Can you tell me if you still use
alignPeriodicBoundaries() when reading MSH2 files? If you do, do you mind if I set
Mesh.IgnorePeriodicity=1 by default to bypass it by default?
In my experience
alignPeriodicBoundaries() is completely broken. Try e.g. the attached .geo file: mesh and save in MSH2 format. Then load the mesh - some nodes are moved to unexpected places.