Moving post-input-refinement to a stand alone function.
Add accessor for MeshBuilder from SimulationBuilder

This is needed for doing post-input refinement when there's
a restart file. We should really refactor SimulationBuilder to
just have accessors for each of the builder modules. I still like
containing everything in SimulationBuilder to keep the Simulation
API simple, but redoing function calls is stupid and everything
in the builder modules should be const anyway.
Make do_mesh_refinement_from_input const
Rename read restart function to something more descriptive
Decide when to do post-input refinement

Based on presence of restart file.
Need to reinit after the mesh refinement
Warning+temporary fix for locally_h_refine+restart
Merge pull request #120 from pbauman/input_refinement_restart_fix

Input refinement restart fix