This PR is a complete redo of how MEDYANSimRunner is used. Before, it was installed as a command line tool. Now it is just a regular Julia package inspired by how build scripts work in BinaryBuilder.jl.

To upgrade inputs to this new version do the following:

1. Add import MEDYANSimRunner to the start of main.jl and add MEDYANSimRunner to the input environment.
2. Add the vector of jobs to run to main.jl, for example, jobs = ["a", "b", "c",]. This should contain what used to be in jobnames.txt.
3. Add abspath(PROGRAM_FILE) == @__FILE__ && MEDYANSimRunner.run_sim(ARGS; jobs, setup, loop, load_snapshot, save_snapshot, done) to the very end of main.jl

To run the simulation, instead of:

medyansimrunner run input output jobnames.txt 3

Do:

julia --project=input -e 'using Pkg; Pkg.instantiate();'
JULIA_LOAD_PATH="@" julia --project=input --startup-file=no input/main.jl --out=output --batch=3 --continue

The output of the simulation is also very different. There is no more list.txt. Instead extra metadata has been added to each snapshot, which is now stored in the traj output subdirectory in snap$(step).zarr.zip files, along with header.json and a new footer.json. Because of this extra metadata, the ZGroup returned by save_snapshot which used to be the root of the snap$(step).zarr.zip files has been moved to the "snap" subgroup.