Markdown reader: parse refs and notes in the same pass.

Previously the markdown reader made one pass for references,
a second pass for notes (which it parsed and stored in the
parser state), and a third pass for the rest.  This patch
achieves a 10% speed improvement by storing the raw notes
on the first (reference) pass, then parsing them when the
notes are inserted into the AST. This eliminates the need
for a second pass to parse notes.

git-svn-id: https://pandoc.googlecode.com/svn/trunk@1629 788f1e2b-df1e-0410-8736-df70ead52e1b

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