Rejuvenate API refs

[Yoshanuikabundi]

This PR goes over the API reference with a fine toothed comb:

• Reorganise the reference to be more objective-focused, rather than grouping data objects separately from the functions that work on them
• Ensure important objects like LigandNetwork, the ligand network loaders, and various abstract base classes are documented.
• Include more comprehensive documentation of the members of documented classes, including classes without docstrings.
• Correctly renders some maths in the docs
• Make type annotations for using score functions more consistent and complete
• Fix typos, add docstrings, and make style consistent across the API reference.
• Remove unimplemented TMCSR scorer from docs
• Switch order of subheadings under "Simulation Campaign Planning"
• Add GufeTokenizable to docs

RTD should build without warnings once OpenFreeEnergy/gufe#220 is merged.

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[codecov]

Codecov Report

Patch coverage: 65.21% and project coverage change: -0.32% ⚠️

Comparison is base (25fb327) 91.29% compared to head (c3250ae) 90.98%.
Report is 40 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #527      +/-   ##
==========================================
- Coverage   91.29%   90.98%   -0.32%     
==========================================
  Files         116      114       -2     
  Lines        7056     6876     -180     
==========================================
- Hits         6442     6256     -186     
- Misses        614      620       +6     

Files Changed	Coverage Δ
openfe/setup/atom_mapping/ligandatommapper.py	91.66% <ø> (ø)
openfe/setup/atom_mapping/lomap_mapper.py	100.00% <ø> (ø)
openfe/setup/atom_mapping/perses_mapper.py	45.45% <ø> (ø)
openfe/setup/atom_mapping/perses_scorers.py	32.25% <ø> (ø)
...lsystem_generator/easy_chemicalsystem_generator.py	100.00% <ø> (ø)
openfe/utils/handle_trajectories.py	0.00% <0.00%> (ø)
openfe/setup/__init__.py	100.00% <100.00%> (ø)
...ork_planner/relative_alchemical_network_planner.py	97.59% <100.00%> (-0.03%)	⬇️
openfe/setup/atom_mapping/lomap_scorers.py	100.00% <100.00%> (ø)
openfe/setup/ligand_network_planning.py	100.00% <100.00%> (ø)
... and 1 more

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