openvax / vaxrank / 25398929091
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Default mhcflurry for linker opt; auto-fill CSV/JSON in --output-dir (#274)

Two ergonomics asks from the running-the-tool feedback loop:

1. Default ``mhcflurry`` predictor when ``--mhc-predictor`` isn't
   set but alleles are available. The per-junction linker
   optimizer needs *some* live MHC predictor to score chimeric
   k-mers — refusing to optimize because the operator didn't pick
   one is worse than optimizing against a sensible default.
   mhcflurry is pip-installable, the same predictor LENS often
   uses, and produces both affinity + presentation scores.
   ``--mhc-predictor`` still wins when set; logged-INFO when the
   default kicks in.

2. Auto-fill canonical CSV / JSON paths inside ``--output-dir`` so
   ``vaxrank --input-lens X --output-dir mydir/`` produces the
   full bundle (FASTAs + manifest + CSV + JSON) instead of just
   the FASTAs. Source-aware filename pick: pipeline writes
   ``ranked_vaccine_peptides.{csv,json}``; LENS / pVACseq writes
   ``neoepitope_predictions.csv`` (the per-(peptide, allele)
   shape natural to the external path; the rich JSON dump only
   makes sense on the pipeline path so it's skipped).
   ``--output-csv`` / ``--output-json-file`` always win when set.

Tests:

- ``test_resolve_mhc_defaults_to_mhcflurry_when_predictor_missing``:
  patches mhctools.MHCflurry to a sentinel (don't load the real
  thing in-process — same libomp risk that pepsickle works
  around in subprocess). Verifies the function instantiates the
  default with the inferred alleles + emits the
  "defaulting to mhcflurry" INFO line.
- ``test_resolve_mhc_warns_when_mhcflurry_default_unavailable``:
  monkeypatches MHCflurry to raise; confirms the targeted
  "predictor missing, alleles available" WARNING fires.
- Four ``_auto_populate_output_paths_from_dir`` branch tests:
  pipeline fills CSV+JSON, external fills neoepitope CSV only,
  explicit paths always win, no-output-dir is a no-op.

Bump version to 2.19.0.
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