dsh-aris-panel 0.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (442) hide show
  1. package/LICENSE +21 -0
  2. package/README.md +98 -0
  3. package/README_CN.md +87 -0
  4. package/dsh/checkout.patch.yml +38 -0
  5. package/dsh/client.js +634 -0
  6. package/dsh/cordis.patch.yml +44 -0
  7. package/dsh/index.mjs +76 -0
  8. package/dsh/run-status.mjs +182 -0
  9. package/dsh/scope-limits.mjs +50 -0
  10. package/dsh/workbench.mjs +291 -0
  11. package/mcp-servers/claude-review/README.md +93 -0
  12. package/mcp-servers/claude-review/run_with_claude_aws.sh +49 -0
  13. package/mcp-servers/claude-review/server.py +718 -0
  14. package/mcp-servers/codex-image2/README.md +65 -0
  15. package/mcp-servers/codex-image2/server.py +893 -0
  16. package/mcp-servers/feishu-bridge/requirements.txt +1 -0
  17. package/mcp-servers/feishu-bridge/server.py +240 -0
  18. package/mcp-servers/gemini-review/README.md +171 -0
  19. package/mcp-servers/gemini-review/server.py +1856 -0
  20. package/mcp-servers/llm-chat/requirements.txt +1 -0
  21. package/mcp-servers/llm-chat/server.py +664 -0
  22. package/mcp-servers/manual-review/README.md +133 -0
  23. package/mcp-servers/manual-review/server.py +910 -0
  24. package/mcp-servers/manual-review/ui.html +279 -0
  25. package/mcp-servers/minimax-chat/requirements.txt +1 -0
  26. package/mcp-servers/minimax-chat/server.py +381 -0
  27. package/package.json +51 -0
  28. package/skills/ablation-planner/SKILL.md +123 -0
  29. package/skills/alphaxiv/SKILL.md +196 -0
  30. package/skills/analyze-results/SKILL.md +46 -0
  31. package/skills/arxiv/SKILL.md +248 -0
  32. package/skills/auto-paper-improvement-loop/SKILL.md +651 -0
  33. package/skills/auto-review-loop/SKILL.md +1137 -0
  34. package/skills/auto-review-loop-llm/SKILL.md +259 -0
  35. package/skills/auto-review-loop-minimax/SKILL.md +302 -0
  36. package/skills/citation-audit/SKILL.md +502 -0
  37. package/skills/claims-drafting/SKILL.md +227 -0
  38. package/skills/comm-lit-review/SKILL.md +297 -0
  39. package/skills/deepxiv/SKILL.md +263 -0
  40. package/skills/dse-loop/SKILL.md +296 -0
  41. package/skills/embodiment-description/SKILL.md +129 -0
  42. package/skills/exa-search/SKILL.md +205 -0
  43. package/skills/experiment-audit/SKILL.md +311 -0
  44. package/skills/experiment-bridge/SKILL.md +376 -0
  45. package/skills/experiment-plan/SKILL.md +249 -0
  46. package/skills/experiment-queue/SKILL.md +431 -0
  47. package/skills/experiment-queue/scripts/build_manifest.py +142 -0
  48. package/skills/experiment-queue/scripts/queue_manager.py +433 -0
  49. package/skills/feishu-notify/SKILL.md +156 -0
  50. package/skills/figure-description/SKILL.md +138 -0
  51. package/skills/figure-spec/SKILL.md +262 -0
  52. package/skills/figure-spec/scripts/figure_renderer.py +799 -0
  53. package/skills/formula-derivation/SKILL.md +280 -0
  54. package/skills/gemini-search/SKILL.md +231 -0
  55. package/skills/grant-proposal/SKILL.md +698 -0
  56. package/skills/idea-creator/SKILL.md +542 -0
  57. package/skills/idea-discovery/SKILL.md +521 -0
  58. package/skills/idea-discovery-robot/SKILL.md +363 -0
  59. package/skills/integrity-forensics/SKILL.md +284 -0
  60. package/skills/interview-cheatsheet/SKILL.md +245 -0
  61. package/skills/invention-structuring/SKILL.md +188 -0
  62. package/skills/jurisdiction-format/SKILL.md +192 -0
  63. package/skills/kill-argument/SKILL.md +437 -0
  64. package/skills/mermaid-diagram/SKILL.md +419 -0
  65. package/skills/meta-apply/SKILL.md +141 -0
  66. package/skills/meta-optimize/SKILL.md +437 -0
  67. package/skills/monitor-experiment/SKILL.md +140 -0
  68. package/skills/novelty-check/SKILL.md +101 -0
  69. package/skills/openalex/SKILL.md +237 -0
  70. package/skills/overleaf-sync/SKILL.md +220 -0
  71. package/skills/paper-claim-audit/SKILL.md +348 -0
  72. package/skills/paper-compile/SKILL.md +266 -0
  73. package/skills/paper-figure/SKILL.md +312 -0
  74. package/skills/paper-illustration/SKILL.md +736 -0
  75. package/skills/paper-illustration-image2/SKILL.md +391 -0
  76. package/skills/paper-illustration-image2/scripts/paper_illustration_image2.py +255 -0
  77. package/skills/paper-plan/SKILL.md +386 -0
  78. package/skills/paper-poster/SKILL.md +19 -0
  79. package/skills/paper-poster-html/DESIGN_FINAL.md +176 -0
  80. package/skills/paper-poster-html/IMPLEMENTATION_CONVENTIONS.md +161 -0
  81. package/skills/paper-poster-html/LICENSES/posterly-MIT.txt +21 -0
  82. package/skills/paper-poster-html/NOTICE.md +57 -0
  83. package/skills/paper-poster-html/SKILL.md +323 -0
  84. package/skills/paper-poster-html/scripts/_posterly/__init__.py +0 -0
  85. package/skills/paper-poster-html/scripts/_posterly/canvas.py +200 -0
  86. package/skills/paper-poster-html/scripts/_posterly/measure.py +588 -0
  87. package/skills/paper-poster-html/scripts/_posterly/polish.py +498 -0
  88. package/skills/paper-poster-html/scripts/_posterly/preflight.py +489 -0
  89. package/skills/paper-poster-html/scripts/_posterly/render.py +215 -0
  90. package/skills/paper-poster-html/scripts/_posterly/textutil.py +16 -0
  91. package/skills/paper-poster-html/scripts/_posterly/verify_final.py +171 -0
  92. package/skills/paper-poster-html/scripts/asset_check.py +897 -0
  93. package/skills/paper-poster-html/scripts/extract_pdf_figures.py +666 -0
  94. package/skills/paper-poster-html/scripts/poster_check.py +251 -0
  95. package/skills/paper-poster-html/scripts/preprocess_figures.py +238 -0
  96. package/skills/paper-poster-html/scripts/render_preview.py +217 -0
  97. package/skills/paper-poster-html/scripts/run_gates.py +556 -0
  98. package/skills/paper-poster-html/scripts/style_check.py +1324 -0
  99. package/skills/paper-poster-html/templates/COMPONENTS.md +462 -0
  100. package/skills/paper-poster-html/templates/README.md +170 -0
  101. package/skills/paper-poster-html/templates/landscape_4col.html +1032 -0
  102. package/skills/paper-poster-html/templates/landscape_hero.html +1046 -0
  103. package/skills/paper-poster-html/templates/portrait_2col.html +947 -0
  104. package/skills/paper-poster-html/templates/tokens/acl.json +9 -0
  105. package/skills/paper-poster-html/templates/tokens/cvpr.json +9 -0
  106. package/skills/paper-poster-html/templates/tokens/generic.json +9 -0
  107. package/skills/paper-poster-html/templates/tokens/iclr.json +9 -0
  108. package/skills/paper-poster-html/templates/tokens/icml.json +9 -0
  109. package/skills/paper-poster-html/templates/tokens/neurips.json +9 -0
  110. package/skills/paper-slides/SKILL.md +635 -0
  111. package/skills/paper-talk/SKILL.md +381 -0
  112. package/skills/paper-write/SKILL.md +604 -0
  113. package/skills/paper-write/templates/IEEEtran.bst +2409 -0
  114. package/skills/paper-write/templates/IEEEtran.cls +6347 -0
  115. package/skills/paper-write/templates/iclr2026.tex +84 -0
  116. package/skills/paper-write/templates/icml2025.tex +87 -0
  117. package/skills/paper-write/templates/ieee_conference.tex +89 -0
  118. package/skills/paper-write/templates/ieee_journal.tex +93 -0
  119. package/skills/paper-write/templates/math_commands.tex +48 -0
  120. package/skills/paper-write/templates/neurips2025.tex +80 -0
  121. package/skills/paper-writing/SKILL.md +916 -0
  122. package/skills/patent-novelty-check/SKILL.md +153 -0
  123. package/skills/patent-pipeline/SKILL.md +344 -0
  124. package/skills/patent-review/SKILL.md +203 -0
  125. package/skills/pixel-art/SKILL.md +137 -0
  126. package/skills/prior-art-search/SKILL.md +146 -0
  127. package/skills/proof-checker/SKILL.md +866 -0
  128. package/skills/proof-orchestrator/NOTICE.md +24 -0
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  130. package/skills/proof-orchestrator/references/audit-output-contract.md +126 -0
  131. package/skills/proof-orchestrator/references/deepseek-routing.md +74 -0
  132. package/skills/proof-orchestrator/references/dispatch-prompts.md +227 -0
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  140. package/skills/render-html/scripts/render_html.py +1006 -0
  141. package/skills/render-html/scripts/templates/academic.html +703 -0
  142. package/skills/render-html/scripts/templates/dashboard.html +333 -0
  143. package/skills/research-lit/SKILL.md +756 -0
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  145. package/skills/research-refine/SKILL.md +770 -0
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  158. package/skills/shared-references/compute-env-contract.md +163 -0
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  160. package/skills/shared-references/evidence-precheck.md +65 -0
  161. package/skills/shared-references/experiment-integrity.md +49 -0
  162. package/skills/shared-references/external-cadence.md +326 -0
  163. package/skills/shared-references/fan-out-pattern.md +366 -0
  164. package/skills/shared-references/injection-hygiene.md +127 -0
  165. package/skills/shared-references/integration-contract.md +461 -0
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@@ -0,0 +1,348 @@
1
+ ---
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+ name: paper-claim-audit
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+ description: "Zero-context verification that every number, comparison, and scope claim in the paper matches raw result files. Uses a fresh cross-model reviewer with NO prior context to prevent confirmation bias. Use when user says \"审查论文数据\", \"check paper claims\", \"verify numbers\", \"论文数字核对\", or before submission to ensure paper-to-evidence fidelity."
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+ argument-hint: "[paper-directory]"
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+ allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob, mcp__codex__codex
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+ ---
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+
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+ # Paper Claim Audit: Zero-Context Evidence Verification
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+
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+ > 🔒 **Do not wrap this skill in `/loop`, `/schedule`, or `CronCreate`.** It is
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+ > verdict-bearing — it judges paper-to-evidence fidelity with a deliberately
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+ > zero-context fresh reviewer. Re-firing that verdict on a wall-clock timer adds
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+ > no new signal (it changes only when the *paper or results* change). Schedule
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+ > the *external wait that precedes it* — paper draft ready → then audit
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+ > **once**. See
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+ > [`shared-references/external-cadence.md`](../shared-references/external-cadence.md).
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+
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+ Verify that every claim in the paper matches raw evidence for: **$ARGUMENTS**
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+
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+ ## Why This Exists
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+
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+ The executor writes experiments AND writes the paper. It "knows" what the results should be. This creates confirmation bias:
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+ - Rounding 84.7% up to 85.3%
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+ - Reporting best seed instead of average
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+ - Citing metrics from a different experiment config
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+ - Claiming "improves by 15%" when the delta is actually 12.8%
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+
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+ A **fresh reviewer with zero prior context** catches these because it has no expectations — it just compares paper text vs raw files.
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+
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+ ## How This Differs From Other Audit Skills
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+
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+ | Skill | Question it answers |
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+ |-------|-------------------|
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+ | `/experiment-audit` | Is the experiment code honest? (fake GT, normalization fraud) |
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+ | `/result-to-claim` | Does the data scientifically support this claim? |
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+ | **`/paper-claim-audit`** | **Does the paper report the data truthfully and precisely?** |
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+
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+ ## Core Principle
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+
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+ **Zero-context, fresh reviewer.** The auditor receives ONLY:
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+ - Paper .tex files (the claims)
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+ - Raw result files (the evidence)
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+
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+ It does NOT receive:
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+ - ❌ EXPERIMENT_LOG.md
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+ - ❌ EXPERIMENT_TRACKER.md
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+ - ❌ AUTO_REVIEW.md
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+ - ❌ NARRATIVE_REPORT.md
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+ - ❌ Any executor summary or interpretation
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+ - ❌ Any prior audit results
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+ - ❌ Any conversation history
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+
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+ This is **stricter than reviewer-independence** — it's zero-context evidence audit.
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+
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+ ## Workflow
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+
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+ ### Step 1: Collect Files (Executor — Claude)
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+
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+ Locate paper and result files WITHOUT reading or interpreting them.
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+
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+ **Paper files** (claims) — paths shown relative to the shell's working
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+ directory so you can find them with `ls`; when writing them into
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+ `audited_input_hashes`, use paths relative to the paper dir (no `paper/`
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+ prefix) per the "Submission Artifact Emission" section below:
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+ ```
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+ paper/main.tex # → hash key: main.tex
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+ paper/sections/*.tex # → hash key: sections/*.tex
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+ paper/tables/*.tex (if separate) # → hash key: tables/*.tex
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+ ```
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+
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+ **Result files** (evidence):
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+ ```
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+ results/*.json, results/*.jsonl, results/*.csv, results/*.tsv
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+ outputs/*.json, outputs/*.csv
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+ wandb-summary.json (if exists)
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+ **/metrics.json, **/eval_results.json
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+ **/config.yaml, **/args.json (experiment configs)
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+ ```
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+
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+ **Exclude** (no summaries, no interpretations):
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+ ```
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+ EXPERIMENT_LOG.md, EXPERIMENT_TRACKER.md, AUTO_REVIEW*.md
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+ NARRATIVE_REPORT.md, PAPER_PLAN.md, findings.md
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+ Any .md file that is an executor-written summary
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+ ```
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+
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+ ### Step 2: Fresh Reviewer Audit (GPT-5.6-Sol — NEW thread, no reply)
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+
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+ **CRITICAL: Use `mcp__codex__codex` (new thread), NEVER `mcp__codex__codex-reply`.** Every run must be a fresh context.
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+
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+ ```
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+ mcp__codex__codex:
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+ model: gpt-5.6-sol
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+ config: {"model_reasoning_effort": "ultra"}
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+ prompt: |
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+ You are a paper-to-evidence auditor. You have ZERO prior context about
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+ this research. You will receive only paper source files and raw result
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+ files. Your job is to verify that every number in the paper exactly
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+ matches the raw evidence.
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+
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+ Paper files to read:
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+ [list .tex file paths]
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+
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+ Result files to read:
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+ [list .json/.csv/.yaml file paths]
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+
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+ ## Audit Protocol
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+
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+ ### A. Extract Every Quantitative Claim
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+ For each number, percentage, comparison, or scope statement in the paper:
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+ - Location (section, table, caption, or inline text)
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+ - Exact claim text
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+ - The number or comparison being made
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+
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+ ### B. Trace Each Claim to Evidence
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+ For each extracted claim, find the supporting raw data:
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+ - Which result file contains this number?
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+ - What is the EXACT value in that file?
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+ - Match status: exact_match / rounding_ok / mismatch
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+
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+ ### C. Check These Specific Failure Modes
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+
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+ 1. **Number inflation**: Paper says 85.3%, raw file says 84.7%
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+ Rule: only standard rounding to displayed precision is allowed
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+
126
+ 2. **Best-seed cherry-pick**: Paper says "achieves 90.2%" but
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+ that's the best of 5 seeds; mean is 87.1%
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+ Rule: check if paper specifies "average" / "best" / "median"
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+
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+ 3. **Config mismatch**: Paper compares Method A vs Baseline B,
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+ but they used different hyperparameters / datasets / splits
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+ Rule: verify config files show same settings for compared methods
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+
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+ 4. **Aggregation mismatch**: Paper says "average over 5 seeds"
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+ but result files show only 3 runs
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+ Rule: count actual runs vs claimed count
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+
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+ 5. **Delta error**: Paper says "improves by 15%" but
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+ actual delta is (85.3 - 73.1) / 73.1 = 16.7%
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+ Rule: verify arithmetic of all relative improvements
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+
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+ 6. **Caption-table mismatch**: Figure caption describes
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+ something different from what the figure/table actually shows
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+ Rule: cross-check every caption against its content
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+
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+ 7. **Scope overclaim**: Paper says "consistently outperforms"
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+ but only tested on 2 datasets
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+ Rule: check if language matches actual evaluation scope
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+
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+ ## Output Format (per claim)
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+ For each claim, report:
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+ - claim_id: sequential number
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+ - location: section/table/figure
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+ - paper_text: exact quote from paper
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+ - paper_value: the number claimed
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+ - evidence_file: which raw file
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+ - evidence_value: the actual number
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+ - status: exact_match | rounding_ok | ambiguous_mapping |
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+ missing_evidence | config_mismatch | aggregation_mismatch |
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+ number_mismatch | scope_overclaim | unsupported_claim
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+ - details: explanation if not exact_match
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+
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+ Overall verdict: PASS | WARN | FAIL
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+ ```
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+
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+ ### Step 3: Write Report (Executor — Claude)
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+
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+ Parse the reviewer's response and write `PAPER_CLAIM_AUDIT.md`:
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+
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+ ```markdown
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+ # Paper Claim Audit Report
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+
173
+ **Date**: [today]
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+ **Auditor**: GPT-5.6-Sol ultra (fresh zero-context thread)
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+ **Paper**: [paper title from tex]
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+
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+ ## Overall Verdict: [PASS | WARN | FAIL]
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+
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+ ## Claims Verified: [N total]
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+ - exact_match: [count]
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+ - rounding_ok: [count]
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+ - ambiguous_mapping: [count]
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+ - missing_evidence: [count]
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+ - mismatch: [count]
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+
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+ ## Issues Found
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+
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+ ### [FAIL/WARN] Claim #N: [description]
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+ - **Location**: Section X / Table Y / Figure Z
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+ - **Paper says**: "..."
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+ - **Evidence shows**: ...
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+ - **Status**: [status]
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+ - **Fix**: [specific correction needed]
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+
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+ ## All Claims (detailed)
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+
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+ | # | Location | Paper Value | Evidence Value | Status |
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+ |---|----------|-------------|---------------|--------|
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+ | 1 | Table 2 | 85.3% | 85.28% | rounding_ok |
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+ | 2 | Abstract | "15% improvement" | 12.8% | number_mismatch |
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+ | ... |
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+ ```
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+
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+ Also write `PAPER_CLAIM_AUDIT.json` for machine consumption.
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+
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+ ### Step 4: Print Summary
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+
208
+ ```
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+ 📋 Paper Claim Audit Complete
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+
211
+ Claims verified: 24
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+ exact_match: 18
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+ rounding_ok: 3
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+ ambiguous: 1
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+ ⚠️ mismatch: 2
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+
217
+ Overall: ⚠️ WARN
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+
219
+ See PAPER_CLAIM_AUDIT.md for details.
220
+ ```
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+
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+ ## When to Run
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+
224
+ 1. **After `/paper-write`** — first check before improvement loop
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+ 2. **After `/auto-paper-improvement-loop`** — recheck if improvement loop changed numbers
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+ 3. **Before submission** — final verification
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+
228
+ ## Integration with Other Skills
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+
230
+ ### Read by `/auto-paper-improvement-loop` (if exists)
231
+
232
+ ```
233
+ if PAPER_CLAIM_AUDIT.json exists:
234
+ read mismatched claims
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+ fix them as priority items in the improvement round
236
+ ```
237
+
238
+ ### Advisory, Never Blocking
239
+
240
+ Same pattern as `/experiment-audit`:
241
+ - `PASS` → continue normally
242
+ - `WARN` → print warning, continue, flag draft as "check numbers before submission"
243
+ - `FAIL` → print alert, continue, but do NOT mark as submission-ready
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+
245
+ ## Render HTML view (auto, when `RENDER_HTML = true`, default)
246
+
247
+ After writing `paper/PAPER_CLAIM_AUDIT.md` and `paper/PAPER_CLAIM_AUDIT.json`, invoke `/render-html` on the audit report so the user has a readable HTML view of the verdict + per-claim breakdown:
248
+
249
+ ```
250
+ /render-html "paper/PAPER_CLAIM_AUDIT.md" --json "paper/PAPER_CLAIM_AUDIT.json"
251
+ ```
252
+
253
+ Uses **full Codex review gate** (audit-class artifact — render-fidelity check matches the skill's existing zero-context cross-model audit invariant). Output lands at `paper/PAPER_CLAIM_AUDIT.html` with embedded source SHA256 and a `.review.json` sidecar carrying the render verdict.
254
+
255
+ **Non-blocking**: if `/render-html` fails (helper missing, Codex MCP unavailable, file write error), log the failure and treat the skill as complete — the JSON + MD verdict files are the canonical outputs; the HTML view is a convenience for human readers.
256
+
257
+ Skip if `RENDER_HTML = false` is set in the project's `CLAUDE.md` or passed as `— render html: false`.
258
+
259
+ ## Key Rules
260
+
261
+ - **Fresh thread EVERY run.** Never use `codex-reply`. Never carry context.
262
+ - **Zero executor interpretation.** Only file paths. No summaries.
263
+ - **Only raw results.** No EXPERIMENT_LOG, no AUTO_REVIEW, no human summaries.
264
+ - **Rounding rule.** Only standard rounding to displayed precision. 84.7% → 84.7% or 85% is OK. 84.7% → 85.3% is NOT OK.
265
+ - **Cross-model.** Reviewer must be a different model family from executor.
266
+
267
+ ## Review Tracing
268
+
269
+ After each `mcp__codex__codex` or `mcp__codex__codex-reply` reviewer call, save the trace following `shared-references/review-tracing.md` (Policy C — forensic; never silently skip). Use `save_trace.sh` (resolved per the chain in `shared-references/integration-contract.md` §2) or write files directly to `.aris/traces/<skill>/<date>_run<NN>/`. Respect the `--- trace:` parameter (default: `full`).
270
+
271
+ ## Submission Artifact Emission
272
+
273
+ This skill **always** writes `paper/PAPER_CLAIM_AUDIT.json`, regardless of
274
+ caller or detector outcome. A detector-negative run (paper has no numeric
275
+ claims) emits verdict `NOT_APPLICABLE`; a paper-with-numeric-claims-but-no-
276
+ raw-results run emits `BLOCKED`. Silent skip is forbidden — `paper-writing`
277
+ Phase 6 and `verify_paper_audits.sh` both rely on this artifact
278
+ existing at a predictable path.
279
+
280
+ The artifact conforms to the schema in `shared-references/assurance-contract.md`:
281
+
282
+ ```json
283
+ {
284
+ "audit_skill": "paper-claim-audit",
285
+ "verdict": "PASS | WARN | FAIL | NOT_APPLICABLE | BLOCKED | ERROR",
286
+ "reason_code": "all_numbers_match | rounding_drift | missing_raw_results | ...",
287
+ "summary": "One-line human-readable verdict summary.",
288
+ "audited_input_hashes": {
289
+ "main.tex": "sha256:...",
290
+ "sections/5.evidence.tex": "sha256:...",
291
+ "/abs/path/to/results/run_2026_04_19.json": "sha256:..."
292
+ },
293
+ "trace_path": ".aris/traces/paper-claim-audit/<date>_run<NN>/",
294
+ "thread_id": "<codex mcp thread id>",
295
+ "reviewer_model": "<resolved — the model that actually ran (target: gpt-5.6-sol)>",
296
+ "reviewer_reasoning": "<resolved — the effort that actually ran (target: ultra)>",
297
+ "generated_at": "<UTC ISO-8601>",
298
+ "details": {
299
+ "total_claims": <int>,
300
+ "mismatches": [ ... per-claim issue records ... ],
301
+ "result_files": [ ... raw files consulted ... ]
302
+ }
303
+ }
304
+ ```
305
+
306
+ ### `audited_input_hashes` scope
307
+
308
+ Hash the **declared input set** passed into this audit invocation — i.e. the
309
+ exact `.tex` files and raw result / config files this run read — not a
310
+ repo-wide union and not the reviewer's self-reported subset. If a caller
311
+ passed only `main.tex` + a single result file, hash those two files and no
312
+ others. The external verifier rehashes these entries; any mismatch flags
313
+ `STALE`.
314
+
315
+ **Path convention** (must match what `verify_paper_audits.sh`
316
+ expects): keys are **paths relative to the paper directory** (the arg
317
+ passed to the verifier) for in-paper files — so `main.tex`, not
318
+ `paper/main.tex` — and **absolute paths** for out-of-paper files such as
319
+ external `results/` dirs. The verifier resolves relative entries via
320
+ `os.path.join(paper_dir, key)`; prefixing with `paper/` produces
321
+ `paper/paper/main.tex` and false-fails as STALE.
322
+
323
+ ### Verdict decision table
324
+
325
+ | Input state | Verdict | `reason_code` example |
326
+ |-------------------------------------------------------|------------------|-----------------------|
327
+ | No numeric claims detected in paper | `NOT_APPLICABLE` | `no_numeric_claims` |
328
+ | Numeric claims detected, no raw result files found | `BLOCKED` | `no_raw_evidence` |
329
+ | All claims reconcile to raw data | `PASS` | `all_numbers_match` |
330
+ | Minor rounding drift only, no material mismatch | `WARN` | `rounding_drift` |
331
+ | Any material mismatch (wrong number, config mismatch) | `FAIL` | `claim_mismatch` |
332
+ | Reviewer invocation failed (network / malformed) | `ERROR` | `reviewer_error` |
333
+
334
+ ### Thread independence
335
+
336
+ Every invocation uses a fresh `mcp__codex__codex` thread. Never
337
+ `codex-reply`. Do not accept prior audit outputs (PROOF_AUDIT, CITATION_AUDIT,
338
+ EXPERIMENT_LOG, AUTO_REVIEW summaries) as input to this audit — the fresh
339
+ thread preserves reviewer independence per
340
+ `shared-references/reviewer-independence.md`.
341
+
342
+ ### Human-readable sibling
343
+
344
+ `paper/PAPER_CLAIM_AUDIT.md` is written alongside the JSON for readers.
345
+ The JSON is authoritative for `verify_paper_audits.sh`; the Markdown
346
+ is for humans. The parent skill (`paper-writing` Phase 6) plus the verifier
347
+ decide whether the verdict blocks finalization — this skill itself never
348
+ blocks; it only emits.
@@ -0,0 +1,266 @@
1
+ ---
2
+ name: paper-compile
3
+ description: "Compile LaTeX paper to PDF, fix errors, and verify output. Use when user says \"编译论文\", \"compile paper\", \"build PDF\", \"生成PDF\", or wants to compile LaTeX into a submission-ready PDF."
4
+ argument-hint: "[paper-directory]"
5
+ allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob
6
+ ---
7
+
8
+ # Paper Compile: LaTeX to Submission-Ready PDF
9
+
10
+ Compile the LaTeX paper and fix any issues: **$ARGUMENTS**
11
+
12
+ ## Constants
13
+
14
+ - **COMPILER = `latexmk`** — LaTeX build tool. Handles multi-pass compilation automatically.
15
+ - **ENGINE = `pdflatex`** — LaTeX engine. Options: `pdflatex` (default), `xelatex` (for CJK/custom fonts), `lualatex`.
16
+ - **MAX_COMPILE_ATTEMPTS = 3** — Maximum attempts to fix errors and recompile.
17
+ - **PAPER_DIR = `paper/`** — Directory containing LaTeX source files.
18
+ - **MAX_PAGES** — Page limit. ML conferences: main body to Conclusion end (excluding references & appendix). ICLR=9, NeurIPS=9, ICML=8. **IEEE venues: references ARE included in page count.** IEEE journal ≈ 12-14 pages, IEEE conference ≈ 5-8 pages (all inclusive).
19
+
20
+ ## Workflow
21
+
22
+ ### Step 1: Verify Prerequisites
23
+
24
+ Check that the compilation environment is ready:
25
+
26
+ ```bash
27
+ # Check LaTeX installation
28
+ which pdflatex && which latexmk && which bibtex
29
+
30
+ # If not installed, provide instructions:
31
+ # macOS: brew install --cask mactex-no-gui
32
+ # Ubuntu: sudo apt-get install texlive-full
33
+ # Server: conda install -c conda-forge texlive-core
34
+ ```
35
+
36
+ Verify all required files exist:
37
+
38
+ ```bash
39
+ # Must exist
40
+ ls $PAPER_DIR/main.tex
41
+
42
+ # Should exist
43
+ ls $PAPER_DIR/references.bib
44
+ ls $PAPER_DIR/sections/*.tex
45
+ ls $PAPER_DIR/figures/*.pdf 2>/dev/null || ls $PAPER_DIR/figures/*.png 2>/dev/null
46
+ ```
47
+
48
+ ### Step 2: First Compilation Attempt
49
+
50
+ ```bash
51
+ cd $PAPER_DIR
52
+
53
+ # Clean previous build artifacts
54
+ latexmk -C
55
+
56
+ # Full compilation (pdflatex + bibtex + pdflatex × 2)
57
+ latexmk -pdf -interaction=nonstopmode -halt-on-error main.tex 2>&1 | tee compile.log
58
+ ```
59
+
60
+ ### Step 3: Error Diagnosis and Auto-Fix
61
+
62
+ If compilation fails, read `compile.log` and fix common errors:
63
+
64
+ **Missing packages:**
65
+ ```
66
+ ! LaTeX Error: File `somepackage.sty' not found.
67
+ ```
68
+ → Install via `tlmgr install somepackage` or remove the `\usepackage` if unused.
69
+
70
+ **Undefined references:**
71
+ ```
72
+ LaTeX Warning: Reference `fig:xyz' on page 3 undefined
73
+ ```
74
+ → Check `\label{fig:xyz}` exists in the correct figure environment.
75
+
76
+ **Missing figures:**
77
+ ```
78
+ ! LaTeX Error: File `figures/fig1.pdf' not found.
79
+ ```
80
+ → Check if the file exists with a different extension (.png vs .pdf). Update the `\includegraphics` path.
81
+
82
+ **Citation undefined:**
83
+ ```
84
+ LaTeX Warning: Citation `smith2024' undefined
85
+ ```
86
+ → Add the missing entry to `references.bib` or fix the citation key.
87
+
88
+ **`[VERIFY]` markers in text:**
89
+ → Search for `[VERIFY]` markers left by `/paper-write`. These indicate unverified citations or facts. Search for the correct information or flag to the user.
90
+
91
+ **Overfull hbox:**
92
+ ```
93
+ Overfull \hbox (12.5pt too wide) in paragraph at lines 42--45
94
+ ```
95
+ → Minor: usually ignorable. If severe (>20pt), rephrase the text or adjust figure width.
96
+
97
+ **BibTeX errors:**
98
+ ```
99
+ I was expecting a `,' or a `}'---line 15 of references.bib
100
+ ```
101
+ → Fix BibTeX syntax (missing comma, unmatched braces, special characters in title).
102
+
103
+ **`\crefname` undefined for custom theorem types:**
104
+ → Ensure `\crefname{assumption}{Assumption}{Assumptions}` and similar are in the preamble after `\newtheorem{assumption}`.
105
+
106
+ ### Step 4: Iterative Fix Loop
107
+
108
+ ```
109
+ for attempt in 1..MAX_COMPILE_ATTEMPTS:
110
+ compile()
111
+ if success:
112
+ break
113
+ parse_errors()
114
+ auto_fix()
115
+ ```
116
+
117
+ For each error:
118
+ 1. Read the error message from `compile.log`
119
+ 2. Locate the source file and line number
120
+ 3. Apply the fix
121
+ 4. Recompile
122
+
123
+ **Stuck after 2 attempts?** If Codex plugin is installed, invoke `/codex:rescue` — Codex can independently read the LaTeX source and `compile.log` to spot issues Claude missed (e.g., conflicting packages, encoding problems, subtle macro errors). If not installed, continue with Claude's own diagnosis.
124
+
125
+ ### Step 5: Post-Compilation Checks
126
+
127
+ After successful compilation, verify the output:
128
+
129
+ ```bash
130
+ # Check PDF exists and has content
131
+ ls -la main.pdf
132
+ # Check page count
133
+ pdfinfo main.pdf | grep Pages
134
+
135
+ # macOS: open for visual inspection
136
+ # open main.pdf
137
+ ```
138
+
139
+ **Visual review (automated):**
140
+ If the compiled PDF exists, read it directly to check visual presentation:
141
+ - Figure quality: readable labels, legible text, distinguishable colors
142
+ - Layout: no orphaned section headers, no awkward page breaks
143
+ - Figures appear near their first text reference (not pages away)
144
+ - Tables: aligned columns, consistent decimal precision
145
+ - No overfull content visibly extending past margins
146
+
147
+ This is a quick visual scan, not a full review — the improvement loop does deeper visual review.
148
+
149
+ **Automated checks:**
150
+
151
+ - [ ] PDF file exists and is > 100KB (not empty/corrupt)
152
+ - [ ] Total page count is reasonable (MAX_PAGES + appendix + references)
153
+ - [ ] No "??" in the PDF (undefined references — grep the log)
154
+ - [ ] No "[?]" in the PDF (undefined citations — grep the log)
155
+ - [ ] Figures are rendered (not missing image placeholders)
156
+
157
+ ```bash
158
+ # Check for undefined references
159
+ grep -c "LaTeX Warning.*undefined" compile.log
160
+
161
+ # Check for missing citations
162
+ grep -c "Citation.*undefined" compile.log
163
+ ```
164
+
165
+ ### Step 6: Page Count Verification
166
+
167
+ **CRITICAL**: Verify paper fits within MAX_PAGES.
168
+
169
+ **For ML conferences (ICLR/NeurIPS/ICML/CVPR/ACL/AAAI):** Main body = first page through end of Conclusion section (not necessarily §5 — could be §6, §7, or §8 depending on structure). References and appendix are NOT counted.
170
+
171
+ **For IEEE venues:** The TOTAL page count (including references) must fit within the limit. There is no separate "main body" counting — everything up to and including the references counts.
172
+
173
+ **Precise check using `pdftotext`:**
174
+ ```bash
175
+ # Extract text and find where Conclusion ends vs References begin
176
+ pdftotext main.pdf - | python3 -c "
177
+ import sys
178
+ text = sys.stdin.read()
179
+ pages = text.split('\f')
180
+ for i, page in enumerate(pages):
181
+ if 'Ethics Statement' in page or 'Reproducibility' in page:
182
+ print(f'Conclusion ends on page {i+1}')
183
+ if any(w in page for w in ['References', 'Bibliography']):
184
+ lines = [l for l in page.split('\n') if l.strip()]
185
+ for l in lines[:3]:
186
+ if 'References' in l or 'Bibliography' in l:
187
+ print(f'References start on page {i+1}')
188
+ break
189
+ "
190
+ ```
191
+
192
+ If Conclusion ends mid-page and References start on the same page, the main body is that page number (e.g., if both are on page 9, main body = ~8.5 pages, which is fine for a 9-page limit since it leaves room for the References header).
193
+
194
+ If over limit:
195
+ - Identify which sections are longest
196
+ - Suggest specific cuts (move proofs to appendix, compress tables, tighten writing)
197
+ - Report: "Main body is X pages (limit: MAX_PAGES). Suggestion: move [specific content] to appendix."
198
+
199
+ ### Step 6.5: Stale File Detection
200
+
201
+ Check for orphaned section files not referenced by `main.tex`:
202
+
203
+ ```bash
204
+ # Find all .tex files in sections/ and check which are \input'ed by main.tex
205
+ for f in paper/sections/*.tex; do
206
+ base=$(basename "$f")
207
+ if ! grep -q "$base" paper/main.tex; then
208
+ echo "WARNING: $f is not referenced by main.tex — consider removing"
209
+ fi
210
+ done
211
+ ```
212
+
213
+ This prevents confusion from leftover files when section structure changes (e.g., old `5_conclusion.tex` left behind after restructuring to 7 sections).
214
+
215
+ ### Step 7: Submission Readiness
216
+
217
+ For conference submission, additional checks:
218
+
219
+ - [ ] **Anonymous**: no author names, affiliations, or self-citations that reveal identity
220
+ - [ ] **Page limit**: main body within MAX_PAGES (to end of Conclusion)
221
+ - [ ] **Font embedding**: all fonts embedded in PDF
222
+ ```bash
223
+ pdffonts main.pdf | grep -v "yes" # should return nothing (or only header)
224
+ ```
225
+ - [ ] **No supplementary mixed in**: appendix clearly after `\newpage\appendix`
226
+ - [ ] **File size**: reasonable (< 50MB for most venues, < 10MB preferred)
227
+ - [ ] **No `[VERIFY]` markers**: search the PDF text for leftover markers
228
+
229
+ ### Step 8: Output Summary
230
+
231
+ ```markdown
232
+ ## Compilation Report
233
+
234
+ - **Status**: SUCCESS / FAILED
235
+ - **PDF**: paper/main.pdf
236
+ - **Pages**: X (main body to Conclusion) + Y (references) + Z (appendix)
237
+ - **Within page limit**: YES/NO (MAX_PAGES = N)
238
+ - **Errors fixed**: [list of auto-fixed issues]
239
+ - **Warnings remaining**: [list of non-critical warnings]
240
+ - **Undefined references**: 0
241
+ - **Undefined citations**: 0
242
+
243
+ ### Next Steps
244
+ - [ ] Visual inspection of PDF
245
+ - [ ] Run `/paper-write` to fix any content issues
246
+ - [ ] Submit to [venue] via OpenReview / CMT / HotCRP
247
+ ```
248
+
249
+ ## Key Rules
250
+
251
+ - **Never delete the user's source files** — only modify to fix errors
252
+ - **Keep compile.log** — useful for debugging
253
+ - **Don't suppress warnings** — report them, let the user decide
254
+ - **If LaTeX is not installed**, provide clear installation instructions rather than failing silently
255
+ - **Font embedding is critical** — some venues reject PDFs with non-embedded fonts
256
+ - **Page count rules differ by venue** — ML conferences: main body to Conclusion (refs excluded). **IEEE venues: total pages including references.**
257
+
258
+ ## Common Venue Requirements
259
+
260
+ | Venue | Style File | Citation | Page Limit | Refs in limit? | Submission |
261
+ |-------|-----------|----------|------------|----------------|------------|
262
+ | ICLR 2026 | `iclr2026_conference.sty` | `natbib` (`\citep`/`\citet`) | 9 pages (to Conclusion end) | No | OpenReview |
263
+ | NeurIPS 2025 | `neurips_2025.sty` | `natbib` (`\citep`/`\citet`) | 9 pages (to Conclusion end) | No | OpenReview |
264
+ | ICML 2025 | `icml2025.sty` | `natbib` (`\citep`/`\citet`) | 8 pages (to Conclusion end) | No | OpenReview |
265
+ | IEEE Journal | `IEEEtran.cls` [journal] | `cite` (`\cite{}`, numeric) | ~12-14 pages (Transactions) / ~4-5 (Letters) | **Yes** | IEEE Author Portal / ScholarOne |
266
+ | IEEE Conference | `IEEEtran.cls` [conference] | `cite` (`\cite{}`, numeric) | 5-8 pages (varies by conf) | **Yes** | EDAS / IEEE Author Portal |