Paper Audit Skill v4.5

paper-audit is deep-review-first. Its core job is to behave like a serious reviewer: find technical, methodological, claim-level, and cross-section issues; keep script-backed findings separate from reviewer judgment; and return a structured issue bundle plus a revision roadmap.

Version 4.5 adds a script-backed PRESUBMISSION layer for final-week mechanical checks (em dashes, AI-tone term frequency, abstract completeness, LaTeX citation/label/equation hygiene, paragraph-shape weak signals, concrete captions). It plugs into existing modes; it is not a separate public mode. See references/PRESUBMISSION_GUIDE.md for mode integration.

Use it for audit and review. Do not use it as the first tool for source editing, sentence rewriting, or build fixing.

What This Skill Produces

• quick-audit: fast submission-readiness screen with script-backed findings, including PRESUBMISSION
• deep-review: reviewer-style structured issue bundle with major/moderate/ minor findings
• gate: PASS/FAIL decision calibrated for submission blockers; PRESUBMISSION Major/Minor findings remain advisory
• re-audit: compare current issue bundle against a previous audit, including mechanical regression findings
• polish: precheck-only handoff into a polishing workflow

The primary product is no longer just a score. For deep-review, the main outputs are:

• final_issues.json
• overall_assessment.txt
• review_report.md
• peer_review_report.md
• revision_roadmap.md

Do Not Use

• direct source surgery on .tex / .typ
• compilation debugging as the main task
• free-form literature survey writing
• paragraph-level related-work rewriting
• cosmetic grammar cleanup without an audit goal

Critical Rules

• Don't rewrite the paper source — paper-audit is a reviewer, not an editor; switch skills explicitly if the user wants prose changes, so review evidence stays separable from edits.
• Don't fabricate references, baselines, or reviewer evidence — invented citations and made-up reviewer voices undermine every other finding in the bundle.
• Distinguish [Script] from [LLM] findings — script-backed items have a deterministic anchor the user can rerun, while LLM findings need a quote or section to be falsifiable.
• Anchor every reviewer finding to a quote, section, or exact textual location — unanchored complaints become impossible to audit on a re-pass.
• Be conservative with OCR noise, formatting quirks, and copy-editing trivia — flagging cosmetic noise inflates the report and buries the real issues.
• Read like a careful reader before flagging — understand the author's intended meaning first so the issue captures a real misread, not a strawman.
• For literature findings, judge whether the gap is evidence-backed and fairly positioned, and don't rewrite the prose inside paper-audit — keep prose rewrites in the format-specific writing skills where they can be reviewed in isolation.
• For PRESUBMISSION, map CRITICAL / MAJOR / MINOR to Critical / Major / Minor script severities; only Critical or failed checklist items can fail gate — otherwise mechanical findings drown out the substantive ones. Full mode-integration matrix lives in references/PRESUBMISSION_GUIDE.md.
• In PDF mode, do not guess source-only hygiene. Report text-proven items and note that LaTeX/Typst source checks were skipped.

Mode Selection

Requested intent	Mode
"check my paper", "quick audit", "submission readiness", "pre-submission review", "投稿前检查"	quick-audit
"review my paper", "simulate peer review", "harsh review", "deep review"	deep-review
"is this ready to submit", "gate this submission", "blockers only"	gate
"did I fix these issues", "re-audit", "compare against old review"	re-audit
"polish the writing, but only if safe"	polish

Legacy aliases still work for one compatibility cycle:

• self-check -> quick-audit
• review -> deep-review

For per-mode workflow steps, input resolution rules, presentation surface rules, and committee focus routing, see references/MODE_GUIDE.md.

Review Standard

Read these references before running reviewer-style work:

1. references/REVIEW_CRITERIA.md
2. references/DEEP_REVIEW_CRITERIA.md
3. references/CHECKLIST.md
4. references/CONSOLIDATION_RULES.md
5. references/ISSUE_SCHEMA.md
6. references/PRE_SUBMISSION_RULES.md
7. references/PRESUBMISSION_GUIDE.md
8. references/MODE_GUIDE.md

The deep-review workflow uses a 16-part issue taxonomy:

1. formula / derivation errors
2. notation inconsistency
3. prose vs formal object mismatch
4. numerical inconsistency
5. missing justification
6. overclaim or claim inaccuracy
7. ambiguity that can mislead a careful reader
8. underspecified methods / missing information
9. internal contradiction
10. self-consistency of standards
11. table structure violations
12. abstract structural incompleteness
13. theory contribution deficiency
14. qualitative methodology opacity
15. pseudo-innovation / straw man
16. paragraph-level argument incoherence

Workflow

Each mode has the same shape: parse $ARGUMENTS, lock the paper path, infer mode/report-style/focus/language if not provided, then run the canonical command. Detailed phase steps are in references/MODE_GUIDE.md.

quick-audit

uv run python -B "$SKILL_DIR/scripts/audit.py" <paper> --mode quick-audit ...

Present Submission Blockers -> Quality Improvements -> checklist; call out PRESUBMISSION mechanical findings with [Script] provenance. Escalate to deep-review when the user wants reviewer-depth critique.

deep-review

Five phases (see references/MODE_GUIDE.md for full detail):

1. Workspace prep:

   uv run python -B "$SKILL_DIR/scripts/prepare_review_workspace.py" <paper> --output-dir ./review_results

2. Phase 0 automated audit:

   uv run python -B "$SKILL_DIR/scripts/audit.py" <paper> --mode deep-review ...

3. Phase 3A committee — dispatch 5 committee agents (editor, theory, literature, methodology, logic) and write committee/consensus.md.
4. Phase 3B section + cross-cutting lanes — section, claims-vs-evidence, notation, evaluation fairness, self-consistency, prior-art, and pre-submission readiness (full/editor focus only).
5. Consolidation:

   uv run python -B "$SKILL_DIR/scripts/consolidate_review_findings.py" <review_dir>
   uv run python -B "$SKILL_DIR/scripts/verify_quotes.py" <review_dir> --write-back
   uv run python -B "$SKILL_DIR/scripts/render_deep_review_report.py" <review_dir>

When the user explicitly asks for journal-review prose, set --report-style peer-review so peer_review_report.md becomes the Primary View while review_report.md stays as the richer evidence bundle.

gate

uv run python -B "$SKILL_DIR/scripts/audit.py" <paper> --mode gate ...

Run EIC Screening (Phase 0.5) using agents/editor_in_chief_agent.md first; report PASS/FAIL; verdict -> EIC -> blockers -> advisory. A desk-reject verdict is a gate blocker. Critical PRESUBMISSION only blocks the gate.

re-audit

Requires --previous-report PATH.

uv run python -B "$SKILL_DIR/scripts/audit.py" <paper> --mode re-audit --previous-report <path> ...
uv run python -B "$SKILL_DIR/scripts/diff_review_issues.py" <old_final_issues.json> <new_final_issues.json>

Present root-cause-aware status labels: FULLY_ADDRESSED, PARTIALLY_ADDRESSED, NOT_ADDRESSED, NEW.

polish

uv run python -B "$SKILL_DIR/scripts/audit.py" <paper> --mode polish ...

If blockers exist, stop and report them. Only proceed into polishing if the precheck is safe.

Output Contract

For deep-review, the final issue schema is:

{
  "title": "short issue title",
  "quote": "exact quote from paper",
  "explanation": "why this matters and what remains problematic",
  "comment_type": "methodology|claim_accuracy|presentation|missing_information",
  "severity": "major|moderate|minor",
  "confidence": "high|medium|low|unverified",
  "source_kind": "script|llm",
  "source_section": "methods",
  "related_sections": ["results", "appendix"],
  "root_cause_key": "shared-normalized-key",
  "review_lane": "claims_vs_evidence",
  "gate_blocker": false,
  "quote_verified": true
}

Always prefer:

• exact quotes over vague paraphrase
• evidence-backed findings over style commentary
• issue bundle + roadmap over raw script dumps

References

File	Purpose
references/MODE_GUIDE.md	per-mode workflow detail, phase steps, committee focus routing
references/PRESUBMISSION_GUIDE.md	PRESUBMISSION mode-integration behavior matrix
references/REVIEW_CRITERIA.md	top-level audit scoring and mapping
references/DEEP_REVIEW_CRITERIA.md	deep-review-specific issue taxonomy and leniency rules
references/CONSOLIDATION_RULES.md	deduplication and root-cause merge policy
references/ISSUE_SCHEMA.md	canonical JSON schema
references/REVIEW_LANE_GUIDE.md	section lanes and cross-cutting lanes
references/PRE_SUBMISSION_RULES.md	final-week mechanical audit rules and term list
references/SUBAGENT_TEMPLATES.md	reviewer task templates
references/QUICK_REFERENCE.md	CLI and mode cheat sheet

Scripts

Script	Purpose
scripts/audit.py	Phase 0 audit and mode entrypoint
scripts/pre_submission_check.py	deterministic PRESUBMISSION mechanical audit layer
scripts/prepare_review_workspace.py	create deep-review workspace
scripts/build_claim_map.py	extract headline claims and closure targets
scripts/consolidate_review_findings.py	deduplicate comment JSONs
scripts/verify_quotes.py	verify exact quote presence
scripts/render_deep_review_report.py	render final Markdown report
scripts/diff_review_issues.py	compare old vs new issue bundles

Reviewer Lanes

Committee agents (deep-review default):

• committee_editor_agent.md
• committee_theory_agent.md
• committee_literature_agent.md
• committee_methodology_agent.md
• committee_logic_agent.md

Default deep-review lanes live in agents/:

• section_reviewer_agent.md
• claims_evidence_reviewer_agent.md
• notation_consistency_reviewer_agent.md
• evaluation_fairness_reviewer_agent.md
• self_consistency_reviewer_agent.md
• prior_art_reviewer_agent.md
• synthesis_agent.md
• editor_in_chief_agent.md — EIC desk-reject screener (used in gate mode)

Specialized deep-review agents (read their files for activation criteria):

• critical_reviewer_agent.md — devil's advocate with C3-C5 checks
• domain_reviewer_agent.md — domain expertise with A1-A7 assessments
• methodology_reviewer_agent.md — methodology rigor with B3-B10 checks
• literature_reviewer_agent.md — evidence-based literature verification (optional, --literature-search)

Examples

• "Review this manuscript like a serious conference reviewer and tell me the biggest validity risks."
• "Run a quick audit on paper.tex and tell me what blocks submission."
• "Gate this IEEE submission and separate blockers from recommendations."
• "Re-audit this revision against my previous report."
• "Audit only the literature positioning and tell me whether the claimed gap is real or fabricated by selective citation."