Fix viscous sponge

[charleskawczynski]

Found in #3817. I'm trying to track down where this came from.

[coderabbitai]

Walkthrough

The change updates the source of the vertical velocity field ᶠu₃ in the additional_tendency! function, switching its input from the time tendency field Yₜ.f.u₃ to the state field Y.f.u₃. Additionally, the reference counter in reproducibility_tests/ref_counter.jl was incremented from 239 to 240, with a corresponding changelog entry noting a bug fix in the viscous sponge. No other logic, structure, or public interface is modified.

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Reviewing files that changed from the base of the PR and between 68107c2 and 627be2a.

📒 Files selected for processing (2)

• reproducibility_tests/ref_counter.jl (2 hunks)
• src/prognostic_equations/remaining_tendency.jl (1 hunks)

✅ Files skipped from review due to trivial changes (1)

• reproducibility_tests/ref_counter.jl

🚧 Files skipped from review as they are similar to previous changes (1)

• src/prognostic_equations/remaining_tendency.jl

⏰ Context from checks skipped due to timeout of 90000ms (12)

• GitHub Check: test (1.11)
• GitHub Check: downstream ClimaCoupler.jl (1.11)
• GitHub Check: test (1.10)
• GitHub Check: downstream ClimaCoupler.jl (1.10)
• GitHub Check: ci 1.11 - windows-latest
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[szy21]

I'm surprised this hasn't caused much problem. Thanks!

[szy21]

I'm going to change the MSE and get this in. (This may help with recent failure in AMIP.)

[akshaysridhar]

Oof; thanks @charleskawczynski