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One way to do this would be to build an application that constructs a complete calibre library from the database without using calibre. You would use the same schema that calibre uses along with compatible file naming conventions. Matching the schema would be made easier by starting with an empty calibre library.
There is no doubt that doing this would be a lot of work, but it is orders of magnitude less work than reinventing calibre.
On the other hand, is calibre the right target? Perhaps an academic bibliography manager would be more appropriate? I suspect that generating bibtek would be a lot easier and possibly more useful.
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