Delete old .md and .html files from /docs

[KatherineCox]

Describe what is not working with the template or is unclear in the documentation
When .Rmds are deleted, the corresponding .md and .html files in /docs are not deleted. This means that pages like this exist in the rendered book.

Please link to the specific course repository you are working on
https://github.com/jhudsl/GDSCN_Book_SARS_Galaxy_on_AnVIL
(also a problem for our other AnVIL guides, but this is the most recent and likely has the most up-to-date version of the template)

To Reproduce

1. Set up repository using template
2. Delete e.g. 02-chapter_of_course.Rmd, and merge/rerender site
3. Visit the url for the deleted content e.g. (course-url)/topic-of-section

Expected behavior
Sections that no longer exist in the .Rmd source files don't exist in the rendered output.

[cansavvy]

It just so happens I already have this change in the works! Its related to #317 and I'll be filing a PR shortly. Thanks for the issue. Let me know if you see anything else!

[KatherineCox]

@cansavvy that will take care of the lingering example files, but I think the problem will still exists if I create a new Rmd and then later decide I don't want that section.

e.g https://jhudatascience.org/AnVIL_Book_Getting_Started/student-account-setup.html shouldn't exist anymore, since we removed it from the .Rmd content

[KatherineCox]

I think we need a way to delete the content of docs every time the book rerenders.

[cansavvy]

Yeah, this has been on my TODO list: See #111

If you'd like to take a whack at it, that'd be great, but I can also bump it up on my priority list.