openvax / vaxrank / 25184242014
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Orthogonal antigen-design axes shared across peptide and mRNA (#256)

Folds #255's intent (split peptide modes into leaf modalities) into a
better factoring: the design space is two orthogonal axes, shared
across vaccine types, instead of a peptide-only ``mode`` enum.

Axes
----
- ``antigen_content`` ∈ {mutation_spanning, minimal_epitope} —
  what each antigen *is*. Mutation-spanning extracts a centered
  window of up to max_antigen_length_aa (the SLP/long-peptide
  content); minimal-epitope extracts the top MHC ligand(s) per
  VaccinePeptide.
- ``antigens_per_construct`` ∈ {1, N} — how many antigens to
  concatenate per construct.

Combined with ``--vaccine-type``, 8 distinct designs are now
expressible — 4 per vaccine type:

  +-------+-------------------+-----+------------------------------+
  | type  | content           | N   | name                         |
  +-------+-------------------+-----+------------------------------+
  | pep.  | mutation_spanning | 1   | SLP (PGV-001 canonical)      |
  | pep.  | mutation_spanning | N   | multi-SLP concatenated       |
  | pep.  | minimal_epitope   | 1   | minimal-ligand peptide       |
  | pep.  | minimal_epitope   | N   | concat-minimal-ligand pool   |
  | mrna  | mutation_spanning | N   | BioNTech FixVac / iNeST      |
  | mrna  | mutation_spanning | 1   | single-antigen mRNA          |
  | mrna  | minimal_epitope   | N   | "string of beads" mRNA       |
  | mrna  | minimal_epitope   | 1   | single-ligand mRNA           |
  +-------+-------------------+-----+------------------------------+

Three of these (concat-minimal-ligand, string-of-beads mRNA,
single-ligand mRNA) were not expressible pre-PR. ``string of beads``
mRNA mirrors Velten et al. 2018's polyepitope mRNA design.

Don't-assume-just-one-matters
------------------------------
Replaced the old ``_top_mutant_epitope(vp) → single`` helper with
``mutant_epitopes_sorted(vp) → list`` and ``top_mutant_epitopes(vp,
n=1) → list``. New ``epitopes_per_... (continued)
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