I installed version nightly 1.0.1 (using the graphical installer) on Windows 10 and, in looking around, I found a settings option to allow Atom to update. I checked that, and in the packages section a bunch of the packages showed updates as being available. I allowed these to be done and after several had downloaded, there was a restart prompt saying that the rest of the packages would be completed afterwards. I restarted, but unfortunately Luna Studio was now broken.
If it’s currently unsafe to allow updates, maybe the option should be disabled so that others don’t end up with a broken environment. If it should be OK to get the updates in principle, can you just confirm that something is currently broken in the particular build I had?