I asked the same question on the Military Aircraft thread, C-Seven replied with the following;

“As far as I know they are indeed to verify the geometry of the plane using vision devices.
Those dots disappear after a while and if they are there it means that the plane went out of production line not a long time ago.
If I’m not mistaken the 113-GT is the Rafale C n°141 equipped with the AESA and it’s a new one.”

Its amazing how much information is in a photograph, once you have time to study them you always find something lurking in one or two that get the little grey cells doing overtime…..
Post your other shots Growler, would love to see them.