Update documentation and usage of stage callbacks (`stage_limiter!` in OrdinaryDiffEq.jl)

Stage callbacks (`stage_limiter!` in OrdinaryDiffEq.jl) were made keyword arguments of `solve` instead of arguments to each algorithm in https://github.com/SciML/OrdinaryDiffEq.jl/pull/3835 (with deprecation path). We should consider to update our examples and documentation when this API has stabilized there.

Review the examples and documentation that use stage_limiter! as an algorithm argument, then compare them with the stabilized solve keyword-argument API described in OrdinaryDiffEq.jl PR #3835. Update the affected usage once that API is stable, and consider the work done when the examples and documentation consistently show the new form without relying on the deprecation path.

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