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. 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.