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In my opinion, a BibTeX like system would work quite well for citations.
Rather than have all citations be inline, or even stuffed in the
References section, there should be a bibliography database with a zingy
interface that'll let users quickly add citations and then quickly
reference them in the article. (Extra points if it's centralized, but
doing it on a per-article basis still would work). On the other hand, I
think footnotes should probably stay inline.
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