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Originally Posted by kovidgoyal
Umm, you can copy the structure directly to the reader. And as of 0.6.8 the save to disk function is fully customizable so you can use it to export whatever directory structure you like to devices.
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Which probably solves all the problems...
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And while I don't use emacs, I use calibre from the command line all the time. Why is the structure not suitable for use from the command line? I find it a breeze to navigate in both vim and bash.
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I got the impression that the current structure was a flat structure and it was sorted on first name of an author.
To optimize for command line use you have to think about things like navigating in shells and file name expansion. For example a director or file name starting wit a capital letter is very inconvenient (which is why I hate Java's convention with file name the same as class name).