Support running VL+CT Integrator as a single stage integrator

[mabruzzo]

Overview

This PR is long-overdue.

• It adds support for running the VL+CT machinery as a single-stage integrator (for reference the VL+CT is a 2-stage predictor-corrector scheme). This will be really useful for debugging (specifically I need to this to help debug a flux-correction bug).
• It also lays the ground-work for introducing Runge-Kutta time-integration in the future (just like in Athena++). But that's a topic for another day

Actual Changes

To accomplish these goals, this PR does the following:

1. It introduces the EnzoMHDIntegratorStageCommands class, which encapsulates all of the functionality that is necessary to update hydro/mhd quantities over an individual stage (the number of stages per timestep depends on the time-integration strategy). This class was necessary since the EnzoMethodMHDVlct class was starting to do too much (and becoming hard to understand). In detail:
   • I moved a bunch of the contents of EnzoMethodMHDVlct::compute into EnzoMHDIntegratorStageCommands::compute_update_stage.
   • While doing this it made sense to migrate a few helper methods, like the compute_flux_ and compute_source_terms_, as well as a bunch of attributes from EnzoMethodMHDVlct to EnzoMHDIntegratorStageCommands.
   • I also migrated a bunch of logic from EnzoMethodMHDVlct's constructor and ``EnzoMethodMHDVlct::timestepover toEnzoMHDIntegratorStageCommands` (I'm less sure that these were optimal choices).
   • EnzoMHDIntegratorStageCommands is ignorant of how the stages in the MHD/Hydro integrator are linked together. That's handled by EnzoMethodMHDVlct. The Method class also tries to take most of the responsibility for interfacing with the rest of Enzo-E
   • The docstrings in the code should hopefully make things pretty clear.
2. I deprecated the Method:mhd_vlct:half_dt_reconstruct_method and Method:mhd_vlct:full_dt_reconstruct_method parameters. The former only existed due to an oversight on my part (it never made any sense for this to exist - the VL+CT scheme doesn't work unless nearest-neighbor reconstruction is used). The latter is replaced by the new Method:mhd_vlct:reconstruct_method. Backwards compatibility has been maintained.
3. I introduced the Method:mhd_vlct:time_scheme method to choose the time integration method. Right now, it defaults to "vl" (the predictor-corrector scheme) and the only other choice is "euler" (the simpler 1-stage integrator for testing purposes). In the future, this could be extended to accept other choices (e.g. for a Runge-Kutta integrator).
4. I updated the website documentation to reflect the changes in the parameters.

PR Dependency

This PR unfortunately needed to build on changes from PR #302 (there would have been too many merge conflicts) and this probably can't be reviewed until that PR is merged (it should be merged soon - just waiting on a reviewer to hit approve after I made their requested changes). I will update this PR when it's ready

EDIT: This is now ready for review.

[gregbryan]

Looks great -- clearly commented.

[jwise77]

Thank you very much for this addition! It is structured well and heavily commented. I'm approving and merging.

[jwise77]

Oops, no merging yet. @mabruzzo Can you resolve the merge conflict and then we can merge after it passes the tests (again).