Use a better method to preprocess R Markdown

[jmclawson]

The render() function from the rmarkdown library will handle any needed calls to Knitr and Pandoc, including passing along more options to handle citations, templates, etc.

This change addresses #64 for .rmd files, but it is possible other filetypes may be better served with the provided render command as well.

[michal-h21]

Thank you!