Fix and test MaterialID in msh2vtu

This introduces more tests to systematically check, if MaterialIDs are properly generated from gmsh physical group tags. Also Fixes a failing case, where a single physical group with a tag != 0 would not reindex to 0 if reindex=True. Also changes the logic from reindex: previously would use a offset to reach 0, i.e. [1,2,4] -> [0,1,3] now it reindexes completely, i.e. [1,2,4] -> [0,1,2]