Add validation for callout boxes

Implement template-specific callout rules. Add tests and fix bugs revealed.

Narrow def of callout: block must have heading.

Simplify way that callout counts are tracked, improve log messages, and add further unit tests of callout validation.

Ensure that callout validation is actually run

Set fig.path in tools/chunk-options.R to send all plots to fig/

default instead of figure/.

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

Improve script to setup labels

Validator should check that required files exist

- Delete GitHub's default label that will not be used
- Create new labels
- Update color for labels

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

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