Centralized setting of chunk options for novice R materials.
Added back fig.path option to novice R lesson 01.
Make jekyll ignore Rmd files.
Added Makefile for converting R Markdown files to Markdown.
Added rmarkdown to list of .PHONY targets.
Fixed a couple of typos. (references to another dataset)
Fixed another typo
Fix goostats error when using options -J 100 -r

goostats was returning an error with the options -J 100 -r in lesson 5.
-J was being passed to head which returned invalid option. To fix this
I add option handeling with getopts.
Merge pull request #631 from swcarpentry/typo-fix

Fixed a couple of typos. (references to another dataset)
Remove newline
Changed rmarkdown to rmd.
Changed one last instance of rmarkdown to rmd.
Merge pull request #633 from jensv/fix-shell-05-script-goostats

Fix shell 05-script goostats option error
Improvements to the Introduction and Simple Patterns sections of intermediate/regex.

Main changes:
- Fixed the links to other sections and the Glossary.
- Added files containing the 'evil' data to data/evil.
- Created some exercises for the Simple Patterns section.
- Corrected a few typos and made some paragraphs clearer.
- Split up the Simple Patterns section into subsections.
- Added the intermediate/regex section to the Makefile.
- Added an index page.
Merge pull request #569 from ctjacobs/creating-lesson-on-regular-expressions

Improvements to intermediate/regex
Merge pull request #626 from jdblischak/display_w_hooks

Makefile for converting R Markdown files to Markdown