feat: redesign around phenotype-driven triage, not variant filtering

A table with filters made the user do the work. Rare disease triage is a different task:
which few variants could explain *this* patient's phenotype, and why. The app now answers
that, and lets a reviewer act on the answer.

Domain
- a case is a proband: a VCF plus the HPO terms observed in the patient (samples -> cases)
- HPO's gene-to-phenotype annotations are loaded as reference data (scripts/load-hpo.py)
- each candidate can be shortlisted or dismissed with a reason and a note

Ranking (app/services/triage.py, 21 tests)
- weighted sum of phenotype match, rarity, consequence severity and the model's score,
  with every component shown next to the candidate
- rarity and consequence filter; phenotype only ranks, because a real diagnosis can sit in
  a gene nobody has annotated yet and filtering on it would hide exactly that case
- ClinVar is deliberately not an input: it appears beside the result as independent
  confirmation, so nothing ranks highly merely because ClinVar already said pathogenic

UI
- the funnel is the headline: variants called -> rare -> coding candidates -> phenotype-matched
- ranked candidates with evidence chips, not a grid of everything; filters are demoted
- a variant panel showing the score breakdown, the matched HPO terms, the raw VEP record and
  links out to Ensembl/gnomAD/ClinVar, with the decision controls
- a printable case report: phenotype, funnel, shortlisted variants with reasons, provenance

API: /cases with phenotypes, /cases/{id}/candidates (funnel + ranked + weights),
/variants/{id}, /variants/{id}/decision, /cases/{id}/report, /phenotypes for the picker.
Scoring moved under the case and now answers 503 with the reason when no model registry is
reachable, instead of a 500.

Verified end to end on a simulated proband (scripts/make-demo-case.sh: real GIAB HG002
background + one real ClinVar 2-star pathogenic NF2 variant). 13 variants called -> 1 coding
candidate, and the planted variant ranks first at 0.80 on phenotype 1.00, rarity 1.00 and
consequence 1.00, with ClinVar agreeing afterwards.

Tests: api 75, ml 18, loader 16, web 27; ruff, mypy, svelte-check, terraform validate, both
kustomize overlays and the Nextflow stub run all clean.

docs/architecture.md

@@ -2,8 +2,9 @@
 
 ```mermaid
 flowchart LR
-  U[Scientist] -->|browser| W[SvelteKit web]
+  U[Scientist] -->|phenotype + VCF| W[SvelteKit web]
   W -->|REST /api| A[FastAPI]
+  H[(HPO gene-phenotype annotations)] --> A
   A --> P[(PostgreSQL / Cloud SQL)]
   A -->|publish vcf-uploaded| Q[Pub/Sub]
   Q --> E[Argo Events sensor]
@@ -12,6 +13,7 @@ flowchart LR
   B -->|reads VCF, VEP cache| G[(GCS bucket)]
   B -->|writes variants, marks job succeeded| P
   AW -.->|exit handler marks job failed| P
+  A -->|rank: phenotype, rarity, consequence, model| C[Ranked candidates -> decisions -> report]
   A -->|models:/rarelens-pathogenicity@production| M[MLflow registry]
   T[ml/train.py] --> M
   GH[GitHub Actions] -->|images via WIF| AR[Artifact Registry]
@@ -19,6 +21,33 @@ flowchart LR
   R --> CD[ArgoCD] --> K[GKE Autopilot]
 ```
 
+## The triage model
+
+A **case** is a proband: a VCF plus the HPO terms observed in that patient. Annotation produces
+variants; the model scores them; ranking then answers the only question that matters — which few
+variants could explain *this* phenotype.
+
+Rarity (<0.1% in gnomAD) and consequence (HIGH or MODERATE) *filter*, which is the usual first
+pass. Phenotype only *ranks*: a real diagnosis can sit in a gene nobody has annotated yet, and
+filtering on phenotype would hide exactly that case. The rank is a weighted sum whose parts are
+shown next to every candidate (`app/services/triage.py`):
+
+| Component | Weight |
+|---|---|
+| phenotype terms of this patient annotated to the gene | 0.35 |
+| rarity in gnomAD | 0.25 |
+| consequence severity | 0.20 |
+| model P(pathogenic) | 0.20 |
+
+**ClinVar is deliberately not an input.** It sits beside the result as independent confirmation, so
+the demo never ranks a variant highly merely because ClinVar already called it pathogenic. On the
+simulated NF2 case the planted variant ranks first on phenotype, rarity and consequence alone, and
+ClinVar agrees afterwards.
+
+Each candidate can be shortlisted or dismissed with a reason and a note; the case report is that
+decision trail plus the funnel counts and the provenance (VEP version, model version, run time).
+There is no authentication, so decisions are shared by everyone who opens the demo.
+
 ## Two deployment tracks
 
 The same images and the same pipeline, deployed two ways (`infra/terraform/variables.tf`):