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paper-review-loop

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UpdatedMay 3, 2026 at 12:58

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.

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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

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.
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.
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.
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."
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.
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.
Readiness-aware behavior. On skeletal drafts, do not pretend the manuscript is close to submission. Produce a revision plan and a conservative refinement of supported sections instead.
Loops are monotonic. Each round should strictly improve the manuscript on at least one named axis, and never silently reintroduce a previously-resolved issue.

Inputs

Primary

output/manuscript/MANUSCRIPT_DRAFT.md — the integrated manuscript from paper-draft.
output/manuscript/sections/*.md — per-section drafts with front matter (section, mode, word_target).
output/PAPER_PLAN.md — manuscript intent and claim-to-evidence map (§12 especially).

Companion artifacts from `paper-draft` (read on demand)

output/manuscript/DRAFT_README.md — mode, venue, paper type, readiness, per-section fidelity.
output/manuscript/CLAIM_SUPPORT_MAP.md — the claim-to-evidence rows this skill must re-verify.
output/manuscript/COVERAGE_GAPS.md — missing experiments, figures, citations flagged at draft time.
output/manuscript/CITATION_GAPS.md — claims missing citations.
output/manuscript/SECTION_NOTES.md — per-section scope decisions and softened claims.
output/manuscript/REVISION_NOTES.md — unfinished items from the drafting pass.
output/manuscript/ABSTRACT_DRAFT.md — stand-alone abstract.

Evidence and context (read as needed)

research_contract.md, program.md — active idea and constraints.
memory/APPROVED_CLAIMS.md, output/LIT_REVIEW_REPORT.md (Gap Analysis + Synthesis sections).
memory/paper-cache/*.json — bibliographic + finding records.
output/EXPERIMENT_LOG.md, output/EXPERIMENT_PLAN.md, output/PROJ_NOTES.md.
output/spatial-analysis/ — ESDA and diagnostic reports.
output/figures/FIGURE_MANIFEST.md, output/figures/FIGURE_CAPTIONS.md.
output/AUTO_REVIEW.md — prior adversarial-review scores and pending fixes.
templates/giscience/, templates/remote_sensing/, templates/geoscience/ — venue guides.
skills/knowledge/academic-writing.md, skills/knowledge/apa-citations.md, skills/knowledge/spatial-methods.md, skills/knowledge/geoai-domain.md.
skills/shared-references/writing-principles.md, skills/shared-references/venue-checklists.md — load only when acting on Abstract / Introduction / Related Work / journal-fit.

Prior-loop state

output/manuscript/REVIEW_LOOP_STATE.json — round counter, unresolved issue ids, prior scores, timestamp.
output/manuscript/REVIEW_REPORT.md, MAJOR_ISSUES.md, MINOR_ISSUES.md, REVISION_LOG.md, NEXT_LOOP_PRIORITIES.md — if present, treated as the incoming queue for this round.

Outputs

All outputs live under output/manuscript/. Filenames are stable across rounds (the skill overwrites); rounds are distinguished by entries inside the files, not by filename suffixes.

File	Purpose
`MANUSCRIPT_REVIEWED.md`	The input draft with inline review annotations (`<!-- REVIEW: ... -->` blocks), for traceability. Not a revised draft.
`MANUSCRIPT_REVISED.md`	The revised manuscript after this round. Becomes the basis for the next loop.
`sections_revised/NN_<name>.md`	Per-section revised drafts, parallel to `sections/`. Used when revising partial or conservative scopes.
`REVIEW_REPORT.md`	Structured reviewer-style report: summary, per-section assessment, per-dimension scores, verdict.
`MAJOR_ISSUES.md`	Ranked list of major issues with diagnosis, evidence pointer, revision action, resolved-yes/no, and carry-over flag.
`MINOR_ISSUES.md`	Ranked list of moderate + minor issues (structure, transitions, wording, terminology).
`REVISION_LOG.md`	What changed in `MANUSCRIPT_REVISED.md` this round, keyed to issue ids, with before/after snippets.
`SECTION_REVIEW_NOTES.md`	Per-section notes on strengths, weaknesses, and revision decisions. Feeds the next round.
`CLAIM_RISK_REPORT.md`	Every claim from `CLAIM_SUPPORT_MAP.md` re-verified against the draft; flags overclaims, softened claims, unsupported claims.
`JOURNAL_FIT_NOTES.md`	Alignment against the target venue's expectations (IJGIS / ISPRS JPRS / RSE / TGIS) — framing, rigor, methods reporting, limitations, declarations.
`NEXT_LOOP_PRIORITIES.md`	What the next round should focus on; carries forward unresolved majors and newly discovered moderates.
`REVIEW_LOOP_STATE.json`	Round counter, prior scores, unresolved issue ids, mode, timestamp.

File-naming conventions are inherited from paper-draft: two-digit section prefixes, no _v2 suffixes, prior versions preserved via git not filenames.

Workflow

The skill has eight phases. Phases 1–4 are diagnosis; Phase 5 is the optional human checkpoint; Phases 6–7 are revision and verification; Phase 8 is handoff. On tight scopes (e.g. mode:language), phases can be compressed but not skipped.

Phase 1 — Load state and scope

Read CLAUDE.md Control Flags. Honour HUMAN_CHECKPOINT.
If REVIEW_LOOP_STATE.json exists with status: in_progress and timestamp within 24 hours: resume. Increment round. Read prior REVIEW_REPORT.md, MAJOR_ISSUES.md, NEXT_LOOP_PRIORITIES.md as the incoming queue.
If not resuming: initialize round = 1, load scope from $ARGUMENTS.
Resolve REVIEW_MODE and section scope:
- No mode given → integrated.
- mode:<x> given → use that mode; other phases still run but are minimized.
Locate the manuscript:
- If $ARGUMENTS is a path → use it.
- Else use MAIN_DRAFT. If absent, emit a stub REVIEW_REPORT.md explaining that paper-draft must run first, and stop.

Phase 2 — Read manuscript and its companion artifacts

Read in this order (cheap → expensive):

DRAFT_README.md — get declared DRAFT_MODE (full / partial / skeleton), venue, paper type, readiness signals, and per-section fidelity.
MANUSCRIPT_DRAFT.md and relevant sections/*.md. Determine whether the draft is full, partial, or skeletal regardless of what DRAFT_README.md claims (cross-check against actual content length, [PLACEHOLDER ...] blocks, and [CITE: ...] tags).
CLAIM_SUPPORT_MAP.md — pull the claim-to-evidence rows; this is the backbone of the claim-risk audit.
COVERAGE_GAPS.md, CITATION_GAPS.md, SECTION_NOTES.md, REVISION_NOTES.md — known-at-draft-time weaknesses.
ABSTRACT_DRAFT.md — the stand-alone abstract.

Phase 3 — Cross-check against `PAPER_PLAN.md`

Open PAPER_PLAN.md. For each plan section that drives the draft, answer a specific question and record the answer in SECTION_REVIEW_NOTES.md:

Plan §	Question to answer about the draft
§1 Title & one-sentence claim	Does the draft's title and abstract-leading sentence match this framing? If drift, is it justified by evidence?
§2 Journal strategy	Does the prose tone match this venue (IJGIS / ISPRS JPRS / RSE / TGIS)?
§3–§4 Motivation + gap	Is the gap explicit in the Introduction? Is prior work's insufficiency named?
§5 Novelty + contributions	Does the Introduction list contributions as numbered outcomes? Do Results and Conclusion return to them with the same numbering?
§6 RQs / hypotheses	Are they stated? Are they answered in Results + Discussion?
§7–§8 Scope + data	Are data sources, CRS, spatial unit, coverage, and caveats stated?
§9 Methodology	Are the algorithmic / workflow steps specific enough for a reader to grasp the shape of the method?
§10 Experiments	Are train/val/test, metrics, baselines, and ablations defined with precision?
§11 Results	Does the lead result match §5's headline claim? Are results ordered by claim, not by figure?
§12 Claim-to-evidence map	For every row, does the draft state the claim at the right strength?
§13–§14 Figures / tables	Is every mentioned figure in `FIGURE_MANIFEST.md`? Are figures referenced by purpose?
§15 Related work synthesis	Is related work cluster-organized or a laundry list?
§16 Discussion	Does Discussion close the loop to the gap, name GIScience / GeoAI / RS implications, address responsible-use where relevant?
§17 Limitations	Are all planned limitations present? None silently dropped?
§18 Reproducibility	Data / code availability statements present?
§20 Abstract blueprint	Abstract hits background → gap → method → data → findings → significance?
§21 Title/framing + paper type	Does the manuscript genuinely behave like that paper type (e.g. system paper actually describes architecture, modules, information flow)?
§25 Readiness	Does the draft acknowledge readiness honestly, or does it pretend it is stronger than the evidence?

Record each answer with a severity tag: ok · moderate · major · placeholder-expected.

Phase 4 — Re-verify evidence (Claim Risk Audit)

Open CLAIM_SUPPORT_MAP.md and walk every row. For each:

Find the claim in the draft (grep by claim id or phrasing).
Compare the strength of the claim's wording to the evidence confidence:
- High-confidence evidence + cautious wording → upgrade to precise ("we observed" → "on the [dataset] holdout, [metric] = [value]").
- Medium-confidence evidence + strong wording → soften ("outperforms" → "is competitive with," "consistent with").
- Low-confidence evidence in Abstract / Results headline → move the claim to Discussion with hedged language, or cut.
- No evidence (—) → the claim must be a marked placeholder or cut. If it is asserted as fact in the current draft, flag as CRITICAL-overclaim.
Check for claims in the draft that are not in CLAIM_SUPPORT_MAP.md — these are almost always unsupported and must be added to the map with evidence located, or softened / cut.
Check for planned claims that are missing from the draft — these may be silently dropped evidence; restore if the plan intended them and evidence supports them.

Emit CLAIM_RISK_REPORT.md with one row per claim, columns: ClaimID · Section · Wording · Evidence · Confidence · Risk · Revision Action.

Never invent evidence. Never invent a citation key. Never invent a metric number. When evidence is genuinely missing, the revision is to soften or remove, not to fabricate.

Phase 5 — Diagnose and classify issues

Run through the review checklist (see templates/REVIEW_CHECKLIST.md) using the REVIEW_MODE:

structural — section presence, order, word balance, paragraph topic sentences, section transitions, heading hierarchy, figure/table placement.
argument — gap clarity, contribution clarity, claim-to-evidence consistency, Introduction → Results → Conclusion coherence, lead results discipline.
novelty — precision of novelty statement, differentiation from nearest prior work, avoidance of "first / state-of-the-art" unless APPROVED_CLAIMS.md supports it.
methods — problem formulation, input/output, unit of analysis, spatial unit, CRS, preprocessing, model/framework specificity, baselines, evaluation metrics, reproducibility detail, system architecture for system papers.
results-discussion — ordering by claim, interpretation discipline, mixed/negative findings honesty, GIScience / GeoAI implications, responsible-use discussion, generalizability conditions, limitations completeness.
journal-fit — venue tone, rigor conventions, expected section presence, declarations (data / code availability), ethics statements.
language — paragraph topic sentences, sentence-length variation, terminology drift, figure/table reference style ("shows" vs. "as can be seen in"), abbreviation management.
integrated — all of the above, prioritized.

Classify each finding into:

Major

weak or missing gap articulation
unclear novelty or novelty unsupported by differentiation
claims whose strength exceeds evidence ("overclaim")
insufficient methods detail to grasp the method
weak experiment description (unclear protocol, unclear metrics, unclear baselines)
results interpreted more strongly than the data support
poor connection to GIScience / GeoAI / remote sensing literature
missing or defanged limitations
mismatch with target journal expectations (tone, structure, declarations)
structural problems (section ordering, missing sections, dangling contributions)

Moderate

repetitive writing, redundant paragraphs across sections
vague section transitions
inconsistent terminology (model / dataset / system / metric names drift)
weak paragraph topic sentences
figure/table references that do not integrate with the narrative
incomplete contextualization of findings against prior work

Minor

awkward wording, local clarity problems
caption / title mismatches
redundant phrases and filler
sentence-level polish needs

Write MAJOR_ISSUES.md and MINOR_ISSUES.md using the schema in templates/ISSUE_RUBRIC.md. Each issue has: id · severity · section · description · evidence · proposed revision · resolved-in-this-round (yes/no) · carry-over (yes/no).

Phase 5.5 — Optional external reviewer pass (`REVIEWER_MODEL`)

If Codex MCP is available and HUMAN_CHECKPOINT does not block it, send the revised-candidate to gpt-5.4 for an independent adversarial read. This is the generator-evaluator separation check.

mcp__codex__codex:
  model: gpt-5.4
  config: {"model_reasoning_effort": "xhigh"}
  prompt: |
    You are reviewing a manuscript draft for [TARGET_VENUE] ([IJGIS | ISPRS JPRS | RSE | TGIS]).
    Paper type: [PAPER_TYPE].
    This is Round [N] of an iterative review loop. Prior unresolved major issues: [...].

    Focus: [REVIEW_MODE].

    Please provide a structured review:
    1. Score 1–10 per dimension: gap clarity, novelty precision, methods rigor, results discipline,
       discussion depth, literature positioning, journal fit, language and flow.
    2. Ranked list of remaining CRITICAL > MAJOR > MODERATE issues, each with a minimum edit.
    3. Claim-risk flags: which sentences in the draft look stronger than the evidence supports?
    4. Verdict: ready / almost / not ready for [TARGET_VENUE].
    5. One paragraph on what is working well — do not just list weaknesses.

    Do not rewrite. Do not fabricate evidence. Be specific to GIScience / GeoAI / remote sensing expectations.

    [Paste MANUSCRIPT_REVIEWED.md content or the scoped section(s).]
    [Paste PAPER_PLAN.md §5, §12, §16, §17, §21 for context.]

If round 2+, use mcp__codex__codex-reply with the saved threadId from REVIEW_LOOP_STATE.json so the reviewer has continuity.

If Codex is unavailable, skip — do not fall back to self-scoring. A cold-read sub-agent (Agent tool) can substitute.

Phase 6 — Human checkpoint (if enabled)

Skip if HUMAN_CHECKPOINT = false.

Present to the user:

per-dimension scores (this round vs. prior round if any)
top 3 major issues with proposed revision summaries
claim-risk flags count (overclaims, unsupported, placeholder-expected)
proposed REVISION_MODE (full / partial / conservative)

Accept: go (apply all revisions) · custom: <instructions> · skip N (skip issue id N) · stop (write artifacts, end loop). Default on no response within the session's interaction budget: go.

Phase 7 — Revise the manuscript

Revision is ordered by severity: Majors → Moderates → Minors. Never polish sentence-level wording before structural arguments are resolved.

Decision rules for the revision:

REVISION_MODE = full — rewrite affected paragraphs/sections end-to-end when structural or argument issues dominate; preserve accepted sections per memory/MEMORY.md and REVIEW_STATE.json.
REVISION_MODE = partial — rewrite only the sections with major issues; surgically edit moderate issues in others.
REVISION_MODE = conservative — when evidence is incomplete or readiness is low, prefer softening, tightening, and marking placeholders over large rewrites. Do not upgrade claims. Do not invent new content to paper over gaps.

Section-specific revision behavior (see templates/SECTION_REVIEW_TEMPLATE.md):

Abstract

Rebuild against plan §20 blueprint: background → gap → method / system → data / case study → headline finding (with one specific number from APPROVED_CLAIMS.md) → significance. One paragraph. No citations. No figure references. Cap per venue: 250 words (IJGIS, TGIS), 300 words (ISPRS JPRS, RSE).

Introduction

Verify the six-paragraph arc: broad problem → GIScience / GeoAI / RS framing → current approaches (named threads) → specific gap → proposed work + numbered contribution list → roadmap. Ensure each contribution is a claim the Results actually supports. Soften "first / novel / state-of-the-art" unless directly supported.

Related Work

Enforce cluster-first synthesis. Each cluster: synthesize the thread → name 3–8 representative studies → state what the cluster does well and where it falls short relative to the gap. Close with a differentiation paragraph naming nearest competing approaches and the dimension of difference.

Data / Study Area

For each dataset: name, provider, spatial coverage, temporal coverage, resolution, variables used, preprocessing, licensing, CRS, spatial unit of analysis. Flag caveats honestly (missingness, class imbalance, geographic bias). Add responsible-use paragraph if plan §16 flags it.

Methods

Ensure problem formulation (task, input, output, unit of analysis), preprocessing, model/framework specificity, baselines and rationale, evaluation metrics with precise definitions, implementation reproducibility notes. For system / agent papers: architecture, module inventory, orchestration logic, artifact flow across skills, harness-level constraints. For spatial methods: neighborhood definition, handling of spatial dependency, MAUP / scale considerations, CRS handling, uncertainty propagation.

Experiments

Train / val / test protocol, spatial cross-validation if used, metric definitions, statistical tests, ablation axes, sensitivity / robustness axes, compute environment. State decision rules when plan §10 supplies them.

Results

Lead with the headline finding stated concretely. Organize by claim, not by figure. Each result: observation → metric / number → source experiment → one-sentence measured interpretation. Separate observation from interpretation. Report mixed / negative findings. Reference only figures in FIGURE_MANIFEST.md. Only cite numbers in APPROVED_CLAIMS.md / EXPERIMENT_LOG.md. Replace overclaims with the strongest defensible wording.

Discussion

Interpret, don't repeat. Structure: (1) what the findings mean mechanistically or conceptually, (2) how they answer the gap, (3) GIScience / GeoAI / RS implications, (4) practical / operational implications when applicable, (5) responsible-use (fairness, geoprivacy, interpretability, reproducibility, representativeness) proportional to plan §16, (6) generalizability — conditions of transfer and non-transfer.

Limitations

Specific, not generic. Mirror plan §17 one-to-one. No "future work will solve everything" framing.

Conclusion

Restate contributions as outcomes in the same numbering used in Introduction. Close with broader significance. 2–4 concrete future-work directions grounded in limitations.

Declarations

Data availability, code availability, ethics, conflict of interest, acknowledgement placeholders per plan §18 and the venue's conventions.

Write revised sections to sections_revised/NN_<name>.md. Assemble MANUSCRIPT_REVISED.md by concatenating in order plus the title block. Do not overwrite sections/*.md — paper-draft owns those.

Maintain terminology consistency: grep for canonical names (model, dataset, system, metric, geographic terms, abbreviations) and normalize drift in the revised draft. Record renames in REVISION_LOG.md.

Phase 8 — Verify, log, and hand off

Mechanical post-revision checks:

Claim closure: every CRITICAL-overclaim in CLAIM_RISK_REPORT.md is either softened in MANUSCRIPT_REVISED.md or carried over with an explicit reason.
Limitation closure: every plan §17 limitation appears in the revised Limitations section.
Figure closure: every figure mentioned in the revised draft exists in FIGURE_MANIFEST.md.
Contribution closure: every numbered contribution in Introduction appears, in the same numbering, in Results and Conclusion.
Terminology closure: grep confirms no mixed casing / spelling for canonical names.
Placeholder discipline: [PLACEHOLDER ...] blocks remain only where evidence is genuinely missing; none have been silently deleted.

Write all output artifacts (see Outputs table). Update REVIEW_LOOP_STATE.json:

{
  "round": 2,
  "review_mode": "integrated",
  "revision_mode": "partial",
  "threadId": "019ce736-...",
  "last_scores": {
    "gap_clarity": 6.5,
    "novelty_precision": 6.0,
    "methods_rigor": 7.0,
    "results_discipline": 6.5,
    "discussion_depth": 6.0,
    "literature_positioning": 6.5,
    "journal_fit": 7.0,
    "language_flow": 7.5
  },
  "unresolved_major_ids": ["M3", "M7"],
  "status": "in_progress",
  "timestamp": "2026-04-14T22:00:00"
}

On the final round of this invocation, set status: completed only if no unresolved majors remain; otherwise leave in_progress so the next invocation resumes cleanly.

Append a one-line entry to output/PROJ_NOTES.md:

YYYY-MM-DD paper-review-loop round=N mode=<...> revision=<...> majors=<open/total> verdict=<ready|almost|not-ready>

Append a cumulative entry to output/AUTO_REVIEW.md with the per-dimension scores and top 3 majors, respecting the generator-evaluator protocol noted in CLAUDE.md.

Decision rules (summary)

Full vs. partial vs. conservative revision: full when structural/argument issues dominate and evidence is mostly in place; partial when only some sections have major issues; conservative when readiness is low or evidence is incomplete.
Handling unsupported claims: soften first; mark as placeholder second; cut third. Never fabricate.
When the plan and the draft disagree: if evidence supports the draft, update SECTION_REVIEW_NOTES.md with a rationale and keep the draft's framing; if evidence supports the plan, revise the draft back toward the plan.
Paper-type adaptation: review criteria shift by PAPER_TYPE (e.g. benchmark papers are held to stricter evaluation-protocol standards; system papers to stricter architecture + information-flow clarity; applied case studies to study-area specificity and practical implications).
Journal adaptation: IJGIS / TGIS emphasize GIScience theory, spatial framing, and scale/MAUP discipline. ISPRS JPRS / RSE emphasize sensor / resolution / preprocessing rigor and quantitative evaluation. Adjust the review accordingly (see templates/JOURNAL_FIT_CHECKLIST.md).
Incomplete drafts: produce MAJOR_ISSUES.md, a revised partial draft, a marked-up section-by-section improvement memo in SECTION_REVIEW_NOTES.md, and NEXT_LOOP_PRIORITIES.md. Do not pretend a skeletal draft is publication-ready.
Round budget: cap at MAX_ROUNDS = 3 per invocation. Diminishing returns beyond three rounds for writing-quality improvements; continuation requires fresh evidence or a new scope.

Style guidance for the revised prose

Formal, scholarly, third-person. First-person plural ("we") is acceptable in Methods and Discussion.
Precise vocabulary. Prefer heterogeneous land-cover patches over diverse landscapes; spatial units of analysis over areas; spatial cross-validation over held-out test.
Paragraphs open with a topic sentence that states a claim, not a transition.
One idea per paragraph; ≤ 180 words except in Methods.
Vary sentence length; do not stack three long sentences.
Define every abbreviation at first use and fix it. Canonical names are frozen at first use across sections.
Present tense for established knowledge; past tense for what you did in the study.
Reference figures by purpose: "the confusion matrix in Fig. 3 shows..." — never "as can be seen in Fig. 3."
State spatial unit of analysis and CRS when they matter for the claim.
Distinguish model family from training regime from evaluation protocol.
For system / agent papers: distinguish engineering novelty, workflow novelty, and scientific contribution — do not conflate.

Contribution framing:

State contributions as outcomes, not promises.
Avoid "first," "state-of-the-art," "outperforms all existing methods" unless APPROVED_CLAIMS.md directly supports it on the named benchmark.
Prefer "to our knowledge, this is the first evaluation of X on Y" over "the first X."

Guardrails (non-negotiable)

Do not:

Fabricate results, metrics, sample sizes, effect sizes, or confidence intervals.
Invent citation keys, authors, years, or venues. Use [CITE: ...] placeholders instead.
Reference figures or tables that are not in FIGURE_MANIFEST.md.
Strengthen a claim beyond what CLAIM_SUPPORT_MAP.md + APPROVED_CLAIMS.md support.
Hide missing experiments behind vague language. Mark them.
Drop a limitation listed in plan §17 without a recorded reason.
Use promotional / startup / hype language ("revolutionary," "game-changing," "unlock," "leverage the power of," "paradigm shift").
Flatten the author's intended contribution into something too generic in the name of "clarity."
Write only sentence-level polish while structural arguments are still broken.
Self-score the draft without a cold reader. Use Codex MCP or a fresh Agent.
Overwrite accepted sections listed in memory/MEMORY.md or output/REVIEW_STATE.json without explicit user instruction.
Overwrite sections/*.md — those are owned by paper-draft. Write to sections_revised/*.md.

Do:

Soften under pressure from evidence.
Revise for publishability, not flashiness.
Prefer one strong paragraph to three weak ones.
Cut before padding.
Make the reasoning behind the revision traceable via REVISION_LOG.md.

Deliverable conventions

Folder layout after one round:

output/manuscript/
├── DRAFT_README.md                 # from paper-draft
├── MANUSCRIPT_DRAFT.md             # from paper-draft (unchanged)
├── MANUSCRIPT_REVIEWED.md          # this skill — with <!-- REVIEW: ... --> annotations
├── MANUSCRIPT_REVISED.md           # this skill — revised draft
├── CLAIM_SUPPORT_MAP.md            # paper-draft
├── CLAIM_RISK_REPORT.md            # this skill
├── COVERAGE_GAPS.md                # paper-draft (this skill may append)
├── CITATION_GAPS.md                # paper-draft (this skill may append)
├── SECTION_NOTES.md                # paper-draft
├── SECTION_REVIEW_NOTES.md         # this skill
├── MAJOR_ISSUES.md                 # this skill
├── MINOR_ISSUES.md                 # this skill
├── REVIEW_REPORT.md                # this skill
├── REVISION_LOG.md                 # this skill
├── JOURNAL_FIT_NOTES.md            # this skill
├── NEXT_LOOP_PRIORITIES.md         # this skill
├── REVIEW_LOOP_STATE.json          # this skill
├── REVISION_NOTES.md               # paper-draft (this skill may append)
├── sections/                       # paper-draft (read-only)
│   ├── 00_title.md
│   ├── 01_abstract.md
│   └── ...
└── sections_revised/               # this skill
    ├── 00_title.md
    ├── 01_abstract.md
    └── ...

Each revised section file keeps the same three-line YAML front matter as paper-draft, with two added fields:

---
section: introduction
mode: full
word_target: 1000
review_round: 2
revision_mode: partial
---

MAJOR_ISSUES.md, MINOR_ISSUES.md, and CLAIM_RISK_REPORT.md follow row schemas in templates/ISSUE_RUBRIC.md and templates/CLAIM_RISK_CHECKLIST.md.

Issue ids are stable across rounds (e.g. M3 stays M3 once assigned). Resolution flips resolved-in-this-round to yes but the row stays in history.

Loop iteration conventions

Monotonic improvement: each round must strictly improve at least one named dimension. Regressions are bugs; investigate before shipping.
Stable issue ids: once M7 exists, it stays M7 across rounds; its status and round-resolved columns change, not its id.
Carry-over flag: unresolved majors move to the top of NEXT_LOOP_PRIORITIES.md.
Round cap: MAX_ROUNDS = 3 per invocation. Beyond that, the skill stops and asks whether new evidence has arrived (new experiments, new figures, new approved claims). Without new evidence, further loops produce diminishing returns.
Compaction recovery: if context fills mid-round, write REVIEW_LOOP_STATE.json and REVISION_LOG.md before compaction; the next session reads them, picks up from the next phase.

Supporting templates

templates/REVIEW_CHECKLIST.md — full review checklist by mode (structural / argument / novelty / methods / results-discussion / journal-fit / language / integrated).
templates/SECTION_REVIEW_TEMPLATE.md — per-section review + revision scaffold.
templates/ISSUE_RUBRIC.md — major / moderate / minor schema, row format, severity criteria.
templates/CLAIM_RISK_CHECKLIST.md — claim-wording-vs-evidence audit, one row per claim.
templates/JOURNAL_FIT_CHECKLIST.md — IJGIS / ISPRS JPRS / RSE / TGIS expectations by section and by paper type.
templates/OUTPUT_CONVENTIONS.md — folder layout, file names, front-matter, round conventions.

Load templates on demand; do not paste their full contents into review outputs.

Composing with other workflows

/paper-plan              → output/PAPER_PLAN.md
/paper-figure-generate   → output/figures/
/paper-draft all         → output/manuscript/         (draft + claim map + gap reports)
/paper-review-loop all   ← you are here               (review + revise + next-loop priorities)
/paper-write             → output/paper/ (LaTeX)
/paper-compile           → output/paper/main.pdf
/submit-check            → venue-compliance gate

Relationship to sibling skills:

paper-draft — writes the first manuscript; owns sections/*.md. This skill never overwrites those.
auto-review-loop — adversarial research-quality review (novelty, rigor, literature, clarity, impact); operates earlier in the pipeline on the research itself, not the manuscript prose. This skill borrows its generator-evaluator discipline.
result-to-claim — the safety gate that populates memory/APPROVED_CLAIMS.md. This skill trusts that file absolutely.
submit-check — final venue-compliance gate (word count, declarations, geo-specific reporting). This skill can precede it; it does not replace it.

Key Rules (summary)

Review is a means, revision is the deliverable. Ship MANUSCRIPT_REVISED.md, not just a report.
Evidence binds claims. CLAIM_RISK_REPORT.md is as important as the revised prose.
Terminology is frozen at first use — the revision normalizes drift, does not introduce new variants.
Never reference a missing figure, never invent a citation, never fabricate a metric.
Readiness-aware: conservative revisions on skeletal drafts; no pretending.
Majors before minors — structure and argument before polish.
Generator-evaluator separation: evaluate with Codex MCP or a fresh Agent, not the drafting context.
Stable issue ids and monotonic improvement across rounds.
Respect memory/MEMORY.md and output/REVIEW_STATE.json — do not overwrite accepted sections.
Overwrite to sections_revised/, never sections/.
Large file handling: if Write fails on size, retry with chunked Bash (cat << 'EOF' > file) without asking.

Acknowledgements

Structure adapted from paper-draft (claim-evidence discipline, readiness-aware modes, output richness), auto-review-loop (generator-evaluator separation, per-dimension scoring, round-state persistence, Codex MCP integration), paper-plan (section backbone and venue selection), and submit-check (venue-compliance sensitivity). GIScience / GeoAI / remote sensing review expectations informed by skills/knowledge/academic-writing.md, skills/knowledge/spatial-methods.md, skills/knowledge/geoai-domain.md, and the shared references in skills/shared-references/.

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

Scope argument: $ARGUMENTS

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

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.
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.
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.
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."
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.
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.
Readiness-aware behavior. On skeletal drafts, do not pretend the manuscript is close to submission. Produce a revision plan and a conservative refinement of supported sections instead.
Loops are monotonic. Each round should strictly improve the manuscript on at least one named axis, and never silently reintroduce a previously-resolved issue.

Inputs

Primary

output/manuscript/MANUSCRIPT_DRAFT.md — the integrated manuscript from paper-draft.
output/manuscript/sections/*.md — per-section drafts with front matter (section, mode, word_target).
output/PAPER_PLAN.md — manuscript intent and claim-to-evidence map (§12 especially).

Companion artifacts from `paper-draft` (read on demand)

output/manuscript/DRAFT_README.md — mode, venue, paper type, readiness, per-section fidelity.
output/manuscript/CLAIM_SUPPORT_MAP.md — the claim-to-evidence rows this skill must re-verify.
output/manuscript/COVERAGE_GAPS.md — missing experiments, figures, citations flagged at draft time.
output/manuscript/CITATION_GAPS.md — claims missing citations.
output/manuscript/SECTION_NOTES.md — per-section scope decisions and softened claims.
output/manuscript/REVISION_NOTES.md — unfinished items from the drafting pass.
output/manuscript/ABSTRACT_DRAFT.md — stand-alone abstract.

Evidence and context (read as needed)

research_contract.md, program.md — active idea and constraints.
memory/APPROVED_CLAIMS.md, output/LIT_REVIEW_REPORT.md (Gap Analysis + Synthesis sections).
memory/paper-cache/*.json — bibliographic + finding records.
output/EXPERIMENT_LOG.md, output/EXPERIMENT_PLAN.md, output/PROJ_NOTES.md.
output/spatial-analysis/ — ESDA and diagnostic reports.
output/figures/FIGURE_MANIFEST.md, output/figures/FIGURE_CAPTIONS.md.
output/AUTO_REVIEW.md — prior adversarial-review scores and pending fixes.
templates/giscience/, templates/remote_sensing/, templates/geoscience/ — venue guides.
skills/knowledge/academic-writing.md, skills/knowledge/apa-citations.md, skills/knowledge/spatial-methods.md, skills/knowledge/geoai-domain.md.
skills/shared-references/writing-principles.md, skills/shared-references/venue-checklists.md — load only when acting on Abstract / Introduction / Related Work / journal-fit.

Prior-loop state

output/manuscript/REVIEW_LOOP_STATE.json — round counter, unresolved issue ids, prior scores, timestamp.
output/manuscript/REVIEW_REPORT.md, MAJOR_ISSUES.md, MINOR_ISSUES.md, REVISION_LOG.md, NEXT_LOOP_PRIORITIES.md — if present, treated as the incoming queue for this round.

Outputs

All outputs live under output/manuscript/. Filenames are stable across rounds (the skill overwrites); rounds are distinguished by entries inside the files, not by filename suffixes.

File	Purpose
`MANUSCRIPT_REVIEWED.md`	The input draft with inline review annotations (`<!-- REVIEW: ... -->` blocks), for traceability. Not a revised draft.
`MANUSCRIPT_REVISED.md`	The revised manuscript after this round. Becomes the basis for the next loop.
`sections_revised/NN_<name>.md`	Per-section revised drafts, parallel to `sections/`. Used when revising partial or conservative scopes.
`REVIEW_REPORT.md`	Structured reviewer-style report: summary, per-section assessment, per-dimension scores, verdict.
`MAJOR_ISSUES.md`	Ranked list of major issues with diagnosis, evidence pointer, revision action, resolved-yes/no, and carry-over flag.
`MINOR_ISSUES.md`	Ranked list of moderate + minor issues (structure, transitions, wording, terminology).
`REVISION_LOG.md`	What changed in `MANUSCRIPT_REVISED.md` this round, keyed to issue ids, with before/after snippets.
`SECTION_REVIEW_NOTES.md`	Per-section notes on strengths, weaknesses, and revision decisions. Feeds the next round.
`CLAIM_RISK_REPORT.md`	Every claim from `CLAIM_SUPPORT_MAP.md` re-verified against the draft; flags overclaims, softened claims, unsupported claims.
`JOURNAL_FIT_NOTES.md`	Alignment against the target venue's expectations (IJGIS / ISPRS JPRS / RSE / TGIS) — framing, rigor, methods reporting, limitations, declarations.
`NEXT_LOOP_PRIORITIES.md`	What the next round should focus on; carries forward unresolved majors and newly discovered moderates.
`REVIEW_LOOP_STATE.json`	Round counter, prior scores, unresolved issue ids, mode, timestamp.

File-naming conventions are inherited from paper-draft: two-digit section prefixes, no _v2 suffixes, prior versions preserved via git not filenames.

Workflow

Phase 1 — Load state and scope

Read CLAUDE.md Control Flags. Honour HUMAN_CHECKPOINT.
If REVIEW_LOOP_STATE.json exists with status: in_progress and timestamp within 24 hours: resume. Increment round. Read prior REVIEW_REPORT.md, MAJOR_ISSUES.md, NEXT_LOOP_PRIORITIES.md as the incoming queue.
If not resuming: initialize round = 1, load scope from $ARGUMENTS.
Resolve REVIEW_MODE and section scope:
- No mode given → integrated.
- mode:<x> given → use that mode; other phases still run but are minimized.
Locate the manuscript:
- If $ARGUMENTS is a path → use it.
- Else use MAIN_DRAFT. If absent, emit a stub REVIEW_REPORT.md explaining that paper-draft must run first, and stop.

Phase 2 — Read manuscript and its companion artifacts

Read in this order (cheap → expensive):

DRAFT_README.md — get declared DRAFT_MODE (full / partial / skeleton), venue, paper type, readiness signals, and per-section fidelity.
MANUSCRIPT_DRAFT.md and relevant sections/*.md. Determine whether the draft is full, partial, or skeletal regardless of what DRAFT_README.md claims (cross-check against actual content length, [PLACEHOLDER ...] blocks, and [CITE: ...] tags).
CLAIM_SUPPORT_MAP.md — pull the claim-to-evidence rows; this is the backbone of the claim-risk audit.
COVERAGE_GAPS.md, CITATION_GAPS.md, SECTION_NOTES.md, REVISION_NOTES.md — known-at-draft-time weaknesses.
ABSTRACT_DRAFT.md — the stand-alone abstract.

Phase 3 — Cross-check against `PAPER_PLAN.md`

Open PAPER_PLAN.md. For each plan section that drives the draft, answer a specific question and record the answer in SECTION_REVIEW_NOTES.md:

Plan §	Question to answer about the draft
§1 Title & one-sentence claim	Does the draft's title and abstract-leading sentence match this framing? If drift, is it justified by evidence?
§2 Journal strategy	Does the prose tone match this venue (IJGIS / ISPRS JPRS / RSE / TGIS)?
§3–§4 Motivation + gap	Is the gap explicit in the Introduction? Is prior work's insufficiency named?
§5 Novelty + contributions	Does the Introduction list contributions as numbered outcomes? Do Results and Conclusion return to them with the same numbering?
§6 RQs / hypotheses	Are they stated? Are they answered in Results + Discussion?
§7–§8 Scope + data	Are data sources, CRS, spatial unit, coverage, and caveats stated?
§9 Methodology	Are the algorithmic / workflow steps specific enough for a reader to grasp the shape of the method?
§10 Experiments	Are train/val/test, metrics, baselines, and ablations defined with precision?
§11 Results	Does the lead result match §5's headline claim? Are results ordered by claim, not by figure?
§12 Claim-to-evidence map	For every row, does the draft state the claim at the right strength?
§13–§14 Figures / tables	Is every mentioned figure in `FIGURE_MANIFEST.md`? Are figures referenced by purpose?
§15 Related work synthesis	Is related work cluster-organized or a laundry list?
§16 Discussion	Does Discussion close the loop to the gap, name GIScience / GeoAI / RS implications, address responsible-use where relevant?
§17 Limitations	Are all planned limitations present? None silently dropped?
§18 Reproducibility	Data / code availability statements present?
§20 Abstract blueprint	Abstract hits background → gap → method → data → findings → significance?
§21 Title/framing + paper type	Does the manuscript genuinely behave like that paper type (e.g. system paper actually describes architecture, modules, information flow)?
§25 Readiness	Does the draft acknowledge readiness honestly, or does it pretend it is stronger than the evidence?

Record each answer with a severity tag: ok · moderate · major · placeholder-expected.

Phase 4 — Re-verify evidence (Claim Risk Audit)

Open CLAIM_SUPPORT_MAP.md and walk every row. For each:

Find the claim in the draft (grep by claim id or phrasing).
Compare the strength of the claim's wording to the evidence confidence:
- High-confidence evidence + cautious wording → upgrade to precise ("we observed" → "on the [dataset] holdout, [metric] = [value]").
- Medium-confidence evidence + strong wording → soften ("outperforms" → "is competitive with," "consistent with").
- Low-confidence evidence in Abstract / Results headline → move the claim to Discussion with hedged language, or cut.
- No evidence (—) → the claim must be a marked placeholder or cut. If it is asserted as fact in the current draft, flag as CRITICAL-overclaim.
Check for claims in the draft that are not in CLAIM_SUPPORT_MAP.md — these are almost always unsupported and must be added to the map with evidence located, or softened / cut.
Check for planned claims that are missing from the draft — these may be silently dropped evidence; restore if the plan intended them and evidence supports them.

Emit CLAIM_RISK_REPORT.md with one row per claim, columns: ClaimID · Section · Wording · Evidence · Confidence · Risk · Revision Action.

Never invent evidence. Never invent a citation key. Never invent a metric number. When evidence is genuinely missing, the revision is to soften or remove, not to fabricate.

Phase 5 — Diagnose and classify issues

Run through the review checklist (see templates/REVIEW_CHECKLIST.md) using the REVIEW_MODE:

structural — section presence, order, word balance, paragraph topic sentences, section transitions, heading hierarchy, figure/table placement.
argument — gap clarity, contribution clarity, claim-to-evidence consistency, Introduction → Results → Conclusion coherence, lead results discipline.
novelty — precision of novelty statement, differentiation from nearest prior work, avoidance of "first / state-of-the-art" unless APPROVED_CLAIMS.md supports it.
methods — problem formulation, input/output, unit of analysis, spatial unit, CRS, preprocessing, model/framework specificity, baselines, evaluation metrics, reproducibility detail, system architecture for system papers.
results-discussion — ordering by claim, interpretation discipline, mixed/negative findings honesty, GIScience / GeoAI implications, responsible-use discussion, generalizability conditions, limitations completeness.
journal-fit — venue tone, rigor conventions, expected section presence, declarations (data / code availability), ethics statements.
language — paragraph topic sentences, sentence-length variation, terminology drift, figure/table reference style ("shows" vs. "as can be seen in"), abbreviation management.
integrated — all of the above, prioritized.

Classify each finding into:

Major

weak or missing gap articulation
unclear novelty or novelty unsupported by differentiation
claims whose strength exceeds evidence ("overclaim")
insufficient methods detail to grasp the method
weak experiment description (unclear protocol, unclear metrics, unclear baselines)
results interpreted more strongly than the data support
poor connection to GIScience / GeoAI / remote sensing literature
missing or defanged limitations
mismatch with target journal expectations (tone, structure, declarations)
structural problems (section ordering, missing sections, dangling contributions)

Moderate

repetitive writing, redundant paragraphs across sections
vague section transitions
inconsistent terminology (model / dataset / system / metric names drift)
weak paragraph topic sentences
figure/table references that do not integrate with the narrative
incomplete contextualization of findings against prior work

Minor

awkward wording, local clarity problems
caption / title mismatches
redundant phrases and filler
sentence-level polish needs

Phase 5.5 — Optional external reviewer pass (`REVIEWER_MODEL`)

If Codex MCP is available and HUMAN_CHECKPOINT does not block it, send the revised-candidate to gpt-5.4 for an independent adversarial read. This is the generator-evaluator separation check.

mcp__codex__codex:
  model: gpt-5.4
  config: {"model_reasoning_effort": "xhigh"}
  prompt: |
    You are reviewing a manuscript draft for [TARGET_VENUE] ([IJGIS | ISPRS JPRS | RSE | TGIS]).
    Paper type: [PAPER_TYPE].
    This is Round [N] of an iterative review loop. Prior unresolved major issues: [...].

    Focus: [REVIEW_MODE].

    Please provide a structured review:
    1. Score 1–10 per dimension: gap clarity, novelty precision, methods rigor, results discipline,
       discussion depth, literature positioning, journal fit, language and flow.
    2. Ranked list of remaining CRITICAL > MAJOR > MODERATE issues, each with a minimum edit.
    3. Claim-risk flags: which sentences in the draft look stronger than the evidence supports?
    4. Verdict: ready / almost / not ready for [TARGET_VENUE].
    5. One paragraph on what is working well — do not just list weaknesses.

    Do not rewrite. Do not fabricate evidence. Be specific to GIScience / GeoAI / remote sensing expectations.

    [Paste MANUSCRIPT_REVIEWED.md content or the scoped section(s).]
    [Paste PAPER_PLAN.md §5, §12, §16, §17, §21 for context.]

If round 2+, use mcp__codex__codex-reply with the saved threadId from REVIEW_LOOP_STATE.json so the reviewer has continuity.

If Codex is unavailable, skip — do not fall back to self-scoring. A cold-read sub-agent (Agent tool) can substitute.

Phase 6 — Human checkpoint (if enabled)

Skip if HUMAN_CHECKPOINT = false.

Present to the user:

per-dimension scores (this round vs. prior round if any)
top 3 major issues with proposed revision summaries
claim-risk flags count (overclaims, unsupported, placeholder-expected)
proposed REVISION_MODE (full / partial / conservative)

Phase 7 — Revise the manuscript

Revision is ordered by severity: Majors → Moderates → Minors. Never polish sentence-level wording before structural arguments are resolved.

Decision rules for the revision:

REVISION_MODE = full — rewrite affected paragraphs/sections end-to-end when structural or argument issues dominate; preserve accepted sections per memory/MEMORY.md and REVIEW_STATE.json.
REVISION_MODE = partial — rewrite only the sections with major issues; surgically edit moderate issues in others.
REVISION_MODE = conservative — when evidence is incomplete or readiness is low, prefer softening, tightening, and marking placeholders over large rewrites. Do not upgrade claims. Do not invent new content to paper over gaps.

Section-specific revision behavior (see templates/SECTION_REVIEW_TEMPLATE.md):

Abstract

Introduction

Related Work

Data / Study Area

Methods

Experiments

Results

Discussion

Limitations

Specific, not generic. Mirror plan §17 one-to-one. No "future work will solve everything" framing.

Conclusion

Restate contributions as outcomes in the same numbering used in Introduction. Close with broader significance. 2–4 concrete future-work directions grounded in limitations.

Declarations

Data availability, code availability, ethics, conflict of interest, acknowledgement placeholders per plan §18 and the venue's conventions.

Phase 8 — Verify, log, and hand off

Mechanical post-revision checks:

Claim closure: every CRITICAL-overclaim in CLAIM_RISK_REPORT.md is either softened in MANUSCRIPT_REVISED.md or carried over with an explicit reason.
Limitation closure: every plan §17 limitation appears in the revised Limitations section.
Figure closure: every figure mentioned in the revised draft exists in FIGURE_MANIFEST.md.
Contribution closure: every numbered contribution in Introduction appears, in the same numbering, in Results and Conclusion.
Terminology closure: grep confirms no mixed casing / spelling for canonical names.
Placeholder discipline: [PLACEHOLDER ...] blocks remain only where evidence is genuinely missing; none have been silently deleted.

Write all output artifacts (see Outputs table). Update REVIEW_LOOP_STATE.json:

{
  "round": 2,
  "review_mode": "integrated",
  "revision_mode": "partial",
  "threadId": "019ce736-...",
  "last_scores": {
    "gap_clarity": 6.5,
    "novelty_precision": 6.0,
    "methods_rigor": 7.0,
    "results_discipline": 6.5,
    "discussion_depth": 6.0,
    "literature_positioning": 6.5,
    "journal_fit": 7.0,
    "language_flow": 7.5
  },
  "unresolved_major_ids": ["M3", "M7"],
  "status": "in_progress",
  "timestamp": "2026-04-14T22:00:00"
}

On the final round of this invocation, set status: completed only if no unresolved majors remain; otherwise leave in_progress so the next invocation resumes cleanly.

Append a one-line entry to output/PROJ_NOTES.md:

YYYY-MM-DD paper-review-loop round=N mode=<...> revision=<...> majors=<open/total> verdict=<ready|almost|not-ready>

Append a cumulative entry to output/AUTO_REVIEW.md with the per-dimension scores and top 3 majors, respecting the generator-evaluator protocol noted in CLAUDE.md.

Decision rules (summary)

Full vs. partial vs. conservative revision: full when structural/argument issues dominate and evidence is mostly in place; partial when only some sections have major issues; conservative when readiness is low or evidence is incomplete.
Handling unsupported claims: soften first; mark as placeholder second; cut third. Never fabricate.
When the plan and the draft disagree: if evidence supports the draft, update SECTION_REVIEW_NOTES.md with a rationale and keep the draft's framing; if evidence supports the plan, revise the draft back toward the plan.
Paper-type adaptation: review criteria shift by PAPER_TYPE (e.g. benchmark papers are held to stricter evaluation-protocol standards; system papers to stricter architecture + information-flow clarity; applied case studies to study-area specificity and practical implications).
Journal adaptation: IJGIS / TGIS emphasize GIScience theory, spatial framing, and scale/MAUP discipline. ISPRS JPRS / RSE emphasize sensor / resolution / preprocessing rigor and quantitative evaluation. Adjust the review accordingly (see templates/JOURNAL_FIT_CHECKLIST.md).
Incomplete drafts: produce MAJOR_ISSUES.md, a revised partial draft, a marked-up section-by-section improvement memo in SECTION_REVIEW_NOTES.md, and NEXT_LOOP_PRIORITIES.md. Do not pretend a skeletal draft is publication-ready.
Round budget: cap at MAX_ROUNDS = 3 per invocation. Diminishing returns beyond three rounds for writing-quality improvements; continuation requires fresh evidence or a new scope.

Style guidance for the revised prose

Formal, scholarly, third-person. First-person plural ("we") is acceptable in Methods and Discussion.
Precise vocabulary. Prefer heterogeneous land-cover patches over diverse landscapes; spatial units of analysis over areas; spatial cross-validation over held-out test.
Paragraphs open with a topic sentence that states a claim, not a transition.
One idea per paragraph; ≤ 180 words except in Methods.
Vary sentence length; do not stack three long sentences.
Define every abbreviation at first use and fix it. Canonical names are frozen at first use across sections.
Present tense for established knowledge; past tense for what you did in the study.
Reference figures by purpose: "the confusion matrix in Fig. 3 shows..." — never "as can be seen in Fig. 3."
State spatial unit of analysis and CRS when they matter for the claim.
Distinguish model family from training regime from evaluation protocol.
For system / agent papers: distinguish engineering novelty, workflow novelty, and scientific contribution — do not conflate.

Contribution framing:

State contributions as outcomes, not promises.
Avoid "first," "state-of-the-art," "outperforms all existing methods" unless APPROVED_CLAIMS.md directly supports it on the named benchmark.
Prefer "to our knowledge, this is the first evaluation of X on Y" over "the first X."

Guardrails (non-negotiable)

Do not:

Fabricate results, metrics, sample sizes, effect sizes, or confidence intervals.
Invent citation keys, authors, years, or venues. Use [CITE: ...] placeholders instead.
Reference figures or tables that are not in FIGURE_MANIFEST.md.
Strengthen a claim beyond what CLAIM_SUPPORT_MAP.md + APPROVED_CLAIMS.md support.
Hide missing experiments behind vague language. Mark them.
Drop a limitation listed in plan §17 without a recorded reason.
Use promotional / startup / hype language ("revolutionary," "game-changing," "unlock," "leverage the power of," "paradigm shift").
Flatten the author's intended contribution into something too generic in the name of "clarity."
Write only sentence-level polish while structural arguments are still broken.
Self-score the draft without a cold reader. Use Codex MCP or a fresh Agent.
Overwrite accepted sections listed in memory/MEMORY.md or output/REVIEW_STATE.json without explicit user instruction.
Overwrite sections/*.md — those are owned by paper-draft. Write to sections_revised/*.md.

Do:

Soften under pressure from evidence.
Revise for publishability, not flashiness.
Prefer one strong paragraph to three weak ones.
Cut before padding.
Make the reasoning behind the revision traceable via REVISION_LOG.md.

Deliverable conventions

Folder layout after one round:

output/manuscript/
├── DRAFT_README.md                 # from paper-draft
├── MANUSCRIPT_DRAFT.md             # from paper-draft (unchanged)
├── MANUSCRIPT_REVIEWED.md          # this skill — with <!-- REVIEW: ... --> annotations
├── MANUSCRIPT_REVISED.md           # this skill — revised draft
├── CLAIM_SUPPORT_MAP.md            # paper-draft
├── CLAIM_RISK_REPORT.md            # this skill
├── COVERAGE_GAPS.md                # paper-draft (this skill may append)
├── CITATION_GAPS.md                # paper-draft (this skill may append)
├── SECTION_NOTES.md                # paper-draft
├── SECTION_REVIEW_NOTES.md         # this skill
├── MAJOR_ISSUES.md                 # this skill
├── MINOR_ISSUES.md                 # this skill
├── REVIEW_REPORT.md                # this skill
├── REVISION_LOG.md                 # this skill
├── JOURNAL_FIT_NOTES.md            # this skill
├── NEXT_LOOP_PRIORITIES.md         # this skill
├── REVIEW_LOOP_STATE.json          # this skill
├── REVISION_NOTES.md               # paper-draft (this skill may append)
├── sections/                       # paper-draft (read-only)
│   ├── 00_title.md
│   ├── 01_abstract.md
│   └── ...
└── sections_revised/               # this skill
    ├── 00_title.md
    ├── 01_abstract.md
    └── ...

Each revised section file keeps the same three-line YAML front matter as paper-draft, with two added fields:

---
section: introduction
mode: full
word_target: 1000
review_round: 2
revision_mode: partial
---

MAJOR_ISSUES.md, MINOR_ISSUES.md, and CLAIM_RISK_REPORT.md follow row schemas in templates/ISSUE_RUBRIC.md and templates/CLAIM_RISK_CHECKLIST.md.

Issue ids are stable across rounds (e.g. M3 stays M3 once assigned). Resolution flips resolved-in-this-round to yes but the row stays in history.

Loop iteration conventions

Monotonic improvement: each round must strictly improve at least one named dimension. Regressions are bugs; investigate before shipping.
Stable issue ids: once M7 exists, it stays M7 across rounds; its status and round-resolved columns change, not its id.
Carry-over flag: unresolved majors move to the top of NEXT_LOOP_PRIORITIES.md.
Round cap: MAX_ROUNDS = 3 per invocation. Beyond that, the skill stops and asks whether new evidence has arrived (new experiments, new figures, new approved claims). Without new evidence, further loops produce diminishing returns.
Compaction recovery: if context fills mid-round, write REVIEW_LOOP_STATE.json and REVISION_LOG.md before compaction; the next session reads them, picks up from the next phase.

Supporting templates

templates/REVIEW_CHECKLIST.md — full review checklist by mode (structural / argument / novelty / methods / results-discussion / journal-fit / language / integrated).
templates/SECTION_REVIEW_TEMPLATE.md — per-section review + revision scaffold.
templates/ISSUE_RUBRIC.md — major / moderate / minor schema, row format, severity criteria.
templates/CLAIM_RISK_CHECKLIST.md — claim-wording-vs-evidence audit, one row per claim.
templates/JOURNAL_FIT_CHECKLIST.md — IJGIS / ISPRS JPRS / RSE / TGIS expectations by section and by paper type.
templates/OUTPUT_CONVENTIONS.md — folder layout, file names, front-matter, round conventions.

Load templates on demand; do not paste their full contents into review outputs.

Composing with other workflows

/paper-plan              → output/PAPER_PLAN.md
/paper-figure-generate   → output/figures/
/paper-draft all         → output/manuscript/         (draft + claim map + gap reports)
/paper-review-loop all   ← you are here               (review + revise + next-loop priorities)
/paper-write             → output/paper/ (LaTeX)
/paper-compile           → output/paper/main.pdf
/submit-check            → venue-compliance gate

Relationship to sibling skills:

paper-draft — writes the first manuscript; owns sections/*.md. This skill never overwrites those.
auto-review-loop — adversarial research-quality review (novelty, rigor, literature, clarity, impact); operates earlier in the pipeline on the research itself, not the manuscript prose. This skill borrows its generator-evaluator discipline.
result-to-claim — the safety gate that populates memory/APPROVED_CLAIMS.md. This skill trusts that file absolutely.
submit-check — final venue-compliance gate (word count, declarations, geo-specific reporting). This skill can precede it; it does not replace it.

Key Rules (summary)

Review is a means, revision is the deliverable. Ship MANUSCRIPT_REVISED.md, not just a report.
Evidence binds claims. CLAIM_RISK_REPORT.md is as important as the revised prose.
Terminology is frozen at first use — the revision normalizes drift, does not introduce new variants.
Never reference a missing figure, never invent a citation, never fabricate a metric.
Readiness-aware: conservative revisions on skeletal drafts; no pretending.
Majors before minors — structure and argument before polish.
Generator-evaluator separation: evaluate with Codex MCP or a fresh Agent, not the drafting context.
Stable issue ids and monotonic improvement across rounds.
Respect memory/MEMORY.md and output/REVIEW_STATE.json — do not overwrite accepted sections.
Overwrite to sections_revised/, never sections/.
Large file handling: if Write fails on size, retry with chunked Bash (cat << 'EOF' > file) without asking.

paper-review-loop

More from this repository

More from this repository

Skill: paper-review-loop

Constants

Core Philosophy

Inputs

Primary

Companion artifacts from paper-draft (read on demand)

Evidence and context (read as needed)

Prior-loop state

Outputs

Workflow

Phase 1 — Load state and scope

Phase 2 — Read manuscript and its companion artifacts

Phase 3 — Cross-check against PAPER_PLAN.md

Phase 4 — Re-verify evidence (Claim Risk Audit)

Phase 5 — Diagnose and classify issues

Phase 5.5 — Optional external reviewer pass (REVIEWER_MODEL)

Phase 6 — Human checkpoint (if enabled)

Phase 7 — Revise the manuscript

Abstract

Introduction

Related Work

Data / Study Area

Methods

Experiments

Results

Discussion

Limitations

Conclusion

Declarations

Phase 8 — Verify, log, and hand off

Decision rules (summary)

Style guidance for the revised prose

Guardrails (non-negotiable)

Deliverable conventions

Loop iteration conventions

Supporting templates

Composing with other workflows

Key Rules (summary)

Acknowledgements

Skill: paper-review-loop

Constants

Core Philosophy

Inputs

Primary

Companion artifacts from paper-draft (read on demand)

Evidence and context (read as needed)

Prior-loop state

Outputs

Workflow

Phase 1 — Load state and scope

Phase 2 — Read manuscript and its companion artifacts

Phase 3 — Cross-check against PAPER_PLAN.md

Phase 4 — Re-verify evidence (Claim Risk Audit)

Phase 5 — Diagnose and classify issues

Phase 5.5 — Optional external reviewer pass (REVIEWER_MODEL)

Phase 6 — Human checkpoint (if enabled)

Phase 7 — Revise the manuscript

Abstract

Introduction

Related Work

Data / Study Area

Methods

Experiments

Results

Discussion

Limitations

Conclusion

Declarations

Phase 8 — Verify, log, and hand off

Decision rules (summary)

Style guidance for the revised prose

Guardrails (non-negotiable)

Deliverable conventions

Loop iteration conventions

Supporting templates

Composing with other workflows

Key Rules (summary)

Companion artifacts from `paper-draft` (read on demand)

Phase 3 — Cross-check against `PAPER_PLAN.md`

Phase 5.5 — Optional external reviewer pass (`REVIEWER_MODEL`)

Companion artifacts from `paper-draft` (read on demand)

Phase 3 — Cross-check against `PAPER_PLAN.md`

Phase 5.5 — Optional external reviewer pass (`REVIEWER_MODEL`)