Ashjuk:
Cause of the behaviour you mention I personally use Calibre only to manage the content on my reader, prepare books for future reading and store allready finished books (to know that they have been finished).
The vast majority of e-papers and books are stored on annother place on the harddisk with my own folder structure.
For my purpose a clean database management system (with just linking to the content) and metadatas on a different place would suit much better.
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