Close #152.

Based on https://github.com/swcarpentry/lesson-example/pull/144/files

Close #186

Close #178

Demo at https://github.com/swcarpentry/lesson-example/pull/132/.

This is based on https://github.com/swcarpentry/lesson-example/pull/127/.

Building `md` from `Rmd` in a script like this will break if the `methods` package is not called and the code includes class object routines. See https://github.com/r-spatial/sf/issues/478

See https://github.com/swcarpentry/workshop-template/issues/410

The consumer was removed by 079d7d50 (Updating contribution guidelines
in boilerplate, 2016-06-26).

1.  Create file `_includes/links.md` with definitions of all links.
2.  Replace links at the bottom of Jekyll'd `.md` files with inclusion of that file.
3.  Modify `bin/lesson_check.py` to load and check definitions in this file.

This eliminates most redundancy in link definitions, though
`CONTRIBUTING.md` and `README.md` still contain their own links, since
they are not Jekyll'd.  Note that we *cannot* put the links into
`_layouts/*.html` (or even `_layouts/something.md`) because of the
order in which Jekyll expands things - we have to explicitly include
it in each page.

1. Checking that `index.md` has `root` set to '.'
2. Checking that `_config.yml` has `root` set to '..'

An internally-defined Markdown link has the form [xxx][yyy].  If the
ID 'yyy' doesn't resolve, the text is left as-is, so we check for
that, then subtract those that reference configuration values using
'{{'.  It's a hack, but it'll catch at least a few things.