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/tests/test_variants.py

@@ -0,0 +1,46 @@
+import uuid
+
+import pytest
+from factories import seed_job
+from httpx import AsyncClient
+
+
+@pytest.mark.parametrize(
+    "paging", [{"limit": 0}, {"limit": -1}, {"limit": 501}, {"offset": -1}]
+)
+async def test_out_of_range_paging_is_422_not_500(client: AsyncClient, paging: dict) -> None:
+    r = await client.get("/api/variants", params={"job_id": str(uuid.uuid4()), **paging})
+    assert r.status_code == 422
+
+
+async def positions(client: AsyncClient, job_id: uuid.UUID) -> list[tuple[str, int, str]]:
+    r = await client.get("/api/variants", params={"job_id": str(job_id)})
+    assert r.status_code == 200, r.text
+    return [(v["chrom"], v["pos"], v["alt"]) for v in r.json()["items"]]
+
+
+@pytest.mark.usefixtures("db")
+async def test_chromosomes_sort_naturally(client: AsyncClient) -> None:
+    job_id = await seed_job([{"chrom": c} for c in ["10", "MT", "2", "X", "chr3", "1", "Y"]])
+    assert [c for c, _, _ in await positions(client, job_id)] == [
+        "1", "2", "chr3", "10", "X", "Y", "MT",
+    ]
+
+
+@pytest.mark.usefixtures("db")
+async def test_same_position_keeps_insertion_order_across_pages(client: AsyncClient) -> None:
+    # Split multiallelics share chrom/pos; without a tiebreak, pages can repeat or skip rows.
+    job_id = await seed_job([{"pos": 5, "alt": a} for a in "CGT"])
+    assert [a for _, _, a in await positions(client, job_id)] == ["C", "G", "T"]
+
+
+@pytest.mark.usefixtures("db")
+async def test_long_vep_strings_are_stored(client: AsyncClient) -> None:
+    clin_sig = ",".join(["conflicting_classifications_of_pathogenicity"] * 8)
+    consequence = (
+        "splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant"
+        "&NMD_transcript_variant&non_coding_transcript_variant"
+    )
+    job_id = await seed_job([{"clinvar_sig": clin_sig, "consequence": consequence}])
+    [v] = (await client.get("/api/variants", params={"job_id": str(job_id)})).json()["items"]
+    assert (v["clinvar_sig"], v["consequence"]) == (clin_sig, consequence)