Use unified CSS from site.

As per swcarpentry/lesson-template#140, but only the core CSS
changes.

Add debugging notes about Git and line endings

Import style for slides from https://github.com/swcarpentry/slideshows

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