[fjtorres]

If you don't want to use the file system (one of the defining features of the reader), you can just drop all the ebooks in the same folder. Same effect as the flat file database front end used by Kindle, Sony, Kobo, etc.

Or, you can use the favorites system to store a single list of file links if you want to store books in nesting folders but don't want to browse that way.

Bear in mind that storing/browsing ebooks in nested folders is a feature; it lets you store and navigate tens of thousands of books in the reader.