Update README.md with commands to ignore VERSION.tex and CITATION.bib
Version 0.3.3 (patch to fix compilation problems)

The previous commit broke compilation of the pdfs by including
the same source into several documents. This commit undoes that
problem by changing 'include' to 'input'.  (This was a problem
when running parallel make).
Small tweak to filenames and dependencies

This commit makes some small changes to the standalone license
and author list and renames the common preamble.
Merge branch 'master' into dev

Conflicts:
	AUTHORS_standalone.tex
	LICENSE_standalone.tex
	Makefile