WIP: Update submodules, API changes, tracer swarm packs, formatting CI

[AstroBarker]

PR Summary

Far overdue, this PR updates parthenon, singularity-eos, and singularity-opac and makes necessary changes to work with their updated versions.

• Updates to MHD (API changes for packing)

• Overhauls to swarm API

  • Tracers use SwarmPacks now
  • Monte Carlo needs refactoring for it (Move Monte Carlo to swarm packs #224)
  • Tracers should be refactored to work on MeshData

• The advection problem's tracers were refactored due to a bug on multiple blocks

• Some updates to BCs, probably more simplification can be done.

• The fast logs of singularity-eos are default disabled.

• Updates neutrino mean opacity API

• Tracers:

  • Use SwarmPacks (as mentioned)
  • Refactored to work on MeshData instead of MeshBlockData
  • tracer swarm variables are SWARM_VARIABLES now, so access with e.g., tv::rho(), tv::rho::name() e.g., (for namespace tv = tracer_variables; to enable type based packing.

• Also, the github ubuntu-latest changed and clang-format-12 was no longer available. I have moved us to installing clang-format with pip, pinned at version 12.0.1. Which was not compatible with ubuntu's v12...

• Weirdness seems to have crept in to the regression testing. Some tests, despite producing an identical gold file (when ran with --upgold) failed tests due to how hdf5 was loaded. Unsure what caused this change, but a fix was implemented.