wrote each command individually

Adding an R package is not obvious if learners have installed Anaconda. Not sure where this lesson might fall in the grand scheme of things, but adding the simple command-line example helps.

If you have an out dated Ruby version. 
They may fail to work with jekyll

Add note about version of Jekyll needed per https://github.com/swcarpentry/styles/issues/195#issuecomment-351056899.

Thanks to @rbavery for the report.

Close #124
Close #125

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.

Updated the setup instructions to reflect the current GitHub interface,
and small changes to the lesson template files.

1.  Adding link using `page.root`.
2.  Adding ID attribute to syllabus.

Replaces #56.

1.  Fixing image link in `setup.md`.
2.  Regenerating all-figures.

Closes #42.