Refactor C++ dolfinx::mesh::Topology

[jorgensd]

Describe new/missing feature

Current Topology initializer just takes in an MPI communicator and a cell type, and then all other information is passed through set_index_map or set_connectivity or original_cell_index.
However, a topology isn't really valid (none of the create_entities or create_connectivity functions can be called without):

• A cell index map
• A vertex index map
• A cell_to_vertex connectivity
• Original cell indices ( Not required for create_*, but for reading external data).

Additionally, users can make invalid connections or index maps through set_index_map and set_connectivity post initialization.

A benefit of this is that we allow for an "adaptive mesh topology".
However, we do not have the same flexibility for the mesh geometry (cannot replace index map or change the size of x, or the indices of the dofmap).

Thus, I propose we refactor topology such that:

• Initializer: Takes in communicator, cell_type, cell_index_map, vertex_index_map, c_to_v and original_cell_indices
• Destruction of connectivity: Sometimes users might want to delete a connectivity after usage. We could have a clear_connectivity(i, j) that removes the connectivity (and guards against removal of c_to_v, c_to_c or v_to_v connectivity).
• Destruction of entities: Can currently be done with set_index_map (which is unsafe). Should be done with a clear_entities(i) with guards against clearing cells or vertices.

Suggested user interface

No response