Project restructure

The purpose of this issue is to build a suite of programs to oversee the full simulation.

The suite will consist of the following programs, each serving a purpose of maintaining the controlled environment for a large scale simulation.

# Setup Program:
Purpose of setup is, given the input generate a first _parthenon_ restart file that will generate the initial state of the simulation, to be used by other programs.

1. Create field solver initial condition and store it in binary file.
2. Create a Hermite Field and store it in another file.
3. This file names will be listed in the restart file to ship it as one package.
4. Generate particle distribution the and store it the restart file.
5. Add plots for the collision coefficients and probabilities to generate particles for quick reference
6. Store and plot configuration space geometry.

The resulting restart file may serve as unified input for other programs. It is also a first simulation snapshot.

# Governing Equations Push:
This program helps to study the deterministic orbit tracing and particle current accumulation for a given snapshot of the simulation state - the restart file. It is here
- To determine how long one needs to run an averaging loop and for how many particles to achieve a smooth current.
- To see whether the collision less push conserves the variables.
- To do a performance comparisons between adaptive and fixed time step pushers, for different time discretizations.

# Avalanche:
This program is needed to determine the optimal $\Delta t_{LA}$ so that the particle distribution growth at each collision samling is within reasonable limits.
- This code is tested against paper results on analytic fields in radial case and on slab
- It produces a new look up table for growth within the given spec

# MHD:
This program simply evolves the fields without any contribution of particles.
- We need it to stay sane

# Hybrid:
This program runs the code and produces snapshots to be studied by other programs
- This one is actually giving results, others are needed to be sure that these results are correct and we know what we are doing.

Start by reading the issue's five program areas: Setup, Governing Equations Push, Avalanche, MHD, and Hybrid. Identify the existing entry points and restart-file flow for each area before making changes. Done means the suite can create and consume the described simulation snapshots and produce the listed validation outputs, but the issue does not name files or tests.

Written by the indexing model from the issue text.