I wrote a pandoc filter that when run on each individual chapter's file, inserts the title block as headings (level 1 for title, level 2 for author, level 3 for date. This is what the HTML writer does).
This lets you run pandoc on each chapter individually (to produce the pandoc'd output plus the formatted title block), and then run pandoc on all the chapters together to compile the single document.
The filter is here on gist (I take no responsibility for malfunctioning code, etc): https://gist.github.com/mathematicalcoffee/e4f25350449e6004014f
You could modify it if you wanted it to format differently (for example like this the author/date appear in the table of contents since they are headings, which is not quite right... but that's a different problem as it happens with the default HTML writer too).
My workflow is now something like this:
FORMAT=latex # as understood by -t <format> in pandoc
FLAGS=--toc # other flags for pandoc, --smart, etc
OUT=pdf # output extension
for f in Chapter*.md; do \
pandoc $FLAGS -t $FORMAT --filter ./chapter.hs $f; \
echo ""; \
done | pandoc $FLAGS --standalone -o thesis.$OUT
where I've chmod +x chapter.hs
and it's in the current directory.
(I additionally have a title.txt
that I stick out the front with the entire thesis' title block (as opposed to each chapter's title block)).
I received some help from the pandoc google group which was great.