Make sure all HTML dependencies can be opt-out

[cderv]

I think this is important that everything we add to activate some feature, or modification over Pandoc behavior for example can be opt-out.

Most of the feature can be using argument - like theme = NULL to remove boostrap dependency for example.
However, some JS script cannot be deactivated yet (like html_dependency_header_attrs()).

I believe this could be something to watch out for: any HTML dependency should be documented and how to opt-in / opt-out.

Related issues:

• Redundant removal of attributes on HTML headers bookdown#865
• Enhancement: support for non-standard RMarkdown directory structures. #1859

[cderv]

Note to self: rstudio/bookdown#865 is a priority to solve for next version