fix: overhaul the platform skeleton, add a serverless deployment track

An end-to-end audit found the repo could not build, test or run as shipped. This
fixes every finding, then adds a Cloud Run track so the demo costs about £1/month
idle instead of ~£150.

CI (red on its first run)
- api: setuptools could not build the package (flat layout with app/ and alembic/)
- web: missing @types/node; `vitest run` exited 1 with no test files
- pipeline: the stub run needed a gitignored VCF, and no process had a stub block
- ruff pinned, mypy configured, DB tests on real Postgres (pgserver locally, service in CI)

ML serving (scores were meaningless)
- the registered model now carries its own feature engineering and returns predict_proba,
  so serving sends raw columns and cannot drift from training
- resolve by registry alias (stages are deprecated in MLflow 3) and record the real
  version; re-scoring upserts instead of failing on the unique constraint
- ClinVar labels parsed from VEP's lowercase terms

Pipeline
- exact ref/alt recovered from a CHROM_POS_REF_ALT VCF ID; loading is idempotent
- job status reaches running/failed/succeeded, so the UI stops polling dead jobs
- DATABASE_URL travels in the environment or a Nextflow secret, never on a command line
- VEP cache and plugins staged as inputs; the gcp profile runs tasks on Google Batch

Deployment
- the API serves /api (matching the ingress); the web app reads its API URL at runtime
- migrations run in an init container under a Postgres advisory lock
- terraform: custom VPC shared with Batch, private Cloud SQL, API enablement, Workload
  Identity bindings, Secret Manager, deletion protection
- serverless track, now the default: Cloud Run services scaling to zero, a Cloud Run job
  for the Nextflow driver, and Neon or Cloud SQL behind one DATABASE_URL secret. GKE and
  Argo remain, behind -var deploy_kubernetes=true. See docs/cloud.md.

Correctness and security
- 409 on duplicate sample names, 422 on bad paging, natural chromosome ordering, wider
  VEP text columns, enum dropped on downgrade, the sample's assembly actually used
- vcf_uri restricted to gs:// objects or files under the data root, blocking option injection
- CORS restricted to configured origins; `make down` no longer deletes volumes

Data
- docs/data.md records the peer-reviewed, openly licensed sources (GIAB HG002, ClinVar,
  gnomAD) with citations and an honest evaluation plan; `make data` fetches a chr22 slice

Verified: api 50 tests, ml 18, loader 16, web 12; ruff, mypy, svelte-check, terraform
validate and both kustomize overlays clean.

pipeline/bin/set_job_status.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+"""Set a job's status, e.g. from the Argo exit handler when a workflow fails.
+
+A succeeded job is never overwritten: the loader's success is the source of truth.
+"""
+import argparse
+import os
+import sys
+
+from load_db import engine_for
+from sqlalchemy import Engine, text
+
+
+def set_status(engine: Engine, job_id: str, status: str, log: str | None) -> None:
+    with engine.begin() as conn:
+        conn.execute(
+            text("""
+                UPDATE jobs
+                SET status = CAST(:status AS jobstatus), log = :log,
+                    finished_at = CASE WHEN :status IN ('succeeded', 'failed') THEN now() END
+                WHERE id = :id AND status <> 'succeeded'
+            """),
+            {"id": job_id, "status": status, "log": log},
+        )
+
+
+def main() -> None:
+    p = argparse.ArgumentParser()
+    p.add_argument("--job-id", required=True)
+    p.add_argument("--status", required=True, choices=["running", "failed"])
+    p.add_argument("--log")
+    a = p.parse_args()
+    url = os.environ.get("DATABASE_URL")
+    if not url:
+        sys.exit("DATABASE_URL is not set")
+    set_status(engine_for(url), a.job_id, a.status, a.log)
+
+
+if __name__ == "__main__":
+    main()