Fellow Atom user here. According to Lee Dohm, Open Source Community Manager at GitHub, "Atom remains key to GitHub. Our product roadmap is set, and the team will continue all of their work." [0]
A product roadmap is set until it changes. "I am altering the deal. Pray I don't alter it any further".
Besides, Microsoft has enough PR skills to avoid unpleasant announcements about redundant products for a while after an acquisition they know to be worrying.
Until they aren't. I really don't see MS putting work into two code editors that are in direct competition with each other. I'm sure they'll let the dust settle for a while, but Atom will vanish from Microsoft's product list. No doubt.
I actually really like Visual Studio Code, I could imagine a great product coming out of the marriage of Code and Atom. I could also imagine infighting killing Atom, but I’ll try to be optimistic.
The really nasty changes always seem to come at the beginning of the second fiscal year after acquisition. So meet me back here in 18 months and we’ll talk.
Besides, Microsoft has enough PR skills to avoid unpleasant announcements about redundant products for a while after an acquisition they know to be worrying.