Goal Completion Audit

The old completion audit claimed support for private Ripple transport, simulation, and output-writer subsystems. Those subsystems have now been removed.

Completed In This Cut

• Removed bespoke Hamiltonian finite-volume advection code.
• Removed Ripple-owned Simulation, callback, diagnostic writer, checkpoint, and dataset writer code.
• Removed JLD2/NCDatasets weak-dependency output extensions.
• Moved vertical Q-transform geometry into the physical RectilinearGrid.
• Reduced examples to the source-only and coupling tutorial path.
• Added direct Oceananigans.Simulation and JLD2Writer coverage.
• Added horizontal physical transport through Oceananigans tracer advection schemes, with WENO integration coverage.

Open

• Transport validation still needs current-coupled and non-periodic cases.
• Publication readiness should be re-audited after those optional gates pass.