Hosted repositories
Set up MFK
Use GitHub’s search features as well as scraping tools to check your own code for potential data leaks.
Identify, configure and audit production branches to
Not allow force pushes.
Only give commit privileges to a small set of users.
Enforce those restrictions on admins & owners too!
Require all commits to be PGP signed (keys known in advance).
Read more recommendations by Mozilla (they learned the hard way, no need to repeat that for ourselves).
As of November 2017, GitHub tracks reported vulnerabilities in certain dependencies and provides security alerts to affected repositories.