Wire reference assembly and GTF steps into organism-scoped stepper, scoped to selected assemblies

Enable existing ReferenceAssemblyStep and GTFStep to appear in ORGANISM-scoped workflows.

- ASSEMBLY_FASTA_URL step: restrict the selectable assembly list to the ones selected in the multi-assembly step (when present, see #1403).
- GENE_MODEL_URL step: allow choosing a GTF for the selected reference assembly, with the same "User upload to Galaxy" option.
- Update buildSteps to include these steps after FASTA_COLLECTION when the workflow declares the relevant parameter variables.
- Update getOrganismScopeConfiguredValues to validate and pass fastaCollection, reference FASTA URL, and geneModelUrl to the Galaxy launch payload.