Support md_extensions or variant in YAML

[hawkrobe]

RMarkdown usually allows you to modify templates with variants or Markdown extensions like this:

---
title: "Habits"
output:
  html_document:
    md_extensions: -autolink_bare_uris+hard_line_breaks
---

I tried to get this to work a few different ways with the cogsci2016 template, but I think the arguments are not getting passed through?

The practical context in which this came up: Markdown sometimes auto-breaks section titles in terrible ways and apparently the only way (?) that you can force a line-break is to use the escaped_line_breaks extension!