Excluding unwanted files from build

Update LAYOUT for changes from #103

Change filters since classes must be explicit

Add examples of links to part of our lessons

Add classes

All classes **must** be explicit because this will make easy
to translate the lessons.

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.

Add input cell question to FAQ

Small improvements to CSS

Close #116.

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