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.

api/app/config.py

@@ -1,5 +1,10 @@
+from pathlib import Path
+
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
+# api/app/config.py -> repo root locally; "/" in the API image, where compose mounts /pipeline.
+REPO_ROOT = Path(__file__).resolve().parents[2]
+
 
 class Settings(BaseSettings):
     model_config = SettingsConfigDict(env_file=".env", extra="ignore")
@@ -7,9 +12,22 @@ class Settings(BaseSettings):
     database_url: str = "postgresql+asyncpg://rarelens:rarelens@localhost:5432/rarelens"
     mlflow_tracking_uri: str = "http://localhost:5000"
     model_name: str = "rarelens-pathogenicity"
-    model_stage: str = "Production"
+    # Registry alias set by `rarelens_ml.train --register` (stages are deprecated in MLflow 3).
+    model_alias: str = "production"
+    # A model artifact URI (gs://...) scores without an MLflow server running; wins over the registry.
+    model_uri: str | None = None
     gcs_bucket: str | None = None          # set in GCP; local uses ./data
     pubsub_topic: str | None = None        # "vcf-uploaded" in GCP; local runs pipeline inline
+    # Serverless track: run the Nextflow driver as a Cloud Run job instead of Argo + Pub/Sub.
+    cloudrun_job: str | None = None
+    gcp_project: str | None = None         # required with pubsub_topic or cloudrun_job
+    gcp_region: str = "europe-west2"
+    pipeline_dir: Path = REPO_ROOT / "pipeline"
+    nextflow_profile: str = "docker"
+    # Local (non-gs://) VCFs must live under this directory.
+    local_data_root: Path = Path("/data")
+    # Browsers calling the API cross-origin; behind the ingress the UI is same-origin.
+    cors_origins: list[str] = ["http://localhost:5173"]
 
 
 settings = Settings()