Excluding unwanted files from build

Change filters since classes must be explicit

Improving support for R Markdown.

1.  Adding `tools/chunk-options.R` with support for Pandoc-based conversion of R Markdown to plain Markdown.
2.  Modifying `Makefile` to handle any R Markdown files that are present.

Changes have been checked by @jdblischak in the `r-novice-inflammation` project.

Small improvements to CSS

Link text validation changes

Changes to link text validation per #58 and #90. Validate link text in index.md (always), or only in headings (reference.md and instructors.md)

Demote msg level when http links skipped

Strip anchor from filenames in error messages

Validator logging QA bugfixes

-   Remove extra space before title of boxes
-   Remove background color of boxes when printing
-   Add "Input", "Output" and "Error" tips for code blocks
    when printing
-   Avoid duplicate lines

Improve logging of YAML header errors

added some challenge CSS

Make validator imports more pythonic

Fix typo

Update License.md md5sum on tools/check based on 2f4703e8

Add requirements.txt necessary to build and run validator

Make filter for id at definitions general

Adding url placeholder

The original plan was to put the URL for this repository in a configuration file that authors could edit when creating actual lessons.  However, it looks like Pandoc only does one level of variable expansion, so variables inside `_includes/footer.html` (which is itself interpolated as a variable) aren't expanded.  Instead, we will tell authors to edit `_includes/footer.html` in the `README.md` in the `gh-pages` branch.

Fix unittest for changes on motivation.md

This solves #77 by add id attribute to every item of a definition.