Add capability to rerun JPEC from an HDF5 file

[jhalpern30]

Currently, we write a decent amount of the outputs from the run to the HDF5 output file in write_outputs_to_HDF5. This is now slightly outdated since some TOML fields have been removed and consolidated into a single file. I think we're at a point where we can dump the outputs in a way + add a method to main where it pulls the TOML info from the HDF5 output. This would be a convenient way of reproducing runs. Unsure as of now if we should also save the equilibrium data, or that would still be on the user.

[logan-nc]

This seems like something Calin could do! What's his github username to assign him?

[jhalpern30]

@calin1989