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lit-review-v2

Lit review v2 synthesis: integrate full 14-topic coverage (incl. new topics 05 and 07)

Metadata

Statusdone
Assignedagent-937
Agent identity3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647
Modelclaude:opus
Created2026-05-06T13:52:42.352834792+00:00
Started2026-05-06T14:04:24.322618287+00:00
Completed2026-05-06T14:23:40.761846459+00:00
Tagslit-review, synthesizer, paper-prep, eval-scheduled
Eval score0.92
└ blocking impact0.90
└ completeness0.95
└ constraint fidelity0.70
└ coordination overhead0.95
└ correctness0.95
└ downstream usability0.90
└ efficiency0.85
└ intent fidelity0.88
└ style adherence0.90

Description

GOAL: Re-integrate the now-complete 14 topical lit reviews into a fresh, comprehensive narrative + bibliography. The previous synthesis (lit-review-synthesis, completed earlier this session) ran with only 12 of 14 topics on disk; this task runs with the full 14 and produces v2 deliverables.

INPUTS:

  • paper_prep/lit_review/topic_01_.md … topic_14_.md (all 14 should be present after upstream tasks complete)
  • paper_prep/lit_review/topic_01_.bib … topic_14_.bib (all 14)
  • paper_prep/synthesis/REFERENCES.bib (existing 24-entry bibliography)
  • paper_prep/synthesis/ABSTRACT_nature.md (anchor; falls back to ABSTRACT_BoG.md)
  • paper_prep/synthesis/CROSSWALK.md (claim-to-substrate map)
  • end-to-end-report/report/12_literature.md (Andrea's literature/novelty ledger)
  • paper_prep/lit_review/SYNTHESIS.md (PRIOR synth output, built from 12 topics — read for continuity but supersede)
  • paper_prep/lit_review/CHRONOLOGY.md (PRIOR — supersede)
  • paper_prep/lit_review/GAPS.md (PRIOR — supersede)
  • paper_prep/synthesis/REFERENCES_v2.bib (PRIOR — supersede)

DELIVERABLES (under paper_prep/lit_review/, REPLACING the v1 versions):

  1. SYNTHESIS_v2.md — narrative history, ~6,000-10,000 words, structured as: Foreword: how to read this document Part I — Cytogenetic and structural foundations (topics 01, 02, 04) Part II — The pseudohomology concept and its variants (topics 03, 05, 06, 13, 14) Part III — Mechanism: meiotic 3D and recombination (topics 07, 08, 09) Part IV — Methods: pangenomes and pedigrees (topics 10, 11, 12) Part V — How this paper sits in the field This should now properly include topics 05 (acrocentric/rDNA/Robertsonian) and 07 (concerted evolution/NAHR) — the two that were missing in the v1 synth.
  2. CHRONOLOGY_v2.md — timeline table.
  3. paper_prep/synthesis/REFERENCES_v3.bib — augmented BibTeX combining REFERENCES.bib + all 14 topic_NN_*.bib; deduplicated, sorted. Should grow from ~24 -> ~150-220 entries.
  4. GAPS_v2.md — open questions and limitations.

ACCEPTANCE:

  • SYNTHESIS_v2.md exists with all 5 parts; topics 05 and 07 are explicitly present in Parts II and III.
  • CHRONOLOGY_v2.md has at least one row per major paper in REFERENCES_v3.bib.
  • REFERENCES_v3.bib has >= 150 deduplicated entries.
  • Single commit: "docs: lit review v2 synthesis with full 14-topic coverage".
  • wg artifact records all 4 deliverables.

DO NOT modify any topic_NN_.md or topic_NN_.bib (read-only inputs). Do NOT delete the v1 synthesis files (SYNTHESIS.md, CHRONOLOGY.md, GAPS.md, REFERENCES_v2.bib) — they remain as historical record.

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