Update half-edge geometry in geometry layer in more places

[hannobraun]

I already made sure the geometry layer is updated in all the obvious places in #2271, but it turns out there were quite a few more that are less obvious.

The problem here is that everywhere a half-edge is updated, by calling update_curve or update_start_vertex, you create a new half-edge, and the new half-edge does not have any geometry associated with it in the geometry layer. That needs to be added manually, which is exactly what I did in this pull request.

This is a pain, and error-prone, but I think it's only relevant during the current transition. I expect that long-term, only Surface, Curve, and Vertex will have geometry associated with them, and since there's no reason to create new instances of those while wanting to keep the geometry, this problem won't be present then (they contain no topological data, so changing the geometry is literally the only reason you'd want to create a new instance).

This is another step towards #2116, as now it's possible to actually use the geometry from the geometry layer. This is the next step, and removing that part of the geometry from the object graph can come right after.