Construction/Size Entities in .msh file
Jean Francois has already helped me quite a bit on this. The issue is that, when I write a .msh file, construction vertices (e.g., centers of circles or points that are put in for size info) are written into the $Entities section and into the $Nodes and $Elements section of the mesh even though they are not a part of the mesh. Initially we thought that we could eliminate them by defining physical groups of all the elements we want and these would be left out but it turned out they were still there-- not just in the model Entities but also the mesh Nodes and Elements listed.
The obvious suggestion of deleting them before making and writing the mesh works in most cases (e.g., OpenCascade factory) but this also fails sometimes or is at best awkward and error prone for users.
Finally, it is possible for us to make our mesh converter filter out all entities that are not part of the topological model of the mesh (e.g., model vertex not used in any model edge, edge not in a face, face not in a volume).
So solutions exist but all are tedious and error prone. It would be highly desirable to have an option only write the model entities that are topologically connected in the construction of the mesh and the actual mesh entities used in the discretization. To be clear it is extremely valuable to have the $Entities section to help us construct a topological model so that was a great addition but it would be nice to have the option to limit the .msh file to not include model and mesh entities that would not be used in a FEM or FVM discretization.