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I went the other way!
I added all my books to the Calibre library which allowed me to vastly improve the catgorisation of my books and eliminate a large number of duplicates as the tagging system is much more powerful thatn the folder based heirarchy I used to use. I then deleted the originals. Having put some effort into getting metadata into a good state I can now search and find material more easily.
I can then use Calibre's facilities to get books out of the Calibre library when needed using virtually any naming convention I want. The books are also already in Calibre if I need a book in another format - it takes just a few clicks to get that new format.
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