added preliminary tagging and numbering of bibliography refs
fixed some list weirdness
Updated docopt and command line options
Fixes to inline reference parsing

These fixes XPATH-ify elements of @axfelix 's regex solution. We can't actually just replace this in text via LXML because when you insert back into a text element it re-encodes the output.

I also fixed an indent error in tei2nlm.py that meant that the reference parser would never trigger.
Basic tests for inline reference handling

Also reformatted existing tests