Update YAML metadata values

Logical values in YAML were unusual: true/false, yes/no, and on/off.

Now it seems necessary to use only true/false, otherwise the GUI won't work...
See https://github.com/rstudio/markdown/commit/e9d9c350072c8fa487d985afa6f5b4b41ebe9aba

In the YAML header of the rmd file, we need to replace:

---
output: 
  html_document: 
    keep_md: yes
    self_contained: yes
---

By:

---
output: 
  html_document: 
    keep_md: true
    self_contained: true
---