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I use Calibre occasionally for research articles and manuals (and regularly for lots of other stuff, such as audiobooks and language learning materials) but wouldn't go with it as my main tool for research. Right now, I'm pretty happy with my simple and slightly chaotic way of organizing scientific publications in regular folders on my hard drive but if I wanted to get a more systematic solution, I would certainly use something like Zotero, Mendeley or Citavi (not only because of metadata download features but also the simplicity of generating references).
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