Symbolic names for boundary ids

This turned out to be a much larger feature than I thought it would be. In any case, I think that it covers all of the places where we input or output boundary indicators in the input file, and it should now be possible to use symbolic names for them as provided by the geometry model.

There is a single place where it is currently still incomplete, namely in parsing the "Prescribed velocity boundary indicators" in Parameters::parse_geometry_dependent_parameters(). This will conflict with my changes to make pressure/traction boundary conditions possible and I would like to defer dealing with this place until this other patch. I promise to get to it.

This patch also addresses issue 126 (https://github.com/geodynamics/aspect/issues/126) whereby we need to initialize the SimulatorAccess object of every plugin before we parse parameters. This is likely about half of the total patch.

With this pull request, I'd like to ask for a code review. After addressing everything, I can then squash the whole thing and commit it as one, instead of the almost 40 individual commits this request consists of.
The manager objects for the various mesh_refinement and postprocessor objects do not have an initialize() function of their own. But they call initialize() right after parse_parameters() on the objects they manage.