Updated a deprecation in mongoose, so that no longer shows up in the console.

In addition, have updated the github provider to use new API urls that were also deprecated and fixed the refresh process when looking to update the list of repos.

In addition, I've made it possible to run /auth/github endpoint (manual for now) to update the accesstoken for github if you have issues with not being able to authenticate. The plan is to make this available via the UI, and eventually to make it automatic.