[fix # 82] Check R packages required by the lesson

Using `site.github.url` to refer to the repository fails to load resources when the GitHub Pages site is accessed via HTTPS, because `site.github.url` is `http` protocol.  This modifies loads of CSS and Javascript files to always use `https`.

Closes #75.

1.  Created `bin/repo_check.py`.
2.  Moved `require()` to `util.py`.
3.  Updated `Makefile` with new target.

add function knitr_fig_path

Only cleaning intermediate R files on demand.

1.  Use site.root for root path if set, otherwise use site.github.url.
2.  Display extra files for workshop-template repo as well as for lessons.