(0.5.0) Updated sediment to work with all grids and model types

[jagoosw]

This PR makes sediment models work with immersed boundary grids and improves sediment testing on all grid and model types.

This breaks the sediment, nitrogen/carbon flux, and sinking flux APIs.

[jagoosw]

Think this is probably the most straightforward way to set this up, and in this case the bottom cell only has to be calculated once

[jagoosw]

I think in the same vein it may be worth modifying PAR integration to only integrate down to the bottom cell since a lot of the globe doesn't reach the bottom of the underlying grid (and at the moment I think we integrate it for the land area too)

[codecov]

Codecov Report

Patch coverage: 76.00% and project coverage change: -0.24% ⚠️

Comparison is base (ef69e24) 63.82% compared to head (3a352ad) 63.58%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #127      +/-   ##
==========================================
- Coverage   63.82%   63.58%   -0.24%     
==========================================
  Files          28       28              
  Lines        1020     1049      +29     
==========================================
+ Hits          651      667      +16     
- Misses        369      382      +13     

Files Changed	Coverage Δ
src/Light/2band.jl	88.88% <ø> (ø)
src/Light/Light.jl	33.33% <ø> (ø)
src/Models/AdvectedPopulations/NPZD.jl	90.90% <50.00%> (-1.10%)	⬇️
src/Boundaries/Sediments/Sediments.jl	65.71% <63.63%> (+6.89%)	⬆️
src/Models/AdvectedPopulations/LOBSTER/LOBSTER.jl	85.00% <66.66%> (+0.78%)	⬆️
...c/Boundaries/Sediments/instant_remineralization.jl	85.00% <100.00%> (+2.64%)	⬆️
src/Boundaries/Sediments/simple_multi_G.jl	90.38% <100.00%> (+0.80%)	⬆️

... and 1 file with indirect coverage changes

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[jagoosw]

Since it's just the codecov failing (and I'm not bothered by the lines in the NPZD model it says aren't being tested as it's just a warning and function no one will probably ever use) I'm happy for this PR to be merged now

[jagoosw]

The example was failing because I'd changed the sediment models to only use flat fields, but we can't output these still due to CliMA/Oceananigans.jl#2770 which I've not fixed yet

[jagoosw]

Nonhydrostatic + RK3 is not getting tested but it should