DMPlex: Reorder global and universal node numbering

Reordering the global and universal node numbering created by the
Plex is required to make DoFs contiguous within each PyOP2 entity
class. The DefaultSF that defines the halo-exchange can then be
derived from the new node numbering exchange.

DMPlex: Cleaning up node renumbering
DMPlex: Creating Halo objects from DMPlex

We derive the receives from the associated PetscSF and the sends are
derived by gathering rank numbers via the PetscSF. The global_to_universal
numbering map is derived directly from the global and universal numbering
sections associated with the FunctionSpace.
DMPlex: Adding support for internal and external facets.

Internal and external facets are marked on the sequential Plex
using DMLabels, from which the auxiliary _Facets object can be
derived. When doing this a permutation needs to be applied to all
cell cones to align DMPlex's local facet numbering with Firedrake.
DMPlex: Adding support for boundary IDs.

Boundary IDs are applied via the Plex label "boundary_ids" and
mimic the previous gmsh-based unit mesh setups.
DMPlex: Switching most remaining unit meshes to use DMPlex.

Build DMPlex objects from coordinate and cell-to-node mapping for
unit triangle, tetrahedron and interval. Only UnitCircle still requires
Gmsh meshing, but _from_file() now uses DMPlex's Gmsh interface.
DMPlex: Creating IcosahedralSphereMesh from DMPlex

This requires proper dimension handling, where topological and
geometric dim can be different.
DMPlex: Adding plex-based extrusion

For extruded function spaces we use sections that point to stacked
vertical dof columns for each point in the base plex. When building
element->dof mappings we then traverse the closure explicitly and add
the DoFs belonging to the first element in the stack according to
explicit extrusion numbering rules.
DMPlex: Relaxing several convergence tolerances
DMPlex: Adding (limited) support for various mesh formats
DMPlex: Disabling tests that require improved Gmsh support in PETSc