/paper-writing-pipeline

name: paper-writing-pipeline
description: "Full paper writing pipeline. Orchestrates paper-plan → paper-figure-generate → paper-draft → paper-review-loop → paper-covert to go from upstream research artifacts to a polished, submission-ready manuscript package (Markdown → LaTeX → PDF + DOCX). Use when user says \"write paper pipeline\", \"paper writing\", or wants the complete paper generation workflow."
argument-hint: [narrative-report-path-or-topic]
allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob, Agent, Skill, mcp__codex__codex, mcp__codex__codex-reply

Paper Writing Pipeline

Orchestrate a complete paper writing workflow for: **$ARGUMENTS**

Overview

This skill chains five sub-skills into a single automated pipeline:

/paper-plan → /paper-figure-generate → /paper-draft → /paper-review-loop → /paper-covert
  (outline)       (figures & prompts)     (Markdown)     (review & revise)    (LaTeX + PDF + DOCX)

Each phase builds on the previous one's output. The pipeline takes upstream research artifacts and produces a polished, reviewed submission package in `output/submission/`.

Artifact Flow

Upstream artifacts (RESEARCH_PLAN, LIT_REVIEW, IDEA_REPORT, FINAL_PROPOSAL,
                    EXPERIMENT_PLAN, EXPERIMENT_RESULT, NARRATIVE_REPORT)
    ↓ Phase 1: paper-plan
output/PAPER_PLAN.md  (§0–§26: outline, claims matrix, figure plan, citations)
    ↓ Phase 2: paper-figure-generate
output/figures/       (PNGs, PDFs, scripts, prompts, FIGURE_MANIFEST.md, FIGURE_CAPTIONS.md)
    ↓ Phase 3: paper-draft
output/manuscript/    (MANUSCRIPT_DRAFT.md, sections/*.md, CLAIM_SUPPORT_MAP.md, COVERAGE_GAPS.md)
    ↓ Phase 4: paper-review-loop
output/manuscript/    (MANUSCRIPT_REVISED.md, sections_revised/*.md, REVIEW_REPORT.md, CLAIM_RISK_REPORT.md)
    ↓ Phase 5: paper-covert
output/submission/    (latex/, pdf/MANUSCRIPT_SUBMISSION_READY.pdf, docx/, SUBMISSION_MANIFEST.md)

---

Constants

• **TARGET_VENUE = `IJGIS`** — Target venue. Supported: `TGIS`, `RSE`, `ISPRS_JPRS`, `AAG_ANNALS`, `IEEE_TGRS`, `ICLR`, `NeurIPS`, `ICML`, `CVPR`, `ACL`, `AAAI`, `ACM`, `IEEE_JOURNAL` (IEEE Transactions / Letters), `IEEE_CONF` (IEEE conferences). Affects template selection, page limit, citation format, and section structure.
• **MAX_REVIEW_ROUNDS = 2** — Number of review→revise rounds in the review loop (Phase 4).
• **REVIEWER_MODEL = `gpt-5.4`** — Model used via Codex MCP for plan review, figure review, draft review, and review loop.
• **AUTO_PROCEED = true** — Auto-continue between phases. Set `false` to pause and wait for user approval after each phase.
• **HUMAN_CHECKPOINT = false** — When `true`, the review loop (Phase 4) pauses after each round's review to let you see the score and provide custom modification instructions. When `false` (default), the loop runs fully autonomously. Passed through to `paper-review-loop`.
• **DRAFT_MODE** — One of `full`, `partial`, `skeleton`. Determined automatically by `paper-draft` based on evidence readiness. Can be forced via argument.

> Override inline: `/paper-writing-pipeline "NARRATIVE_REPORT.md" — venue: NeurIPS, human checkpoint: true` > IEEE example: `/paper-writing-pipeline "NARRATIVE_REPORT.md" — venue: IEEE_JOURNAL`

---

Inputs

This pipeline accepts one of:

1. **`output/NARRATIVE_REPORT.md`** (best) — structured research narrative with claims, experiments, results, figure plans, verified citations. Produced by `generate-report`. 2. **Upstream research artifacts** — the pipeline's `paper-plan` phase will read all available artifacts (`RESEARCH_PLAN.md`, `output/LIT_REVIEW_REPORT.md`, `output/IDEA_REPORT.md`, `output/refine-logs/FINAL_PROPOSAL.md`, `output/EXPERIMENT_PLAN.md`, `output/EXPERIMENT_RESULT.md`, `output/NARRATIVE_REPORT.md`) and build the plan from whatever exists. 3. **Existing `output/PAPER_PLAN.md`** — skip Phase 1, start from Phase 2. 4. **Existing `output/manuscript/MANUSCRIPT_DRAFT.md`** — skip Phases 1–3, start from Phase 4 (review loop). 5. **Existing `output/manuscript/MANUSCRIPT_REVISED.md`** — skip Phases 1–4, start from Phase 5 (conversion).

The more detailed the input (especially figure descriptions, quantitative results, and verified claims in `memory/APPROVED_CLAIMS.md`), the better the output.

Skip Logic

Before starting, check which artifacts already exist to determine the entry point:

| Artifact exists | Skip to | Condition | |---|---|---| | `output/submission/MANUSCRIPT_SUBMISSION_READY.pdf` | Done | Ask user if they want to rebuild | | `output/manuscript/MANUSCRIPT_REVISED.md` | Phase 5 | Unless user requests re-review | | `output/manuscript/MANUSCRIPT_DRAFT.md` | Phase 4 | Unless user requests re-draft | | `output/figures/FIGURE_MANIFEST.md` | Phase 3 | Unless user requests re-generation | | `output/PAPER_PLAN.md` | Phase 2 | Unless user requests re-planning | | None of the above | Phase 1 | Full pipeline |

When resuming, always read `handoff.json` first — it records the last completed phase and any pending issues.

---

Pipeline

Phase 1: Paper Plan

Invoke `paper-plan` to create the structural outline:

Skill: paper-plan "$ARGUMENTS"

**What this does:**

• Reads all available upstream artifacts (RESEARCH_PLAN, LIT_REVIEW_REPORT, IDEA_REPORT, FINAL_PROPOSAL, EXPERIMENT_PLAN, EXPERIMENT_RESULT, NARRATIVE_REPORT) — each is optional
• Determines venue and paper type from arguments, RESEARCH_PLAN, or defaults
• Loads venue-specific template from `templates/`
• Builds the full §0–§26 plan per `templates/PAPER_PLAN_TEMPLATE.md`:
• One-paragraph summary and one-sentence claim
• Target journal strategy and audience
• Research gap and contributions (with "not claiming" boundary)
• Research questions and hypotheses
• Data and methodological plan
• Experiment inventory and results summary
• **Claims-Evidence Matrix** (§12) — the backbone mapping every claim to evidence
• **Figure & Table Plan** (§13–§14) — with hero figure detail
• Related work synthesis in t