I just looked into Calibre Companion, and while it seems like a great tool, it's still not really solving the problem I'm having with Mantano. When I try to read a book out of Calibre Companion, it imports it into Mantano, and I once again have missing covers and no tags on all the PDF files, even though Calibre Companion has everything complete. It's pretty frustrating; there seems to be no way to import PDFs into Mantano without losing more than half the metadata! But I really like Mantano's tag + collection system, as well as their highlighting feature... *sigh*
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