For comparison, The Project Gutenberg library is designed around machine accessibility and the accessibility of a large number of materials like a Calibre Library, but is arranged as follows:
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Originally Posted by http://www.gutenberg.org/wiki/Gutenberg:Mirroring_How-To
The main collection uses a set of numbered subdirectories. For example, eBook #12345 would have all associated files under 1/2/3/4/12345/. The generated content is all in one directory, with files named according to their eBook source: pg12345-images.epub and pg12345.txt.utf8. This is not "friendly" for users to browse, since it contains a very large number of files.
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To be clear, I am not proposing the current structure be changed, but perhaps linkable Libraries ( or better awareness of alternates ) and the alternate use of containers rather than folders for data retention.