This is somehwat geared toward my specific preferences as a social scientist, but my cookiecutter template contains pretty much everything you need for academic

This is somehwat geared toward my specific preferences as a social scientist, but my cookiecutter template contains pretty much everything you need for academic writing using pandoc: https://bitbucket.org/jboy1/cookiecutter-pandoc-paper https://bitbucket.org/jboy1/cookiecutter-pandoc-paper You can also consult Kieran Healy's guide here: http://plain-text.co http://plain-text.co (again, this targets social scientists)