update URLs to reflect consolidation to carpentries organization

Add links.md to files in boilerplate

Makefile: add docker-serve target

Move CODE_OF_CONDUCT.md to boilerplate

remove permalink that breaks asset includes

gitIgnore for R

Closes swcarpentry/styles#283

`site.email` is used as:

_includes/lesson_footer.html:	        <a href="mailto:{{ site.email }}">Contact</a>
_includes/workshop_footer.html:	<a href="mailto:{{ site.email }}">Contact</a>

Therefore, it does not make sense to have `mailto` in the `email` itself.

Will also match https://raw.githubusercontent.com/swcarpentry/lesson-example/gh-pages/CONDUCT.md

Rename CoC file to align with GitHub's Community Profile expectation

See https://help.github.com/articles/about-community-profiles-for-public-repositories/.

Fix lesson_check.py

Run lesson-fixme from within lesson-check

Change shebang to Python3

Close swcarpentry/styles#271

Make Jekyll ignore .Rproj

Port of https://github.com/swcarpentry/r-novice-inflammation/commit/9da857efb16d7351127f2d5c46fc0af660654506.

Close swcarpentry/styles#274

Improve .travis.yml to build the lesson

Remove root and layout from YAML for boilerplate

Remove unnecessary super call

Use Python3-style class declaration

util.py: make functions return NotImplemented