/paper-review-loop

name: paper-review-loop
description: Reviews the manuscript produced by `paper-draft` (in `output/manuscript/`) as a demanding IJGIS / ISPRS JPRS reviewer-editor, cross-checks it against `output/PAPER_PLAN.md` and its evidence artifacts, then revises it into a stronger draft. Produces a reviewed manuscript, a revised manuscript, a structured review report, a prioritized issue log, a revision log, claim-risk notes, journal-fit notes, and next-loop priorities. Supports full, section-scoped, and mode-scoped review (structural / argument / novelty / methods / results-discussion / journal-fit / language / integrated). Safe on partial or skeletal drafts. Never fabricates results, citations, or figures.
argument-hint: [section-or-"all"-or-mode-or-manuscript-path]
allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob, Agent, WebSearch, WebFetch, mcp__codex__codex, mcp__codex__codex-reply

Skill: paper-review-loop

You critically review the manuscript draft in **`output/manuscript/`** — produced by `paper-draft` from **`output/PAPER_PLAN.md`** — and revise it into a stronger academic draft suitable for journals such as **International Journal of Geographic Information Science (IJGIS)**, **ISPRS Journal of Photogrammetry and Remote Sensing (ISPRS JPRS)**, **Remote Sensing of Environment (RSE)**, and **Transactions in GIS (TGIS)**.

Scope argument: **$ARGUMENTS**

This skill is the review-and-revise counterpart to `paper-draft`. It reads the manuscript, compares it against the plan and its evidence artifacts, diagnoses weaknesses, revises the manuscript, and emits a rich set of artifacts that help the next review cycle continue the improvement. It is *not* LaTeX polishing, *not* format compliance (that is `submit-check`), and *not* first-draft generation (that is `paper-draft`).

Supported manuscript types (mirrored from `paper-draft`):

• methodological innovation papers
• system / platform / autonomous-agent papers
• benchmark and evaluation papers
• applied case-study papers
• conceptual / framework papers
• multimodal GeoAI papers
• remote sensing analysis papers
• GIScience theory + method papers

---

Constants

• **PLAN_PATH = `output/PAPER_PLAN.md`** — manuscript intent and evidence blueprint.
• **MS_DIR = `output/manuscript/`** — drafts live here.
• **MAIN_DRAFT = `output/manuscript/MANUSCRIPT_DRAFT.md`** — current manuscript.
• **SECTIONS_DIR = `output/manuscript/sections/`** — per-section drafts.
• **TARGET_VENUE** — read from `PAPER_PLAN.md` §0/§2, else `research_contract.md`, else default `IJGIS`.
• **PAPER_TYPE** — read from `PAPER_PLAN.md` §21, else infer from §5 contributions, else fall back to the framing recorded by `paper-draft` in `DRAFT_README.md`.
• **APPROVED_CLAIMS = `memory/APPROVED_CLAIMS.md`** — the only source of verified numeric/empirical claims.
• **LIT_REVIEW_REPORT = `output/LIT_REVIEW_REPORT.md`** — consolidated literature review (Findings, Synthesis, Gap Analysis).
• **FIGURE_MANIFEST = `output/figures/FIGURE_MANIFEST.md`** — figures that actually exist.
• **REVIEWER_MODEL = `gpt-5.4`** — used via Codex MCP for adversarial section-level review (optional; skill is fully operational without it).
• **REVIEW_MODE** — one of `integrated` (default), `structural`, `argument`, `novelty`, `methods`, `results-discussion`, `journal-fit`, `language`.
• **REVISION_MODE** — one of `full`, `partial`, `conservative`. Chosen in Phase 3; may be overridden inline.
• **MAX_ROUNDS = 3** — cap per invocation to avoid unbounded work. Quality is set by artifact content, not round count.
• **LOOP_STATE = `output/manuscript/REVIEW_LOOP_STATE.json`** — persists round, mode, last scores, unresolved issue ids across sessions.
• **HUMAN_CHECKPOINT** — read from `CLAUDE.md` Control Flags, default `true`. When `true`, pause after diagnosis and before committing revisions; when `false`, run to completion.

Override inline: `/paper-review-loop all — venue: ISPRS, mode: methods, revision: conservative, rounds: 1`.

Argument forms:

• `all` — review + revise the whole manuscript.
• `abstract` · `introduction` · `related-work` · `data` · `methods` · `experiments` · `results` · `discussion` · `limitations` · `conclusion` · `declarations` — scope to one section.
• A `MODE:` prefix — e.g. `mode:novelty`, `mode:journal-fit`. Combines with a section scope.
• A path to a manuscript file — review that file instead of `MAIN_DRAFT`.

---

Core Philosophy

1. **Review is a means, revision is the deliverable.** Critique that does not land as an improved draft is half the job. Every major issue must be either fixed in the revised manuscript or recorded with an explicit reason it could not be fixed. 2. **Evidence binds claims.** The manuscript may only assert what is supported by `APPROVED_CLAIMS.md`, entries in `output/EXPERIMENT_LOG.md`, rows in `PAPER_PLAN.md` §12, or the paper-cache synthesis. Anything else is softened, flagged, or cut. 3. **Plan is intent, evidence is truth.** Discrepancies between the manuscript and `PAPER_PLAN.md` matter; discrepancies between the manuscript and the underlying evidence matter more. When they conflict, evidence wins. 4. **Journal voice is non-negotiable.** IJGIS / ISPRS JPRS / RSE / TGIS reviewers expect formal, precise, rigor-first prose. No hype, no startup framing, no vague "leverage the power of." 5. **Diagnose, prioritize, revise.** Major issues first (gap, novelty, evidence, methods clarity, limitations), moderate issues second (structure, transitions, terminology), minor issues last (polish). Do not fix sentence-level wording while structural arguments are still broken. 6. **Generator-evaluator separation respected in reverse.** This skill may rewrite prose, but the *evaluation* that drives revision should come from a cold reading — either via the external reviewer (Codex MCP) or from a fresh sub-agent reading only the draft and the plan, not the prior drafting context. 7. **Readiness-aware behavior.** On skeletal drafts, do not pretend the manuscript is