Tria socket & parameter cleanup

[landinjm]

This is a big PR since I decided to refactor/rewrite a lot of the parameters.

Fundamentally, one thing has changed in how we handle parameters from file. We now have a 5 step process.

1. Predeclare (new)
2. Preassign (new)
3. Declare
4. Assign
5. Validate (optional)

The pre steps are necessary so I can use type polymorphism on the mesh classes. With the two extra steps we do a first pass over the parameter file before deciding what sections to check later on. I imagine these will also be useful for other things down the line.

Some of the parameter names have changed, but everything remains backwards compatible. The only breaking change is the access of mesh dimensions in applications. Now, to get the size of a rectangular you have to cast the mesh to whatever your mesh type is. We could make a safer version of this for users later on.

const auto &mesh = dynamic_cast<const RectangularMesh<dim> &>(
      *get_user_inputs().spatial_discretization.mesh);

const dealii::Tensor<1, dim> &mesh_size = mesh.upper_bound - mesh.lower_bound;

Additionally, size is no longer a member for rectangular meshes. There is only upper and lower bounds.

Closes #572 ParameterBase now exists and see above
Closes #606 ParameterBase now exists and see above
Closes #441 MeshBase now exists and see above
Closes #714 This can be set with the UserInputParameters constructor
Closes #1118 This can be set with the UserInputParameters constructor
Closes #959 MeshBase now exists and see above
Closes #671
Closes #502
Closes #713 'MeshBase` requires the definition of a distance function
Closes #146 Parameters are there. Restarts aren't

[landinjm]

Core library compiles. Now there's just a bunch of annoying things to do to make sure the applications compile :(

[landinjm]

I also gave up on UserConstants because I hate that class and don't want to deal with it

[landinjm]

All the applications, compile. I ran a few in debug and everything seemed fine.

Nucleation application is broken for unrelated reasons. See #1189

[landinjm]

@fractalsbyx when do you think you'll get a chance to look this over? I'm hoping to get this out to get restarts and file input out tomorrow.

[fractalsbyx]

@landinjm I have been working on it today. I will submit a PR of changes prob tonight.

[landinjm]

Cool thanks!