openvax / vaxrank / 25772707551
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Docs: README cleanup — restructure intro, link refs, break dense sections (#288)

* README: de-slop the lead-in; section restructure; reference links

Several content + structure changes driven by review feedback:

**Top-of-doc rewrite**
- Drop the ASCII-art "Architecture" diagram. Replace with a
  ``## Features`` bullet list — what the tool does, not how the
  CLI dispatches internally.
- Move Quick Start up to follow Features (was buried at line 278).
- Fold the "Vaxrank always ranks; multi-mode subdirs" dispatch
  detail into the "Vaccine types and output modes" section where
  it belongs, not the intro.
- Add a Contents ToC near the top so the 850-line README is
  navigable.

**Vaccine designs section**
- Break the giant grouped code-fence into per-design code blocks
  separated by prose: SLP / multi-epitope peptide / minimal-epitope
  peptide / FixVac mRNA / string-of-beads mRNA / top-N ligands /
  both modalities. Each design gets a one-paragraph explanation
  before its example.
- Link the reference column entries to DOIs / PubMed: PGV-001
  (Bortman 2025), Sahin 2017, Rojas 2023. Replace the unsourced
  "Velten 2018" with [Thomson 1996 PNAS]
  (https://www.pnas.org/doi/10.1073/pnas.94.26.14660) for
  string-of-beads — the codebase comment was incorrect.

**Vaccine types and output modes**
- Convert the dense 5-row output table into ``###`` subsections
  (Analysis reports / Neoepitope report / Peptide constructs /
  mRNA constructs / External-input mode / Manifest schema). The
  mRNA constructs row was a single packed cell with 20+ flags;
  now its flags are grouped by what they configure (construct
  anatomy / polyA tail / linker optimization / codon optimization).

**Linker library**
- Link every primary-source citation in the linker table to its
  DOI / PMID (Huston 1988, Arai 2001, Hosaka 1991, Livingston
  Vaccine 2001 + J Immunol 2002, Aguilar-Gurrieri 2023, Yang 2015,
  Donnelly 2001, Kim 2011, Sahin 2017).

**Legacy support**
- Move the... (continued)
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