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I've found the problem: it's in the float-coarsening of the geometric angle of elevation in Refraction::innerRefractionForward that breaks things. I've tried removing all this coarsening from this method, so that calculations are all done in double, and now nothing wobbles.
To reproduce, try the following steps:
The screenshots of Thebe, as an extreme example:
I would suppose a problem with precision of projection, but given that without atmosphere everything is OK, the problem apparently is elsewhere.
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