My previous reply has made me think ...
If I wanted to use Calibre with my custom file structure without keeping an extra copy of the book in its internal directory I might do something like this:
- Install Calibre on Linux (I am already on Linux) or install it on Mac OSx, or install it on recent version of Windows (Win 7 or newer) and study
http://en.wikipedia.org/wiki/Symboli..._symbolic_link
- Create my own directory structure.
- Copy the book there
- Create a:
-- link or a symlink to the file (Linux)
-- an Alias (on Mac OSX)
-- NTFS symbolic link
http://en.wikipedia.org/wiki/NTFS_symbolic_link , you might need an external software here to make it bearable
- drop link / symlink / an alias / NTFS symmbolic link to the Calibre and create a book record.
- you might also create a custom column to store the location(s) of the file in your alternative location, so you can automate some operations
This way you can have your own file structure. There ani't such thing as free lunch. So your use of Calibre got just more complicated. When you use conversion tools, for example, you would need to copy the files over to the alternative place.