Upgrade to Hermes-3

[johnomotani]

Switch to using Hermes-3 instead of Hermes-2.

Example simulation is similar but not identical to the Hermes-2 version. Some differences are due to differences in the model implemented in the source code (e.g. in the sheath closures), some (may be) due to me not having spent any time trying to make the inputs match.

Todo:

• Hermes-3 submodule needs updating once Option for density and energy sinks for all species with sheath closure bendudson/hermes-3#37 is merged so that Hermes-3 includes the bugfix in Initialise second boundary cells of phi when phi_boundary_relax=false bendudson/hermes-3#36 to avoid random crashes.
• Replace the compiled manual pdf (is currently the Hermes-2 manual) with the Hermes-3 one once Option for density and energy sinks for all species with sheath closure bendudson/hermes-3#37 is approved and merged.
• Add note in README.md that the example input file is the same as the Hermes-3 2d turbulence example (which was copied from the one created in this project by modifying Hermes-3's Blob2d-Te-Ti example).