1.  Moving YAML parsing to bin/util.py.
2.  Adding bin/extract_figures.py.
3.  Adding Makefile targets to regenerate image inclusion file.
4.  Adding _extras/figures.md to display all images.

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.

- the "--slide-level 2" allows to generate consistent html structure
- one should only use "##" but never "#" for now

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