What an odd thing.
Looks to me like a bellows type structure with a clear roof for light and opaque sides for security. Potentially on a rolling structure for moving entire projects around with some amount of obscurity. I can imagine such a thing inside hangars with multiple projects that don't want watchers. You can get similar things for cars - including inflatable cocoons for controlled atmosphere, however they are not mobile.
I have to assume that USAF know what's overhead that airfield every moment of the day, so I then have to assume that this was a deliberate act to send a message.
The other thought I had was that the aircraft had somehow become immobile after leaving the hangar (from tyres to system to engine problems I suppose) and required a cover to protect against the elements until it could be recovered. Presumably skin materials could be very delicate. There is also still the point of being obscured from overlooking vantage points by guys who go out with telescopes attached to their cameras.