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/terraform/cloudsql.tf

@@ -1,8 +1,10 @@
 resource "google_sql_database_instance" "pg" {
-  name             = "rarelens-pg"
-  database_version = "POSTGRES_16"
-  region           = var.region
-  deletion_protection = false
+  count               = var.deploy_cloud_sql ? 1 : 0
+  name                = "rarelens-pg"
+  database_version    = "POSTGRES_16"
+  region              = var.region
+  deletion_protection = var.deletion_protection
+  depends_on          = [google_service_networking_connection.private_services]
 
   settings {
     tier              = "db-f1-micro" # lab budget; bump for real use
@@ -16,14 +18,20 @@ resource "google_sql_database_instance" "pg" {
 }
 
 resource "google_sql_database" "rarelens" {
+  count    = var.deploy_cloud_sql ? 1 : 0
   name     = "rarelens"
-  instance = google_sql_database_instance.pg.name
+  instance = google_sql_database_instance.pg[0].name
 }
 
 resource "google_sql_user" "api" {
+  count    = var.deploy_cloud_sql ? 1 : 0
   name     = "rarelens"
-  instance = google_sql_database_instance.pg.name
-  password = random_password.pg.result
+  instance = google_sql_database_instance.pg[0].name
+  password = random_password.pg[0].result
 }
 
-resource "random_password" "pg" { length = 32 }
+resource "random_password" "pg" {
+  count   = var.deploy_cloud_sql ? 1 : 0
+  length  = 32
+  special = false # embedded in DATABASE_URL, where characters like @ / # % would break parsing
+}