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So you put trustworthy, secret projects on GitHub instead of hosting them in-house?

yes, my bad, should have listened to IT

The idea was that it's more likely our servers get hacked than a breach at github. Guess I was wrong.

Microsoft built its business by selling software products. If they had meddled with Fortune 500 companies running their business-critical information on top of Windows, Microsoft wouldn't be here now. There are situations to be wary of MS, but I don't think this is one.

In Europe there are real worries about state-driven industrial espionage.

We shouldn't be worried that our developers coding habits will get connected with linked-in and fed into the surveillance state (which MS is big part of)?

Microsoft is not gonna give a fuck about your shitty little repos or anyones for that matter. What makes you think they are gonna put time and effort into mining people's code?