BREAKING: Change output format and when step is changed

[nhz2]

This should help prevent over 1000 files from being in a directory, which can be an issue on some file systems.

Instead of storing snapshots in "traj/snap<i>.zarr.zip" they are now in "traj/<i÷1000>/<i%1000 zero padded to 3 digits>.zip" so for example, "traj/0/000.zip", "traj/0/001.zip" ... "traj/42/999.zip".

There is a function step_path(step::Int)::String to convert, for example, from 1 to "0/001.zip" and a function steps_traj_dir(traj::String)::Vector{Int} that
returns the snapshot steps from low to high found in the traj directory.

This PR also removes the deprecated run_sim function.

Lastly, when the simulation is run, the step variable is now updated before the calling loop instead of after.
This means the first call to loop gets step = 1 instead of step = 0