What term do we use to describe the gesture that we find when someone wakes up and flexes her arms?
The technical term for this is pandiculation
A stretching and stiffening of the trunk and extremities, as when fatigued and drowsy or on waking, often accompanied by yawning. Wiktionary
However, this would not be understood by most speakers, and it would normally be refered to as just stretching.
Are you looking for something more specific than stretch?
1 : to extend (one's limbs, one's body, etc.) in a reclining position
You could call it a morning stretch or a wake-up stretch, but I don't how common those are, and either could easily mean a yoga-like stretch intended as light exercise done after waking up.