openvax / vaxrank / 25400188094
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Config flatten: drop vaccine_constructs wrapper; manufacturability under peptide (#273) (#275)

Phase 1 of the config-shape refactor. User-facing YAML is now in
its post-2.19 shape; pre-2.19 layouts still load with one-cycle
deprecation warnings.

YAML restructure:

- ``vaccine_constructs:`` wrapper dropped. Modality sections live
  at the top level: ``peptide:`` / ``mrna:`` (and any future
  ``dna:``).
- ``manufacturability:`` is now a sub-section of ``peptide:``.
  Solid-phase peptide-synthesis rules don't apply to mRNA, so
  scoping them under the modality they describe makes that
  contract visible in the YAML itself.
- Antigen-design knobs (``antigen_content``,
  ``epitopes_per_antigen``, ``candidates_per_slot``,
  ``min_antigen_length_aa``, ``max_antigen_length_aa``) absorbed
  into ``vaccine_peptides:`` — they're antigen *design*, not
  construct-assembly, and apply to every modality.
- ``default.yaml`` rewritten to match. Modality sub-trees ship
  uncommented (reflecting the in-code defaults) so a copy of the
  bundled config is a no-op starting point.

Schema:

- ``VaxrankConfigSchema`` now declares ``peptide`` and ``mrna``
  as top-level fields. ``ManufacturabilityConfigSchema`` is a
  field on ``PeptideConstructConfigSchema``. The legacy
  ``VaccineConstructsConfigSchema`` is gone (the wrapper has no
  reason to exist once antigen-design knobs move out).
- Modality registry: new ``vaxrank/modalities.py`` is the single
  source of truth for the set of registered modalities. Loader
  back-compat migration reads the registered names from there;
  adding ``dna:`` is one entry.

Loader migrations (one DeprecationWarning per legacy form):

- ``vaccine_peptides.manufacturability`` →
  ``peptide.manufacturability``
- top-level ``manufacturability`` → ``peptide.manufacturability``
- ``vaccine_constructs.<modality>`` → top-level ``<modality>:``
- ``vaccine_constructs.<antigen-design knob>`` →
  ``vaccine_peptides.<knob>``

Mixed layouts (both legacy ... (continued)
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