Update creating solution field in Formulation.py.

Update to new interface for creating solution field (and subfields) in
Formulation.py. Add setupSolnDof() to integrator as empty virtual
method.
Merge branch 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith into knepley/upgrade-petsc-interface

* 'knepley/upgrade-petsc-interface' of github.com:geodynamics/pylith:
  Mesh: Fix DMPlexCheckSkeleton() for submeshes