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.

infra/k8s/overlays/gcp/kustomization.yaml

@@ -1,21 +1,53 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
-resources: [../../base]
+# Project-specific values use the __GCP_PROJECT__ placeholder: run `make gcp-configure PROJECT=<id>`
+# once and commit. Image tags are then bumped by .github/workflows/deploy.yml after each green CI.
+# Generated ConfigMaps must share the Deployments' namespace, or their hashed names are not
+# propagated to envFrom references.
+namespace: rarelens
+resources: [../../base, ../../../argo-workflows]
+configurations: [kustomizeconfig.yaml]
 images:
-  - { name: rarelens/api, newName: europe-west2-docker.pkg.dev/PROJECT/rarelens/api, newTag: latest }
-  - { name: rarelens/web, newName: europe-west2-docker.pkg.dev/PROJECT/rarelens/web, newTag: latest }
+  - { name: rarelens/api, newName: europe-west2-docker.pkg.dev/__GCP_PROJECT__/rarelens/api, newTag: latest }
+  - { name: rarelens/web, newName: europe-west2-docker.pkg.dev/__GCP_PROJECT__/rarelens/web, newTag: latest }
+  - { name: rarelens/pipeline, newName: europe-west2-docker.pkg.dev/__GCP_PROJECT__/rarelens/pipeline, newTag: latest }
+  - { name: rarelens/loader, newName: europe-west2-docker.pkg.dev/__GCP_PROJECT__/rarelens/loader, newTag: latest }
+configMapGenerator:
+  - name: api-config
+    literals: [PUBSUB_TOPIC=vcf-uploaded, GCP_PROJECT=__GCP_PROJECT__]
+  - name: pipeline-config
+    # Referenced by name from the Argo WorkflowTemplate, which kustomize does not rewrite.
+    options: { disableNameSuffixHash: true }
+    literals: [GCP_PROJECT=__GCP_PROJECT__, GCP_REGION=europe-west2, GCS_BUCKET=__GCP_PROJECT__-rarelens-data]
+# api-secrets and pipeline-secrets come from Secret Manager: `make gcp-secrets PROJECT=<id>`.
 patches:
   - target: { kind: ServiceAccount, name: rarelens-api }
     patch: |
       - op: add
         path: /metadata/annotations
-        value: { iam.gke.io/gcp-service-account: [email protected] }
+        value: { iam.gke.io/gcp-service-account: rarelens-api@__GCP_PROJECT__.iam.gserviceaccount.com }
+  - target: { kind: ServiceAccount, name: rarelens-pipeline }
+    patch: |
+      - op: add
+        path: /metadata/annotations
+        value: { iam.gke.io/gcp-service-account: rarelens-pipeline@__GCP_PROJECT__.iam.gserviceaccount.com }
   - target: { kind: Deployment, name: api }
     patch: |
       - op: add
-        path: /spec/template/spec/containers/-
+        path: /spec/template/spec/initContainers/0
         value:
           name: cloud-sql-proxy
           image: gcr.io/cloud-sql-connectors/cloud-sql-proxy:2.13.0
-          args: ["--structured-logs", "--port=5432", "PROJECT:europe-west2:rarelens-pg"]
-          securityContext: { runAsNonRoot: true }
+          # Native sidecar: starts (and passes its startup probe) before the migrate init
+          # container, then keeps running alongside the API.
+          restartPolicy: Always
+          args:
+            - --structured-logs
+            - --private-ip
+            - --port=5432
+            - --health-check
+            - --http-address=0.0.0.0
+            - __GCP_PROJECT__:europe-west2:rarelens-pg
+          startupProbe: { httpGet: { path: /startup, port: 9090 }, periodSeconds: 1, failureThreshold: 60 }
+          securityContext: { runAsNonRoot: true, allowPrivilegeEscalation: false }
+          resources: { requests: { cpu: 100m, memory: 128Mi }, limits: { cpu: 500m, memory: 256Mi } }

infra/k8s/overlays/gcp/kustomizeconfig.yaml

@@ -0,0 +1,4 @@
+# Teach the `images:` transformer where Argo WorkflowTemplates keep their images.
+images:
+  - path: spec/templates/container/image
+    kind: WorkflowTemplate