To be clear: The accepted answer is correct. Try it first. However, it may be unnecessarily complex for some use cases, particularly if you encounter obnoxious errors such as 'fatal: bad revision --prune-empty', or really don't care about the history of your repo.
An alternative would be:
This will of course remove all commit history branches, and issues from both your github repo, and your local git repo. If this is unacceptable you will have to use an alternate approach.
Call this the nuclear option.