arda 2.28.0 — the integrations speak airrflow

Breaking: all three runners speak nf-core/airrflow's vocabulary, not an arda-only one

process ARDA → ARDA_ASSIGN, a drop-in for CHANGEO_ASSIGNGENES + CHANGEO_MAKEDB, and
params.regime is gone — the mode now comes from --library_generation_method. A second
arda-only name for the library protocol was a second place to get it wrong, and getting it wrong
is a silent 2–4× slowdown rather than an error. arda.samples.read_sheet reads both dialects, so
one samplesheet drives Nextflow, Snakemake and arda cluster with no translation step.
Migration table in integrations/nextflow/arda/README.md.

⛔ sc_10x_genomics is refused with a message: arda cells takes one per-molecule UMI consensus
FASTQ with the barcode in the record name, not a raw 10x read pair.

Added

• arda markup --d-prior PATH — score against a fitted D prior without overwriting a file
  inside the installed database. Implies --d-posterior; a path that is not there raises.
• arda resolve-ties --loci IGK,IGL — whether widening the V call helps is a property of the
  locus. Exact v_gene-set agreement against an arda igblast truth, eleven arms:
  IGK .5707 → .9373, IGL +5.5 pt, TRB +4.0 pt, and IGH −0.6 to −14.9 pt. Named loci are
  widened, every other row is copied through untouched.
• arda igblast --receptor ig|tr|both — a library whose receptor type is known no longer pays
  a whole IgBLAST pass over the other one. both stays the default.

Documented: what an IG V call means when the read is short

v_gene recall against an IgBLAST truth is .1170 on reads covering under 60 nt of V germline and
.9896 on reads covering 200 nt or more — and .9896 is the TRA amplicon's .9867, so there is no
IG-specific deficit at that coverage. Position beats length, somatic hypermutation does not order
this, and no threshold ships. docs/usage.rst.

Fixed

• A d_prior table arda scenarios wrote could not be read back: the generator emits a #
  provenance line above the header and load_d_prior skipped line 1 by position.
• The Nextflow Dockerfile's acceptance check grepped arda rnaseq --help for four flags that moved
  to arda map in 2.16.0 — every docker build failed on a correct install.
• The Cys104 junction gate no longer discards a junction over one substitution in its first two
  bases: +144 correct junctions and one extra over-extension across 92,466 truth junctions,
  held-out locus included.
• build_germline_dbs ignored locus.v_shared, so IgBLAST never saw a TRDV germline when marking
  up chimeric scaffolds: complete markup 7/483 → 49/483 with every V call correct.

Full detail in CHANGELOG.md.