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Agree on that, but it defeats the purpose of calibre managing a book as a logical entity. Furthermore, the links are hardcoded as such they will break as soon as you move or rename directories, right? Which is a HUGE no go for me. Sorry to be so frank.
Maybe I am puristic, but I want to have one folder for one book. Like the internal structure of calibre. No matter how much and how strange the additional material may be. I buy statistics and coding books and they - almost always - have a bunch of strangely formatted items. To have all lecture slides being copied to the e-reader would be great to study paperless.
I want to trust calibres directory to contain everything ebook-related. So for me it is definately a shortcoming of a otherwise great software. A simple tickbox "manage folder" would suffice and I have to manually select one or more files that constitute "the book". To have that I see the best way are zip files.
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