@J. R. Hartley said: "Wonder which new and exciting way they're gonna fuck it up."
They'll integrate it with Linkdin, Skype, Azure and MS developer tools.
Their press release said: "... bring Microsoft’s developer tools and services to new audiences."
Expect to see Github features appearing which hook your code repos directly into MS Azure for deployment. Your Github rankings will be reflected in your Linkdin profile. If you don't have a Linkdin profile, one will be automatically created for you based on your Github data. Skype will be integrated into team meetings for projects. MS Visual Studio will have deep integration into GitHub beyond just being a Git client.
So, you'll still be able to use Github via the web interface and via the command line Git client, but every possible Microsoft service that can be integrated into Github will be to the degree that a software developer could work through the life of an entire project without ever leaving the Microsoft walled garden.
Microsoft just paid a staggering amount for Github (three times as much as press analysts were speculating) and they will be looking for ways to make that back. Introducing a variety of forms of vendor lock-in in order to sell other goods and services is the obvious choice here.
I'm looking into what is involved in setting up a Gitlab account. I won't pull my open source projects from Github, but I won't use it as the sole public repo any more. Just like a lot of Youtubers have come to the realisation that they need to diversify their options rather than being at the mercy of Youtube's latest policies, I'm going to make sure that I can pull the plug on Github at any time if necessary just like I did with Sourceforge.
P.S. Don't be surprised if Amazon come out with some sort of response to this.