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docs: an Applications-in-practice section - #189
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… a real pipeline Appends a worked real-world case to docs/COOKBOOK.adoc: the concrete situation in an amplicon-sequencing pipeline in production use where the type, the OND discipline or the algebra earns its keep -- and what the untyped or undisciplined alternative gets wrong. Documentation only; no code changes. Generated by Mistral Vibe. Co-Authored-By: Mistral Vibe <vibe@mistral.ai>
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Review comments at @docs/COOKBOOK.adoc:
- Around line 761-767: Revise the CNO passage to describe the type-level
treatment as proposed, not as an existing guarantee in MetaManifold. Remove
claims of a machine-checked answer unless the cookbook links to a
MetaManifold-specific proof or type-check artifact.
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…app's code (CodeRabbit, PR #189) The section read as though MetaManifold already provides a typed machine-checked guarantee; its implementation enforces both rules with status symbols and guarded control flow, held by tests. The passage now says that plainly, names the type-level treatment as the modelled endpoint checked in this repository (proofs/agda/OND.agda, proofs/agda/CNO.agda), and links the concrete app-side artifacts at their pins: the status logic in src/analysis/analysis.jl (7d5e9a4) and the complete-separation refusal asserted in test/unit/test_differential.jl. The closing sentence claims a machine-checked account of the failure paths, not a machine-checked answer shipped by the app. Generated by Mistral Vibe. Co-Authored-By: Mistral Vibe <vibe@mistral.ai>
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What this adds
An Applications in practice section in
docs/COOKBOOK.adoc: one worked real-world case that shows the OND side: significance statuses become a type where an unrun test cannot publish; the CNO side: the complete-separation refusal certified as an operation that provably computes nothing -- grounded in MetaManifold, an amplicon-sequencing pipeline in production use, because the value of the discipline is clearest on a live pipeline rather than a toy.The section answers the question a newcomer actually has: what is this for in the real world, and what goes wrong without it? It is deliberately short, states what the undisciplined alternative gets wrong, and links the concrete case.
What this leaves out
Documentation only. No code, no API, no claim changes anywhere else in the repo. The commit is signed.
Versions tested
Not applicable -- documentation.
Generated by Mistral Vibe.
Co-Authored-By: Mistral Vibe vibe@mistral.ai
Summary by CodeRabbit