paper-review-lite-codex

name: paper-review-lite-codex description: Cross-model adversarial pre-submission audit. Claude and Codex independently apply the paper-review-lite specification, then each cross-checks the other's findings; surviving issues are annotated by confidence. argument-hint: "[path to paper or describe manuscript to review]" context: fork # Claude Code: run skill in a forked subagent context (isolated from conversation history). See https://code.claude.com/docs/en/skills#frontmatter-reference allowed-tools: - Read - Write - Edit - Bash - Agent

Paper Pre-Submission Review (Lite, Cross-Model Adversarial)

This is the cross-model sibling of paper-review-lite, itself the in-session, Claude-Code-native counterpart to presubmit (our port of the reviewer2 adversarial peer-review pipeline). The heritage carries over wholesale. Sub-agents adopt a Critical-Reviewer posture, every finding is grounded in a verbatim quote, and a verification cascade filters hallucinations before they reach the final report.

The new mechanic is cross-model adversarial verification. Two reviewers — Claude (the orchestrator) and Codex (GPT-5.4, invoked via Bash codex exec — see § Codex invocation mechanism) — independently apply the same paper-review-lite specification to the same paper. Each then plays Blue Team to the other's Red Team. Two different model families have different blind spots, so:

• Mutual catches (both teams flag the issue, both cross-checks confirm) are high-confidence.
• Asymmetric catches (one team flags, the other's cross-checker confirms against the paper) survive at standard confidence and often surface real but easy-to-miss problems.
• Asymmetric refutations (one team flags, the other's cross-checker refutes against the paper) are dropped by default. The orchestrator can override by re-reading the manuscript directly, but the burden is on the override.
• Quote-failed findings (the cross-checker cannot find the cited verbatim span) are dropped as hallucinations.

This is the heavier sibling. Roughly 22 model calls total (9 Claude Red Team, 9 Codex Red Team, 4 cross-model Blue Team) plus orientation and synthesis by the orchestrator. Reach for it before submission when you want maximum adversarial pressure and a second model family's blind spots. For the heaviest standalone deliverable — Red Team personas (Breaker, Butcher, Shredder, Collector, Void), math audits, code-replication checks, resumable, cost-tracked — use presubmit.

Codex invocation mechanism

Claude Code has no native codex:codex-rescue subagent. Every "spawn Codex" reference below means: use the Bash tool to invoke codex exec directly. Pattern (substitute OUTPUT_PATH with the agent's output file path and inline the prompt body inside the heredoc):

codex exec \
  --sandbox workspace-write \
  --skip-git-repo-check \
  -C "$(dirname OUTPUT_PATH)" \
  "$(cat <<'CODEXEOF'
<the XML prompt template for this agent, with PAPER_PATH and OUTPUT_PATH substituted as literals>
CODEXEOF
)" < /dev/null

Required:

• < /dev/null — closes stdin. Without it, codex exec hangs indefinitely on "Reading additional input from stdin..." even when the prompt is passed as a CLI argument. This is the single most common failure mode.
• run_in_background: true on every Bash call. Eleven parallel Codex calls per run (9 Phase 2 + 2 Phase 3) make foreground execution impractical.
• timeout: 600000 (10 minutes) as a harness backstop. If a call hangs for any reason, the harness kills it.

After each Codex Bash task notifies completion, Read its output file. Treat any of the following as a Codex agent failure (skip that finding's contribution in adjudication, log the failure in the report):

• Exit code ≠ 0.
• No session file appeared in ~/.codex/sessions/ (Codex did not actually start).
• The OUTPUT_PATH file is missing or empty.

Instructions

1. Orientation (orchestrator, before any review agent launches)

Run the orientation step from paper-review-lite § 1 verbatim. Read the paper yourself to determine source format (LaTeX, Pandoc, Word), SI location, figure paths, replication archive, bibliography format, and design family. Use this to write specific review prompts that name actual file paths and section names. Generic prompts produce shallow reviews from both model families.

For experimental manuscripts, also invoke methods-reporting in audit mode so its 45-item checklist becomes the baseline for Agents 1, 2, 6, 7, and 8 on both teams (matching paper-review-lite § 1). For conjoint, list-experiment, topic-modeling, LLM-classification, or VLM-OCR manuscripts, invoke the matching sibling skill and fold its checklist into Agent 9 on both teams.

2. Orchestration contract

Create this scratch layout in the paper's working directory.

.review-tmp/
├── claude/
│   ├── agent-1-content.md
│   ├── agent-2-numbers.md
│   ├── agent-3-references.md
│   ├── agent-4-dois.md
│   ├── agent-5-writing.md
│   ├── agent-6-consort.md
│   ├── agent-7-prereg.md
│   ├── agent-8-figures.md
│   └── agent-9-archive.md
├── codex/
│   ├── agent-1-content.md   (same dimensions, Codex output)
│   ├── ...
│   └── agent-9-archive.md
└── cross-check/
    ├── claude-checks-codex-content.md     (covers Codex agents 1, 2, 6, 7)
    ├── claude-checks-codex-technical.md   (covers Codex agents 3, 4, 5, 8, 9)
    ├── codex-checks-claude-content.md
    └── codex-checks-claude-technical.md

Both teams write independently to their own subdirectory. Cross-checkers read the other team's subdirectory. Use absolute paths when spawning Codex sub-agents — codex exec's -C flag sets the working directory, but absolute PAPER_PATH and OUTPUT_PATH values in the prompt remove ambiguity when the paper lives outside that CWD.

3. Phase 2 — Dual independent Red Team (18 parallel calls)

Launch all 18 review calls in a single message.

• 9 Claude sub-agents via the Agent tool (default subagent_type). Use the agent prompts from paper-review-lite § 2 (Agents 1–9) verbatim, but redirect output to .review-tmp/claude/agent-N-*.md instead of the original .review-tmp/agent-N-*.md.
• 9 Codex sub-agents via the Bash tool, following the pattern in § Codex invocation mechanism. Use the Codex Phase 2 template below as the prompt body, one call per dimension. Output to .review-tmp/codex/agent-N-*.md.

Both teams apply the same dimension definitions, the same Critical-Reviewer posture, and the same severity rubric ([CRITICAL], [RECOMMENDED], [MINOR]) from paper-review-lite § 2. The point of running two model families on one specification is to compare independent applications of one standard, not to give them different jobs. Neither team sees the other's findings during Phase 2.

One carve-out — Codex Agent 4 (DOI audit) has no web access. The codex exec sandbox cannot perform the web searches that the Agent 4 prompt asks for. Tell Codex's Agent 4 to limit itself to offline checks (DOI present/absent, format validity, internal consistency with the entry) and to tag entries NEEDS WEB VERIFICATION instead of attempting lookups; live DOI resolution and missing-DOI searches are the Claude team's Agent 4's job (it has WebSearch/WebFetch).

Agents 6 (CONSORT) and 7 (pre-registration) are required for experimental manuscripts and marked NA for non-experimental ones on both teams.

4. Phase 3 — Cross-model adversarial verification (4 parallel calls)

Each model verifies the other's findings. Cross-checkers do not add new findings; that was Phase 2's job. They verify, refute, or downgrade.

Claude cross-checks Codex (2 sub-agents via Agent).

• Sub-agent A reads .review-tmp/codex/agent-{1,2,6,7}-*.md and the manuscript. Writes .review-tmp/cross-check/claude-checks-codex-content.md.
• Sub-agent B reads .review-tmp/codex/agent-{3,4,5,8,9}-*.md plus the manuscript, bibliography, and archive. Writes .review-tmp/cross-check/claude-checks-codex-technical.md.

For each Codex [CRITICAL] or [RECOMMENDED] finding, the cross-checker verifies the cited verbatim quote appears at the cited location, verifies the issue against the actual paper, flags any Codex finding that Claude also flagged independently in .review-tmp/claude/ (mutual catch — note for synthesis), and steel-mans the paper. When the paper anticipates or partially addresses the concern, note it for severity downgrade.

Codex cross-checks Claude (2 sub-agents via Bash following § Codex invocation mechanism).

• Sub-agent C reads .review-tmp/claude/agent-{1,2,6,7}-*.md. Writes .review-tmp/cross-check/codex-checks-claude-content.md.
• Sub-agent D reads .review-tmp/claude/agent-{3,4,5,8,9}-*.md. Writes .review-tmp/cross-check/codex-checks-claude-technical.md.

Use the Codex Phase 3 template below. Same verification protocol.

5. Phase 4 — Adjudication and synthesis (orchestrator, direct)

Build the consolidated Pre-Submit Report by adjudicating across teams.

• Mutual. Both teams flagged it; both cross-checkers confirmed. Mark [CRITICAL ✓✓] or [RECOMMENDED ✓✓]. Highest-confidence findings.
• Asymmetric, cross-confirmed. One team flagged; the other team's cross-checker confirmed against the paper. Retain at original severity. Mark [CRITICAL ✓] or [RECOMMENDED ✓]. These often surface real but easy-to-miss problems.
• Asymmetric, cross-refuted. One team flagged; the other team's cross-checker refuted against the paper. Default action is to drop. The orchestrator can override by re-reading the manuscript directly, in which case retain at one tier below original severity with the note "single-team finding, cross-refuted, retained after orchestrator re-read at file:line".
• Quote-failed. The cross-checker could not find the cited verbatim span. Drop as hallucination on the finder's side.

Apply the synthesis rules from paper-review-lite § 4 in order. Deduplicate within-team first (multiple agents on the same team flagging the same underlying issue). Then deduplicate across-team (a mutual catch is one entry, not two). Then demote self-conceded critiques (any finding whose own description includes language conceding the point). Then write a single-line Recommendation at the top of the report. Then write the Editor's Note (3–6 paragraph prose memo). Then the issue lists. Then the journal-readiness checklist. Then "What Still Needs Your Input".

The Critical Issues and Recommended Changes tables get one extra column compared to the original paper-review-lite report.

| Severity | Confidence                                      | Location | Issue | Fix |
|----------|-------------------------------------------------|----------|-------|-----|
| CRITICAL | Mutual (Claude + Codex)                         | …        | …     | …   |
| CRITICAL | Asymmetric: Codex only, confirmed by Claude     | …        | …     | …   |
| CRITICAL | Asymmetric: Claude only, cross-refuted, retained after orchestrator re-read | … | … | … |

Everything else in the report follows the paper-review-lite § 4 format exactly. Top-line Recommendation, then Editor's Note, then Critical / Recommended / Minor lists, then Strengths, then Journal-Readiness Checklist, then What Still Needs Your Input.

Codex Phase 2 template (one per dimension, 9 total)

Use the XML block below as the prompt body inside the Bash invocation from § Codex invocation mechanism. Substitute DIMENSION_INSTRUCTIONS with the verbatim text of the corresponding agent from paper-review-lite § 2 (the full text of Agent 1, Agent 2, …, Agent 9 — do not paraphrase). Substitute PAPER_PATH with the absolute manuscript path and OUTPUT_PATH with the absolute path to the Codex agent's output file under .review-tmp/codex/.

<task>
You are a Critical Reviewer auditing the manuscript at PAPER_PATH for the dimension below.

Posture (required): adversarial but fair. Find every place the argument is weaker than the paper presents it to be. Attack the argument or the data, not the authors. Framing like "fraudulent" or "incompetent" is out of scope. "The claim on line X is not supported by the evidence on line Y" is in scope.

Dimension:

DIMENSION_INSTRUCTIONS

Write your findings to OUTPUT_PATH. Do not write to any other file.

A second model (Claude) is independently performing the same review on the same paper for the same dimension. You will not see its findings. After both passes complete, each model's findings will be verified by the other. Findings without a verbatim quote will be dropped as hallucinations during cross-check.
</task>

<output_format>
Structured list, not prose. For each issue:
- Severity: [CRITICAL] / [RECOMMENDED] / [MINOR]
- Location: file path and line number, or section name
- Issue: one sentence describing the problem
- Fix: one sentence describing what to do
- Quote: a verbatim span (≤ 2 sentences) from the manuscript that supports the finding. REQUIRED for every [CRITICAL] and [RECOMMENDED] finding. Optional for [MINOR].

Severity rubric (apply consistently):
- [CRITICAL] — blocks submission. Wrong numbers, broken references, missing ethics or data-availability statement when required, silent pre-registration deviation, anonymization failure, unreproducible main result.
- [RECOMMENDED] — will draw reviewer complaint. Unsupported claim, missing robustness check, undefined threshold, missing limitation, insufficient figure caption, undocumented exclusion.
- [MINOR] — polish. Style, typography, citation format, wording consistency.
</output_format>

<action_safety>
Scope. Read PAPER_PATH and any files it references (bibliography, archive, SI). Write only to OUTPUT_PATH. Do not edit the manuscript or any other file.
</action_safety>

<default_follow_through_policy>
Apply the dimension end-to-end without stopping for confirmation.
If the finding is unambiguous, record it.
If the finding requires author knowledge to confirm (embargo status, IRB number), record it as [RECOMMENDED] with the caveat "requires author confirmation".
Do not ask clarifying questions mid-run.
</default_follow_through_policy>

Codex Phase 3 template (cross-check Claude's findings)

Used for sub-agents C and D in Phase 3. Substitute PAPER_PATH, INPUT_FILES (a comma-separated list of .review-tmp/claude/agent-N-*.md paths the cross-checker should read), and OUTPUT_PATH.

<task>
You are a verification cross-checker. Another model (Claude) has produced findings about the manuscript at PAPER_PATH. Your job is to verify each finding against the actual manuscript.

Read the findings file(s) at INPUT_FILES. For each [CRITICAL] or [RECOMMENDED] finding, output one verdict entry.

1. QUOTE CHECK. Does the cited verbatim quote appear at the cited location in PAPER_PATH? If not, verdict is "QUOTE FAILED — drop as hallucination".
2. ISSUE CHECK. Does the issue itself hold up against the actual paper text? If the issue does not exist, is already addressed elsewhere in the paper, or is a misreading, verdict is "REFUTED" with a one-sentence explanation citing the paper line that refutes it.
3. STEEL-MAN. If the issue is real, note whether the paper anticipates or partially addresses the concern. If it does, verdict is "CONFIRMED, downgrade one severity tier — partially addressed at <file:line>".
4. OTHERWISE. Verdict is "CONFIRMED".

Do not add new findings of your own. You are verifying, not reviewing.

Write your verdicts to OUTPUT_PATH.
</task>

<inputs>
Findings to verify: INPUT_FILES
Manuscript: PAPER_PATH
</inputs>

<output_format>
For each finding in the input files, one entry.
- Source finding: <Claude agent N, severity, location>
- Quote check: PASS / FAIL
- Issue check: CONFIRMED / REFUTED / DOWNGRADE
- Evidence: one sentence citing the paper line that supports the verdict.
- Original severity vs. recommended severity (if downgrade)
</output_format>

<action_safety>
Read PAPER_PATH and the files listed in INPUT_FILES. Write only to OUTPUT_PATH. Do not edit the manuscript or the input files.
</action_safety>

<default_follow_through_policy>
Process every finding in the input files end-to-end. Do not ask clarifying questions mid-run.
</default_follow_through_policy>

Quality Checks

• Orientation completed by the orchestrator before any review agent launches. Paper structure, SI location, archive location, and design family identified.
• For experimental manuscripts, methods-reporting invoked in audit mode and its 45-item checklist made the baseline for Agents 1, 2, 6, 7, and 8 on both teams.
• For domain-specific manuscripts (conjoint, list-experiment, topic-modeling, text-classification, VLM-OCR), the relevant sibling skill is invoked and its checklist folded into Agent 9 on both teams.
• Three subdirectories created under .review-tmp/. claude/, codex/, cross-check/.
• All 18 Phase 2 calls (9 Claude + 9 Codex) launched in a single parallel message.
• Both teams use the same dimension prompts and severity rubric from paper-review-lite § 2. No model gets a different job.
• Codex sub-agents called via Bash following § Codex invocation mechanism (codex exec ... < /dev/null, run_in_background: true, timeout: 600000). Absolute paths used for PAPER_PATH and OUTPUT_PATH in the prompt.
• Agents 6 and 7 marked NA on both teams for non-experimental or non-preregistered manuscripts.
• All 4 Phase 3 cross-check calls launched in a single parallel message after all 18 Phase 2 output files exist.
• Phase 3 cross-checkers do not add new findings. Verify, refute, or downgrade only.
• Adjudication produces one entry per underlying issue. Across-team deduplication done after within-team deduplication.
• .review-tmp/ (all three subdirectories) deleted after the final report was delivered, unless the user asked to keep it.
• Quote-failed findings dropped as hallucinations on the finder's side.
• Asymmetric, cross-refuted findings dropped by default. Retention requires an explicit orchestrator re-read of the manuscript and a note on the entry.
• Final report annotates each retained Critical / Recommended issue with confidence. Mutual, Asymmetric-confirmed, or Asymmetric-after-adjudication.
• Synthesis applies paper-review-lite § 4 rules. Single-line Recommendation at top, Editor's Note (3–6 paragraphs) before issue lists, Strengths section present, journal-readiness checklist filled, "What Still Needs Your Input" populated with author-knowledge items.
• Every retained issue cites file path and line number, or section name.
• Report distinguishes objective errors from subjective suggestions.

When to reach for this skill vs. siblings