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.

pipeline/modules/load_db.nf

@@ -3,11 +3,18 @@ process LOAD_DB {
     input:
         path tsv
         val job_id
-        val db_url
     output: stdout
 
+    // DATABASE_URL reaches the task through its environment (docker profile) or a Nextflow
+    // secret (gcp profile); it never appears on a command line or in .command.sh.
     script:
+    def dry_run = job_id == 'dry-run' ? '--dry-run' : ''
     """
-    load_db.py --tsv $tsv --job-id $job_id --db-url '$db_url'
+    load_db.py --tsv $tsv --job-id $job_id $dry_run
+    """
+
+    stub:
+    """
+    echo "stub: would load $tsv for job $job_id"
     """
 }

pipeline/modules/normalise.nf

@@ -3,9 +3,16 @@ process NORMALISE {
     input:  path vcf
     output: path "${vcf.simpleName}.norm.vcf.gz", emit: vcf
 
+    // Split multiallelics, then set each ID to CHROM_POS_REF_ALT. VEP echoes the ID back as
+    // Uploaded_variation, and the loader takes exact VCF alleles from it (VEP trims indels).
     script:
     """
-    bcftools norm -m -both -Oz -o ${vcf.simpleName}.norm.vcf.gz $vcf
-    bcftools index -t ${vcf.simpleName}.norm.vcf.gz
+    bcftools norm -m -both -Ou $vcf \\
+        | bcftools annotate --set-id '%CHROM\\_%POS\\_%REF\\_%FIRST_ALT' -Oz -o ${vcf.simpleName}.norm.vcf.gz
+    """
+
+    stub:
+    """
+    touch ${vcf.simpleName}.norm.vcf.gz
     """
 }

pipeline/modules/vep.nf

@@ -1,16 +1,31 @@
 process VEP {
     tag "$vcf.simpleName"
     publishDir params.outdir, mode: 'copy'
-    input:  path vcf
+    input:
+        path vcf
+        path cache          // staged as an input so it is visible inside the container
+        path plugin_data    // assets/NO_FILE when plugins are not configured
     output:
         path "${vcf.simpleName}.vep.tsv",      emit: tsv
         path "${vcf.simpleName}.vep_summary.html"
 
     script:
+    // Plugins run only when --vep_plugin_data names a directory holding the plugin modules
+    // (INSTALL.pl -a p -g CADD,AlphaMissense -r <dir>) and the data files named in params.
+    def plugins = plugin_data.name == 'NO_FILE' ? '' : [
+        "--dir_plugins ${plugin_data}",
+        "--plugin CADD,snv=${plugin_data}/${params.cadd_snv},indels=${plugin_data}/${params.cadd_indels}",
+        "--plugin AlphaMissense,file=${plugin_data}/${params.alphamissense}",
+    ].join(' ')
     """
     vep -i $vcf -o ${vcf.simpleName}.vep.tsv --tab \\
-        --assembly ${params.assembly} --cache --dir_cache ${params.vep_cache} --offline \\
-        --everything --pick --af_gnomade --plugin CADD --plugin AlphaMissense \\
+        --assembly ${params.assembly} --cache --offline --dir_cache ${cache} \\
+        --everything --pick ${plugins} \\
         --stats_file ${vcf.simpleName}.vep_summary.html --fork ${task.cpus}
     """
+
+    stub:
+    """
+    touch ${vcf.simpleName}.vep.tsv ${vcf.simpleName}.vep_summary.html
+    """
 }