Calibre will always have limited use for academics without an easy and accurate way to export its metadata into the most common citation managers of Endnote and Zotero. It makes sense for Calibre to have this integration to involve this large international community of "professional" readers ... Calibre has better metadata extraction than either one of those two programs.
Both of them take BibTeX, RIS, plain text, I believe, and a few others. I'll look into the command line tools and let you know the results.
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