Markdown writer: Allow footnotes/refs at the end of blocks, sections

This allows footnotes and refs to be placed at the end of blocks and
sections. Note that we only place them at the end of blocks that are at
the top level and before headers that are the top level. We add an
environment variable to keep track of this. Because we clear the
footnotes and refs when we use them, we also add a state variable to
keep track of the starting number.

Finally, note that we still add any remaining footnotes at the end. This
takes care of the final section, if we are placing at the end of a
section, and will always come after a final block as well.

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