1.  Adding `tools/chunk-options.R` with support for Pandoc-based conversion of R Markdown to plain Markdown.
2.  Modifying `Makefile` to handle any R Markdown files that are present.

Changes have been checked by @jdblischak in the `r-novice-inflammation` project.

Uses the filter-out Make text function

"Returns all whitespace-separated words in text that do not match any of
the pattern words, removing the words that do match one or more."

http://www.gnu.org/software/make/manual/make.html#Text-Functions