I am in the progress of reorganizing my library.
First I have a folder for original download and updated version. The original download folder contains one folder per author, then one folder for series (if the author has series) and the books (no matter their format) in there.
The updated version has two folders, HTML and MOBI. The HTML contains one folder per author, one folder per series and one folder per book (and in there the EPUB directory structure and files). the MOBI contains the same layout as the original download folder, but this one only contains mobi files.
These files are on an external HD which I backup to a network drive. And the mobi's are also on two SD cards (which are mirror images of each other, and that includes a backup of my PDA).
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