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As it's coming up in other contexts, there's the question of what the best way of doing references is on the Wiki.
Traditional texts and articles have a list of references at the end of the article, with small indications such as references numbers in the text. The need for full references is clearly to provide enough detail to find the exact source listed, but presumably its done this way for the following reasons:
Paper is a static medium (a full reference can't appear in a mouse-over). Putting all very long lines inline in the text would break up normal reading, so putting them at the end moves them out of the way.
It's easy for authors and readers to scan through an alphabetical ref list and look somehting up, spot something that they think ought to be there isn't, etc.
To what extent do these apply to the wiki (in principle, ignoring for the moment Instiki limitations)? It's possible to "hide" the full reference details as referring to them comes up in the main text, and have means of making them visible, eg, mouseover. It's also possible to automatically compile a secondary list of references (either at the end or on a separate page) from the text, so it doesn't sacrifice the utility of point (2). So the traditional reasons for reference structuring don't apply. Why might we want to keep things that way:
Tradition/familiarity ourselves or judgement by readers who use those criteria.
Similarly, if wiki material is intended to migrate to a traditional format, eg, a printed version or submitted as a journal article.
It provides somewhere to stick references that aren't explicitly mentioned in the text.
I certainly find the current layout difficult at times, since it's often time consuming to find the reference a mention in the main text refers to. (Mea culpa in that I haven't bothered to learn how to do markdown reference-links. However no-one else seems to have done it either.) Certainly on a page which has multiple "orthogonal" sections, it'd be nice if it was acceptable to put references only of relevance to that section at the end of a section. Being more radical, it might be interesting to come up with some guidelines for when it's appropriate to put references in as they come up in a text block, and if so how.