Restarts from HDF5 checkpoints

[kpwelsh]

Currently some of our code pretends to support restarting. Despite it being an important functionality for HPC users that expect long running jobs (1day+), we don't really support it.

We should consolidate the solver state into a single object and support periodically creating checkpoints that we can restart from. These should probably be HDF5 files to support exporting/importing the exact solver state as structured binary data.