Replace references to master branch (#2210)

Commit history before merge:

* Replace references to master branch
* Update .flake8 to reference docs on RTD

  We're moving away from GitHub as a documentation host to only RTD because
  it's makes our lives easier creating good docs. I know this link is dead right now,
  but it won't be once we release a new version with the documentation reorganization
  changes (which should be soon!).

Co-authored-by: Richard Si <63936253+ichard26@users.noreply.github.com>