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/data.md

@@ -28,6 +28,7 @@ benchmarks variant callers against, so it is both realistic and unambiguously sh
 | **gnomAD** v4 | allele frequency feature and filter | `gs://gcp-public-data--gnomad`, `s3://gnomad-public-us-east-1` | free use, no restriction | Chen et al., *Nature* 625:92–100, 2024. [10.1038/s41586-023-06045-0](https://doi.org/10.1038/s41586-023-06045-0); Karczewski et al., *Nature* 581:434–443, 2020. [10.1038/s41586-020-2308-7](https://doi.org/10.1038/s41586-020-2308-7) |
 | **1000 Genomes** 30x | optional cohort/trio data | EBI FTP, `s3://1000genomes` | fully open, no access restriction | Byrska-Bishop et al., *Cell* 185(18):3426–3440.e19, 2022. [10.1016/j.cell.2022.08.004](https://doi.org/10.1016/j.cell.2022.08.004) |
 | **MANE Select** | one transcript per gene, if transcript choice ever matters | Ensembl/RefSeq | open | Morales et al., *Nature* 604:310–315, 2022. [10.1038/s41586-022-04558-8](https://doi.org/10.1038/s41586-022-04558-8) |
+| **Human Phenotype Ontology** gene-to-phenotype | what the phenotype half of the ranking matches against (`make hpo`) | `purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` | free to use with attribution | Gargano et al., *Nucleic Acids Res* 52(D1):D1333–D1346, 2024. [10.1093/nar/gkad1005](https://doi.org/10.1093/nar/gkad1005) |
 
 ## Tools and scores
 
@@ -40,6 +41,24 @@ benchmarks variant callers against, so it is both realistic and unambiguously sh
 Neither score is required: `rarelens_ml.features` treats a missing CADD or AlphaMissense value as
 NaN and LightGBM handles it, so the pipeline runs without the plugin data.
 
+## The simulated proband
+
+`make demo-case` builds `data/proband-simulated.vcf.gz`: real GIAB HG002 variants as background
+plus one real ClinVar 2-star pathogenic variant in a disease gene (NF2 by default, giving
+neurofibromatosis type 2). Spiking a known variant into a public genome is how phenotype-driven
+triage tools are benchmarked, every input is public, and the file's header says SIMULATED. It is
+not a patient, and no part of it is invented: both the background and the planted variant are real
+published records.
+
+The point of it is that the case has a right answer, so the ranking can be checked rather than
+admired. Give the case the phenotype of the planted disease and the planted variant should rank
+first — on phenotype, rarity and consequence, with ClinVar agreeing only afterwards.
+
+**Caveat when running without a VEP cache.** `VEP_DATABASE=true` queries Ensembl's public database
+instead of the 25 GB cache. It returns no gnomAD frequencies, so every variant looks absent from
+gnomAD and the rarity term stops discriminating. Fine for showing the mechanics; use the cache for
+anything you would quote.
+
 ## Evaluating the model honestly
 
 The model trains on ClinVar labels and is scored on ClinVar-labelled variants, which is exactly