openvax / vaxrank / 25396797037

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mRNA output ergonomics: naming, separators, ranking-report (#270) (#271)

* default.yaml: rewrite header for the post-2.17 layout

The header still mixed pre-mRNA language ("frozen config groups",
``EpitopeConfig`` / ``VaccineConfig`` class names) with post-mRNA
content. Section is now described in user terms:

- modality-agnostic vs peptide-only is called out per section,
- ``manufacturability``'s actual role (tie-break + report
  auto-skip) is documented instead of an outdated
  ``-> VaccineConfig`` mapping that no longer holds,
- the resolution order (CLI > per-modality > cross-modality >
  built-in default) is named once at the top so the per-section
  text doesn't have to re-state it.

* mRNA output ergonomics: naming, separators, dropped-count (#270 part 1)

First batch of fixes from the issue. Touches the mRNA writer + CLI
plumbing; the broader items (mRNA ranking-decisions report,
configurable antigen-name template) ride in follow-up commits on
this branch.

- Construct names: ``seq_NNN`` -> ``mrna_NNN``. Mixed peptide+mRNA
  outputs in the same downstream pipeline collide on a bare
  ``seq_001``; modality-stamped names mirror the peptide writer's
  ``peptide_NNN`` scheme.
- FASTA ``antigens=`` field now uses ``;`` instead of ``,``. Comma
  is a token boundary in many FASTA-parsing tools' description-line
  handlers; ``;`` is the GenBank convention for compound description
  fields.
- ``layers.csv`` -> ``mrna-sequence-parts.csv``. ``layers`` next to
  ``cds.fasta`` / ``full.fasta`` is too cryptic; the new name spells
  out what each row describes.
- ``--mrna-max-constructs`` cap warning now reports the dropped
  count: ``dropping 379 / 384 ranked antigen(s) past the cap``
  rather than the legacy single-name ``including X``. Operators
  can tell whether they lost 1 or 379.

Tests pin the FASTA ``;``-separator format, the dropped-count
warning shape, and the cross-modality construct-name pattern
(``mrna|peptide_NNN``).

Bump version to 2.18.0.
... (continued)
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