on a suggestion of @sritchie73 and @aammd

Thanks to ocefpaf for request that.

Pandoc had some changes in the last versions.
Having a variable for Pandoc will help
maintainers to handle different versions of Pandoc.

This is based on 966a0322 from gh-pages.

Thanks to @ChristinaLK to report the problem.

First should come the common workflow tasks, then commands for internal/debugging use.

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.