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/main.py

@@ -1,8 +1,9 @@
 from contextlib import asynccontextmanager
 
-from fastapi import FastAPI
+from fastapi import APIRouter, FastAPI
 from fastapi.middleware.cors import CORSMiddleware
 
+from app.config import settings
 from app.routers import jobs, predictions, samples, variants
 
 
@@ -14,13 +15,19 @@ async def lifespan(app: FastAPI):
 
 app = FastAPI(title="rarelens API", version="0.1.0", lifespan=lifespan)
 app.add_middleware(
-    CORSMiddleware, allow_origins=["*"], allow_methods=["*"], allow_headers=["*"]
+    CORSMiddleware,
+    allow_origins=settings.cors_origins,
+    allow_methods=["GET", "POST"],
+    allow_headers=["content-type"],
 )
 
-app.include_router(samples.router, prefix="/samples", tags=["samples"])
-app.include_router(jobs.router, prefix="/jobs", tags=["jobs"])
-app.include_router(variants.router, prefix="/variants", tags=["variants"])
-app.include_router(predictions.router, prefix="/predictions", tags=["predictions"])
+# The ingress forwards /api/* to this service unchanged, and local dev uses the same prefix.
+api = APIRouter(prefix="/api")
+api.include_router(samples.router, prefix="/samples", tags=["samples"])
+api.include_router(jobs.router, prefix="/jobs", tags=["jobs"])
+api.include_router(variants.router, prefix="/variants", tags=["variants"])
+api.include_router(predictions.router, prefix="/predictions", tags=["predictions"])
+app.include_router(api)
 
 
 @app.get("/health", tags=["ops"])