Posted by JSWolf
How is the same number of directories instead of the same number of files any different? It's not. And it's less neat when you want to delete a book using the Reader's delete function yet the directory remains.
This thread is in the Kindle Forum
There are at least one associated file to each ebook file on a kindle. My K3 normally has two, annotations/reading position(.mbp or .han) and also page numbers(.apnx), but there can be others as well. (And I think the Touch and PW uses a slightly different format).