Resolve non-manifold geometric situations

[sloriot]

These correspond to self-intersection in the mesh produced for example by orient_polygon_soup() and stitch boundary cycles or duplicate_non_manifold_vertices().

One way to solve it is to raise water in the n sheets of each non-manifold situations (n-1 might be sufficient but to be symmetric it is advised to do it for all of them).
I have some code around doing it.