graph LR
    P0["−1. Discovery\n(question · novelty · design · pre-reg)"] --> P1[1. Literature Search]
    P1 --> P2[2. Outline]
    P2 --> P25[2.5 Tables/Figures]
    P25 --> P3[3. Draft]
    P3 --> P4[4. Humanize]
    P4 --> P5[5. References]
    P5 --> P6[6. Quality Review]
    P6 --> P65["6.5 Adversarial Review"]
    P65 --> P7[7. Pre-Submission]
    P65 -.->|KILL| P0
    P7 --> P8["8. Revision ①"]
    P8 --> P9["9. Post-Acceptance"]
    P7 -.-> P10["10. Rejection → Resubmit"]
    P10 -.-> P1

flowchart TD
    subgraph "Per-Phase Loop (max 3 iterations)"
        A["Phase N Complete"] --> B{"Quality Gate"}
        B -->|PASS| C["→ Phase N+1"]
        B -->|FAIL iter < 3| D["Generate feedback.md"]
        D --> E["Fixer Agent\n(revision_mode)"]
        E --> B
        B -->|FAIL iter ≥ 3| F["⚠ Escalate to User"]
    end

    style B fill:#f9a825,stroke:#f57f17,color:#000
    style C fill:#66bb6a,stroke:#388e3c,color:#fff
    style F fill:#ef5350,stroke:#c62828,color:#fff

flowchart LR
    subgraph "Phase 1"
        G1["📚 Literature\n≥10 papers\nAll DOIs valid"]
    end
    subgraph "Phase 2"
        G2["📋 Outline\nAll IMRAD sections\n≥2 citations mapped"]
    end
    subgraph "Phase 2.5"
        G25["📊 Tables/Figures\nAll designs complete\nJournal limits OK"]
    end
    subgraph "Phase 3"
        G3["✍️ Section Draft\nScore ≥80%\nMust Fix = 0"]
    end
    subgraph "Phase 4"
        G4["🔍 Humanize\nHigh-priority\nAI patterns = 0"]
    end
    subgraph "Phase 5"
        G5["📖 References\nFabrication = 0\nOrphan cites = 0"]
    end
    subgraph "Phase 6"
        G6["🔗 Cross-Section\nPASS or\nCONDITIONAL_PASS"]
    end
    subgraph "Phase 7"
        G7["📦 Submission\nAll docs ready\nWord count OK"]
    end

    G1 --> G2 --> G25 --> G3 --> G4 --> G5 --> G6 --> G7

flowchart TB
    subgraph P1["Phase 1 — Literature Search (3 parallel)"]
        L1[PubMed Searcher]
        L2[Google Scholar Searcher]
        L3[Domain DB Searcher]
    end

    subgraph P3["Phase 3 — Drafting (grouped parallel)"]
        direction LR
        D1[Methods] --> D3[Intro]
        D2[Results] --> D4[Conclusion]
    end

    subgraph P4["Phase 4 — Humanize (up to 6 parallel)"]
        H1[Humanizer × N sections]
    end

    subgraph P6["Phase 6 — Quality Review"]
        R1[Section Reviewer ×N]
        R2[Quality Gate — opus]
    end

    L1 & L2 & L3 --> MERGE["Merge Matrix"]
    MERGE --> D1 & D2
    D3 & D4 --> H1
    H1 --> R1
    R1 --> R2

/paper-writer

{project-dir}/
├── README.md                        # Project dashboard (status, timeline, links)
├── 00_literature/                   # Literature search & matrix
├── 01_outline.md                    # Paper skeleton
├── sections/                        # Manuscript sections (writing order)
│   ├── 02_methods.md ... 08_title.md
├── tables/                          # Tables (numbered)
├── figures/                         # Figures + captions
├── supplements/                     # Supplementary materials
│   ├── supplementary-tables/
│   ├── supplementary-figures/
│   └── appendices/
├── data/                            # Research data (raw → processed → analysis)
│   ├── raw/                         # Original data (READ-ONLY, gitignored)
│   ├── processed/                   # Cleaned, de-identified
│   ├── analysis/                    # Statistical output
│   └── data-dictionary.md
├── ethics/                          # IRB, consent, protocol, registration
├── submissions/                     # Submission history (v1_bmj/, v2_lancet/, ...)
│   └── v1_{journal}/               # Compiled manuscript + cover letter + declarations
├── revisions/                       # Revision rounds (r1/, r2/, ...)
│   └── r1/                          # Reviewer comments + response + diff
├── coauthor-review/                 # Co-author feedback tracking
├── correspondence/                  # Editor & reviewer communication log
├── references/                      # Formatted reference list
├── checklists/                      # Quality gates, reporting guideline tracking
└── log/                             # Decisions, meetings, timeline

paper-writer/
├── SKILL.md                           # Main workflow definition
├── CHANGELOG.md                       # Version history
├── README.md                          # This file
├── README.ja.md                       # Japanese documentation
├── requirements.txt                   # Python dependencies for utility scripts
│
├── templates/                         # 37 files — Section templates
│   ├── project-init.md                # Project initialization (Original Article)
│   ├── project-init-case.md           # Project initialization (Case Report)
│   ├── research-question.md           # Question forge and FINER scoring
│   ├── study-design.md                # Study design, variables, power, feasibility
│   ├── preregistration.md             # Pre-registration lock template
│   ├── human-loop-ledger.md           # Human/AI accountability ledger
│   ├── literature-matrix.md           # Literature comparison matrix
│   ├── methods.md                     # Methods writing guide
│   ├── results.md                     # Results writing guide
│   ├── introduction.md                # Introduction writing guide
│   ├── discussion.md                  # Discussion writing guide
│   ├── conclusion.md                  # Conclusion writing guide
│   ├── abstract.md                    # Abstract writing guide (Original Article)
│   ├── cover-letter.md                # Cover letter template
│   ├── submission-ready.md            # Pre-submission checklist
│   ├── case-report.md                 # Case presentation (CARE-compliant)
│   ├── case-introduction.md           # Case report introduction
│   ├── case-abstract.md               # Case report abstract (CARE format)
│   ├── review-article.md              # Review article structure guide
│   ├── sr-outline.md                  # Systematic review outline
│   ├── sr-data-extraction.md          # SR data extraction template
│   ├── sr-prisma-flow.md              # PRISMA flow diagram
│   ├── sr-grade.md                    # GRADE evidence assessment
│   ├── sr-rob.md                      # Risk of bias assessment
│   ├── sr-prospero.md                 # PROSPERO registration template
│   ├── sr-screening-pipeline.md       # Dual-screening execution pipeline
│   ├── response-to-reviewers.md       # Response to reviewers template
│   ├── revision-cover-letter.md       # Revision cover letter
│   ├── declarations.md                # Declarations (ethics, COI, funding, AI disclosure)
│   ├── graphical-abstract.md          # Graphical abstract guide
│   ├── title-page.md                  # Title page template
│   ├── highlights.md                  # Key points / highlights (JAMA, BMJ, etc.)
│   ├── limitations-guide.md           # Limitations section guide
│   ├── acknowledgments.md             # Acknowledgments template
│   ├── proof-correction.md            # Post-acceptance proof correction guide
│   ├── data-management.md             # Data management (raw/processed/analysis)
│   └── analysis-workflow.md           # Data analysis workflow guide
│
├── references/                        # 30 files — Reference materials
│   ├── ai-for-science-model.md        # Research-engine operating model
│   ├── novelty-check.md               # Live-literature novelty check
│   ├── adversarial-review.md          # Design/manuscript red-team review
│   ├── imrad-guide.md                 # IMRAD structure and writing principles
│   ├── section-checklist.md           # Per-section quality checklist
│   ├── citation-guide.md              # Citation formatting and management
│   ├── citation-verification.md       # Citation verification guide
│   ├── reporting-guidelines.md        # Reporting guidelines summary
│   ├── reporting-guidelines-full.md   # 20+ reporting guidelines with checklists
│   ├── humanizer-academic.md          # AI writing detection (EN 18 + JP 13 patterns)
│   ├── statistical-reporting.md       # Statistical reporting guide
│   ├── statistical-reporting-full.md  # Extended SAMPL guide
│   ├── journal-selection.md           # Journal selection strategy
│   ├── pubmed-query-builder.md        # PubMed search query builder
│   ├── multilingual-guide.md          # Multilingual support guide
│   ├── coauthor-review.md             # Co-author review process
│   ├── ai-disclosure.md               # ICMJE 2023 AI disclosure guide
│   ├── tables-figures-guide.md        # Tables and figures creation guide
│   ├── keywords-guide.md              # Keywords and MeSH selection strategy
│   ├── supplementary-materials.md     # Supplementary materials strategy
│   ├── hook-compatibility.md          # Claude Code hook compatibility
│   ├── submission-portals.md          # Submission portal guide
│   ├── open-access-guide.md           # OA models, APCs, CC licenses
│   ├── clinical-trial-registration.md # Clinical trial registration guide
│   ├── abstract-formats.md            # Journal-specific abstract formats
│   ├── word-count-limits.md           # Word count limits by journal
│   ├── coi-detailed.md               # COI categories, CRediT taxonomy, ORCID
│   ├── desk-rejection-prevention.md   # Desk rejection prevention
│   ├── journal-reformatting.md        # Journal reformatting and cascading strategy
│   └── master-reference-list.md       # Master URL list (100+ links, 13 categories)
│
├── scripts/                           # 8 files — Utilities & Analysis
│   ├── compile-manuscript.sh          # Compile sections into single manuscript
│   ├── word-count.sh                  # Word count utility
│   ├── forest-plot.py                 # Forest plot generator
│   ├── sr-dedup.py                    # SR record parsing and de-duplication
│   ├── sr-pdf-link.py                 # Link full-text PDFs to records by DOI
│   ├── sr-prisma-count.py             # PRISMA flow counts and consistency checks
│   ├── table1.py                      # Table 1 generator (baseline characteristics)
│   └── analysis-template.py           # Statistical analysis template (t-test, logistic, survival)
│
├── tests/
│   └── test_scripts.py                # Regression tests for utility scripts
│
└── .github/workflows/
    └── tests.yml                      # CI: syntax checks + regression tests

git clone https://github.com/kgraph57/paper-writer-skill.git ~/.claude/skills/paper-writer

// Add to "skills" in ~/.claude/settings.json
{
  "skills": {
    "paper-writer": {
      "path": "~/.claude/skills/paper-writer"
    }
  }
}

python -m py_compile scripts/*.py
bash -n scripts/*.sh
python -m unittest discover -s tests -v