Citation Node Improvements

[rowanc1]

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There are a few improvements that I would like to improve regarding citations:

1. make them part of the root tree, included in a single back-matter element (for easy access and not searching the whole tree). These would be CitationDefinition nodes (similar to footnotes).
2. Remove the References object, and chase that through the exports code (should simplify things with a few utilities).
3. Move from raw HTML as the citation to mdast (right now this is a security hole).
4. Change the new ArticleProvider in the theme, to actually just take the article.
5. Write the upgrade/downgrade scripts.

This would also likely solve some of the problems around citations in parts not being rendered. I was prompted on this issue thinking about data citations (which are reported differently in an academic context), and trying to add more information about the citation source (e.g. zenodo vs datacite).