feat: Phase 4 — Boman scorer, consensus report, 89 AMP nominees, nomination report - #13

Implements the Boman (2003) interaction-potential-based activity scorer as
a second independent predictor alongside the existing physicochemical heuristic.
Adds model disagreement signal to flag uncertain nominations.

- scoring/boman.py: boman_index(), boman_activity_score(), gravy_score(), model_disagreement()
  - Published Boman 2003 Table 1 potentials (transparent, no training)
  - tanh normalization to [0,1]; disagreement = |activity − boman_activity|
- features/physchem.py: boman_index and gravy added to compute_features() output
- pipeline.py: boman_activity and disagreement stored in raw_scores
- scoring/ensemble.py: disagreement-aware selection reasons and failure modes
- schemas/candidate.schema.json: boman_activity and disagreement as optional score fields
- tests/test_boman_scorer.py: 37 tests covering all four functions + pipeline integration
- docs/METHODS.md, EXPERT_REVIEW_PACK.md: document second scorer and uncertainty signal

Candidates with disagreement < 0.20 have dual-scorer consensus (more robust).
Candidates with disagreement >= 0.30 are flagged for extra scrutiny.

Surfaces the Boman index vs. activity-likeness disagreement signal in the
human-readable batch pack and expert review documents.

- batch_pack.py: scorer_consensus_report() — new 5th sub-report
  - Labels each candidate: high_consensus (<0.20), moderate, uncertain (≥0.30)
  - Sorted by disagreement ascending (strongest consensus first)
  - Gracefully handles candidates without boman_activity in scores
  - generate_batch_pack() → batch_pack_version 1.1, includes scorer_consensus
  - Summary adds n_high_consensus, n_uncertain_disagreement, mean_scorer_disagreement
  - write_batch_pack_markdown() → Section 5 Scorer Consensus table
- tests/test_batch_pack.py: 11 new tests (TestScorerConsensusReport)
  - Updated _make_candidate helper to include boman_activity/disagreement
  - Updated TestWriteBatchPackMarkdown to assert "Scorer Consensus" in markdown
  - Updated TestGenerateBatchPack to assert scorer_consensus key present

314 tests pass.

…results

Reflects the actual Phase 3 run output: 89 candidates selected, all evidence
certificates schema-validated, dual-scorer consensus data from v0.2 pipeline.

Key changes:
- Top-20 table now includes Boman activity and disagreement columns (live data)
- Batch statistics include mean Boman (0.503), mean disagreement (0.311)
- Explains scientifically why high disagreement is expected for helical AMPs:
  activity scorer rewards amphipathic character; Boman index penalizes hydrophobic
  residues — these are different mechanistic models, not a data quality issue
- Adds "Suggested pilot candidates" table ranked by Boman × low-disagreement:
  SEED-003 tryptophan-rich 11-mers prioritized for first synthesis round
- Reviewer questions updated to cover dual-scorer methodology
- Limitations table updated to reflect current two-scorer state
- 6.2 asks expert: do SEED-003 11-mers look more promising than SEED-005 14-mers?

Complete scientific documentation of how the 89 Phase 3 candidates were
found, scored, filtered, and selected. Suitable for sharing with expert
reviewers and as a pre-publication methods record.

Sections:
1. Abstract (89 nominees, computational only, no bio claims)
2. Motivation (cationic AMPs, why short variants, why this approach)
3. Seed templates (5 seeds, family rationale, published sources)
4. Candidate generation (3 strategies, conservative groups, rng_seed=2024, 383 total)
5. Scoring pipeline (6 dimensions with formulas and references)
   - Activity-likeness (Scorer 1: heuristic)
   - Boman activity (Scorer 2: Boman 2003 potentials, independent)
   - Model disagreement (|act - boman| uncertainty proxy)
   - Safety proxy (hemolysis risk flags)
   - Synthesis feasibility
   - Novelty (Levenshtein vs 45 curated references)
   - Ensemble (pre-registered weights)
6. Selection criteria (hard filters + ranking + greedy diversity)
7. Results
   - 89 selected from 383 (pass-rate 23%)
   - Per-seed breakdown: SEED-003 best Boman (0.538), SEED-005 best ensemble (0.863)
   - Novelty distribution: 9 high, 58 mid, 22 low
   - Top-10 table with dual-scorer columns
   - Suggested 5-candidate pilot (Boman × low-disagreement criterion)
8. Evidence trail (all artifacts with locations)
9. Reproducibility (make phase3 from clean checkout)
10. What we do not know (mandatory integrity section)
11. Safety and dual-use assessment
12. Next steps (human gates only)
13. References (Boman 2003, Eisenberg 1984, Kyte-Doolittle 1982, Zasloff 1987...)