@research-copilot/plugin 1.1.17 → 1.1.18

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 (799) hide show
  1. package/dist/.claude-plugin/plugin.json +1 -1
  2. package/dist/.codex-plugin/plugin.toml +1 -1
  3. package/dist/.cursor-plugin/plugin.json +1 -1
  4. package/dist/.gemini-plugin/plugin.json +1 -1
  5. package/dist/.opencode-plugin/plugin.json +1 -1
  6. package/dist/.windsurf-plugin/plugin.json +1 -1
  7. package/dist/skills/ablation-planner/SKILL.md +126 -0
  8. package/dist/skills/alphaxiv/SKILL.md +186 -0
  9. package/dist/skills/analyze-results/SKILL.md +45 -0
  10. package/dist/skills/arxiv/SKILL.md +210 -0
  11. package/dist/skills/auto-paper-improvement-loop/SKILL.md +574 -0
  12. package/dist/skills/auto-review-loop/SKILL.md +370 -0
  13. package/dist/skills/auto-review-loop-llm/SKILL.md +247 -0
  14. package/dist/skills/auto-review-loop-minimax/SKILL.md +290 -0
  15. package/dist/skills/benchmark-paper-template/SKILL.md +142 -0
  16. package/dist/skills/benchmark-paper-template/references/benchmark-design.md +180 -0
  17. package/dist/skills/benchmark-paper-template/references/checklist.md +113 -0
  18. package/dist/skills/benchmark-paper-template/references/construction-pipeline.md +127 -0
  19. package/dist/skills/benchmark-paper-template/references/experiments.md +159 -0
  20. package/dist/skills/benchmark-paper-template/references/gap-analysis.md +86 -0
  21. package/dist/skills/benchmark-paper-template/references/instantiation-template.md +194 -0
  22. package/dist/skills/benchmark-paper-template/references/orchestrator-notes.md +96 -0
  23. package/dist/skills/benchmark-paper-template/references/paper-structure.md +209 -0
  24. package/dist/skills/citation-audit/SKILL.md +494 -0
  25. package/dist/skills/claims-drafting/SKILL.md +239 -0
  26. package/dist/skills/comm-lit-review/SKILL.md +299 -0
  27. package/dist/skills/comm-lit-review/references/domain-taxonomy.md +57 -0
  28. package/dist/skills/comm-lit-review/references/output-template.md +37 -0
  29. package/dist/skills/comm-lit-review/references/source-policy.md +99 -0
  30. package/dist/skills/comm-lit-review/references/venue-tiering.md +112 -0
  31. package/dist/skills/composer/SKILL.md +840 -0
  32. package/dist/skills/composer/references/section_guides.md +675 -0
  33. package/dist/skills/composer/references/writing_standards.md +629 -0
  34. package/dist/skills/composer/scripts/chapter_quality_check.py +470 -0
  35. package/dist/skills/composer/scripts/final_evaluation.py +550 -0
  36. package/dist/skills/deepxiv/SKILL.md +142 -0
  37. package/dist/skills/dse-loop/SKILL.md +277 -0
  38. package/dist/skills/embodiment-description/SKILL.md +129 -0
  39. package/dist/skills/exa-search/SKILL.md +192 -0
  40. package/dist/skills/experiment-audit/SKILL.md +262 -0
  41. package/dist/skills/experiment-bridge/SKILL.md +316 -0
  42. package/dist/skills/experiment-plan/SKILL.md +249 -0
  43. package/dist/skills/experiment-queue/SKILL.md +380 -0
  44. package/dist/skills/experiment-queue/scripts/build_manifest.py +142 -0
  45. package/dist/skills/experiment-queue/scripts/queue_manager.py +426 -0
  46. package/dist/skills/feishu-notify/SKILL.md +155 -0
  47. package/dist/skills/figure-description/SKILL.md +138 -0
  48. package/dist/skills/figure-designer/SKILL.md +207 -0
  49. package/dist/skills/figure-designer/references/design-rules.md +99 -0
  50. package/dist/skills/figure-designer/references/experimental-results.md +127 -0
  51. package/dist/skills/figure-designer/references/motivated-example.md +138 -0
  52. package/dist/skills/figure-designer/references/solution-overview.md +145 -0
  53. package/dist/skills/figure-designer/references/tools.md +124 -0
  54. package/dist/skills/figure-spec/SKILL.md +252 -0
  55. package/dist/skills/figure-spec/scripts/figure_renderer.py +799 -0
  56. package/dist/skills/formula-derivation/SKILL.md +280 -0
  57. package/dist/skills/gemini-search/SKILL.md +205 -0
  58. package/dist/skills/grant-proposal/SKILL.md +625 -0
  59. package/dist/skills/humanizer/AGENTS.md +25 -0
  60. package/dist/skills/humanizer/SKILL.md +621 -0
  61. package/dist/skills/idea-creator/SKILL.md +311 -0
  62. package/dist/skills/idea-discovery/SKILL.md +340 -0
  63. package/dist/skills/idea-discovery-robot/SKILL.md +362 -0
  64. package/dist/skills/idea-evaluator/SKILL.md +265 -0
  65. package/dist/skills/idea-evaluator/references/fatal-flaws.md +192 -0
  66. package/dist/skills/idea-evaluator/references/five-dimensions.md +251 -0
  67. package/dist/skills/idea-evaluator/references/lifecycle-capability-matching.md +177 -0
  68. package/dist/skills/idea-evaluator/references/paradigm-elephant.md +112 -0
  69. package/dist/skills/idea-evaluator/references/paradigm-examples.md +107 -0
  70. package/dist/skills/idea-evaluator/references/paradigm-first-principles.md +115 -0
  71. package/dist/skills/idea-evaluator/references/paradigm-hamming.md +137 -0
  72. package/dist/skills/idea-evaluator/references/paradigm-shift-probe.md +160 -0
  73. package/dist/skills/idea-evaluator/references/paradigm-technology-cycle.md +116 -0
  74. package/dist/skills/idea-evaluator/references/worked-examples.md +206 -0
  75. package/dist/skills/interview-cheatsheet/SKILL.md +245 -0
  76. package/dist/skills/intro-drafter/SKILL.md +250 -0
  77. package/dist/skills/intro-drafter/references/contribution-patterns.md +116 -0
  78. package/dist/skills/intro-drafter/references/flowchart.md +204 -0
  79. package/dist/skills/intro-drafter/references/paper-types.md +155 -0
  80. package/dist/skills/intro-drafter/references/running-example.md +133 -0
  81. package/dist/skills/intro-drafter/references/worked-examples.md +161 -0
  82. package/dist/skills/invention-structuring/SKILL.md +188 -0
  83. package/dist/skills/jurisdiction-format/SKILL.md +192 -0
  84. package/dist/skills/kill-argument/SKILL.md +384 -0
  85. package/dist/skills/llm-wiki/.mise.toml +2 -0
  86. package/dist/skills/llm-wiki/.nvmrc +1 -0
  87. package/dist/skills/llm-wiki/AGENTS.md +132 -0
  88. package/dist/skills/llm-wiki/CHANGELOG.md +459 -0
  89. package/dist/skills/llm-wiki/CLAUDE.md +109 -0
  90. package/dist/skills/llm-wiki/HERMES.md +44 -0
  91. package/dist/skills/llm-wiki/SKILL.md +1133 -0
  92. package/dist/skills/llm-wiki/assets/graph-demo.gif +0 -0
  93. package/dist/skills/llm-wiki/assets/graph-preview.png +0 -0
  94. package/dist/skills/llm-wiki/deps/LICENSE-d3.txt +13 -0
  95. package/dist/skills/llm-wiki/deps/LICENSE-marked.txt +44 -0
  96. package/dist/skills/llm-wiki/deps/LICENSE-purify.txt +568 -0
  97. package/{LICENSE → dist/skills/llm-wiki/deps/LICENSE-roughjs.txt} +1 -1
  98. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/SKILL.md +261 -0
  99. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/references/config/first-time-setup.md +106 -0
  100. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/cdp.ts +179 -0
  101. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/constants.ts +13 -0
  102. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/defuddle-converter.ts +58 -0
  103. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/html-to-markdown.ts +135 -0
  104. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/legacy-converter.ts +629 -0
  105. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/main.ts +314 -0
  106. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/markdown-conversion-shared.ts +305 -0
  107. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/media-localizer.ts +317 -0
  108. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/package.json +14 -0
  109. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/paths.ts +29 -0
  110. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/vendor/baoyu-chrome-cdp/package.json +9 -0
  111. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/vendor/baoyu-chrome-cdp/src/index.test.ts +307 -0
  112. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/vendor/baoyu-chrome-cdp/src/index.ts +523 -0
  113. package/dist/skills/llm-wiki/deps/d3.min.js +2 -0
  114. package/dist/skills/llm-wiki/deps/marked.min.js +6 -0
  115. package/dist/skills/llm-wiki/deps/purify.min.js +3 -0
  116. package/dist/skills/llm-wiki/deps/rough.min.js +7 -0
  117. package/dist/skills/llm-wiki/deps/youtube-transcript/SKILL.md +47 -0
  118. package/dist/skills/llm-wiki/deps/youtube-transcript/scripts/get_transcript.py +72 -0
  119. package/dist/skills/llm-wiki/docs/design/oriental-atlas/DESIGN.md +183 -0
  120. package/dist/skills/llm-wiki/docs/design/oriental-atlas/design-brief.md +170 -0
  121. package/dist/skills/llm-wiki/docs/design/oriental-atlas/oriental-editorial-atlas.html +1908 -0
  122. package/dist/skills/llm-wiki/docs/design/oriental-atlas/reviews/result-review.md +68 -0
  123. package/dist/skills/llm-wiki/docs/plans/2026-06-15-omp-tool-status-events-phased-plan.md +655 -0
  124. package/dist/skills/llm-wiki/docs/plans/2026-06-15-omp-tool-status-events-progress.json +913 -0
  125. package/dist/skills/llm-wiki/docs/spark/2026-06-15-omp-tool-status-events-design.md +174 -0
  126. package/dist/skills/llm-wiki/install.ps1 +87 -0
  127. package/dist/skills/llm-wiki/install.sh +722 -0
  128. package/dist/skills/llm-wiki/package-lock.json +10309 -0
  129. package/dist/skills/llm-wiki/package.json +24 -0
  130. package/dist/skills/llm-wiki/packages/graph-engine/package.json +33 -0
  131. package/dist/skills/llm-wiki/packages/graph-engine/src/anim/.gitkeep +1 -0
  132. package/dist/skills/llm-wiki/packages/graph-engine/src/anim/index.ts +179 -0
  133. package/dist/skills/llm-wiki/packages/graph-engine/src/diff.ts +121 -0
  134. package/dist/skills/llm-wiki/packages/graph-engine/src/graph-node.ts +37 -0
  135. package/dist/skills/llm-wiki/packages/graph-engine/src/index.ts +140 -0
  136. package/dist/skills/llm-wiki/packages/graph-engine/src/model/atlas.ts +18 -0
  137. package/dist/skills/llm-wiki/packages/graph-engine/src/model/index.ts +6 -0
  138. package/dist/skills/llm-wiki/packages/graph-engine/src/model/labels.ts +11 -0
  139. package/dist/skills/llm-wiki/packages/graph-engine/src/model/learning.ts +8 -0
  140. package/dist/skills/llm-wiki/packages/graph-engine/src/model/legacy-helpers.ts +1373 -0
  141. package/dist/skills/llm-wiki/packages/graph-engine/src/model/queue.ts +7 -0
  142. package/dist/skills/llm-wiki/packages/graph-engine/src/model/storage.ts +4 -0
  143. package/dist/skills/llm-wiki/packages/graph-engine/src/model/visibility.ts +9 -0
  144. package/dist/skills/llm-wiki/packages/graph-engine/src/render/.gitkeep +1 -0
  145. package/dist/skills/llm-wiki/packages/graph-engine/src/render/index.ts +59 -0
  146. package/dist/skills/llm-wiki/packages/graph-engine/src/render/legend.ts +25 -0
  147. package/dist/skills/llm-wiki/packages/graph-engine/src/render/model.ts +593 -0
  148. package/dist/skills/llm-wiki/packages/graph-engine/src/render/preview.ts +65 -0
  149. package/dist/skills/llm-wiki/packages/graph-engine/src/render/search.ts +48 -0
  150. package/dist/skills/llm-wiki/packages/graph-engine/src/render/static-renderer.ts +2783 -0
  151. package/dist/skills/llm-wiki/packages/graph-engine/src/render/toolbar.ts +40 -0
  152. package/dist/skills/llm-wiki/packages/graph-engine/src/render/viewport.ts +272 -0
  153. package/dist/skills/llm-wiki/packages/graph-engine/src/select/.gitkeep +1 -0
  154. package/dist/skills/llm-wiki/packages/graph-engine/src/select/index.ts +189 -0
  155. package/dist/skills/llm-wiki/packages/graph-engine/src/sim/index.ts +298 -0
  156. package/dist/skills/llm-wiki/packages/graph-engine/src/sim/pins.ts +96 -0
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  160. package/dist/skills/llm-wiki/packages/graph-engine/src/types.ts +313 -0
  161. package/dist/skills/llm-wiki/packages/graph-engine/test/anim.test.ts +100 -0
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  164. package/dist/skills/llm-wiki/packages/graph-engine/test/learning.test.ts +259 -0
  165. package/dist/skills/llm-wiki/packages/graph-engine/test/preview.test.ts +56 -0
  166. package/dist/skills/llm-wiki/packages/graph-engine/test/queue.test.ts +114 -0
  167. package/dist/skills/llm-wiki/packages/graph-engine/test/render-model.test.ts +322 -0
  168. package/dist/skills/llm-wiki/packages/graph-engine/test/runtime-state.test.ts +281 -0
  169. package/dist/skills/llm-wiki/packages/graph-engine/test/search-and-legend.test.ts +111 -0
  170. package/dist/skills/llm-wiki/packages/graph-engine/test/select.test.ts +168 -0
  171. package/dist/skills/llm-wiki/packages/graph-engine/test/sim.test.ts +123 -0
  172. package/dist/skills/llm-wiki/packages/graph-engine/test/themes.test.ts +62 -0
  173. package/dist/skills/llm-wiki/packages/graph-engine/test/toolbar.test.ts +64 -0
  174. package/dist/skills/llm-wiki/packages/graph-engine/test/viewport.test.ts +167 -0
  175. package/dist/skills/llm-wiki/packages/graph-engine/tsconfig.json +17 -0
  176. package/dist/skills/llm-wiki/packages/graph-engine/vite.config.ts +15 -0
  177. package/dist/skills/llm-wiki/platforms/claude/CLAUDE.md +37 -0
  178. package/dist/skills/llm-wiki/platforms/claude/companions/llm-wiki-upgrade/SKILL.md +95 -0
  179. package/dist/skills/llm-wiki/platforms/codex/AGENTS.md +23 -0
  180. package/dist/skills/llm-wiki/scripts/adapter-state.sh +424 -0
  181. package/dist/skills/llm-wiki/scripts/build-graph-data.sh +395 -0
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  191. package/dist/skills/llm-wiki/scripts/lint-runner.sh +217 -0
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@@ -0,0 +1,370 @@
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+ ---
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+ name: "auto-review-loop"
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+ description: "Autonomous multi-round research review loop. Repeatedly reviews using a secondary Codex agent, implements fixes, and re-reviews until positive assessment or max rounds reached. Use when user says \"auto review loop\", \"review until it passes\", or wants autonomous iterative improvement."
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+ ---
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+
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+ # Auto Review Loop: Autonomous Research Improvement
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+
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+ Autonomously iterate: review → implement fixes → re-review, until the external reviewer gives a positive assessment or MAX_ROUNDS is reached.
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+
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+ ## Context: $ARGUMENTS
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+
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+ ## Constants
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+
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+ - MAX_ROUNDS = 4
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+ - POSITIVE_THRESHOLD: score >= 6/10 AND verdict ∈ {"ready", "almost"} — both must hold, matching the operative STOP CONDITION below. Verdict vocabulary is {"ready", "almost", "not ready"}. (Earlier wording used "or" + a stale verdict set; the AND form is authoritative.)
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+ - REVIEW_DOC: `review-stage/AUTO_REVIEW.md` (cumulative log) *(fall back to `./AUTO_REVIEW.md` for legacy projects)*
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+ - **OUTPUT_DIR = `review-stage/`** — All review-stage outputs go here. Create the directory if it doesn't exist.
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+ - REVIEWER_MODEL = `gpt-5.5` — Model used via a secondary Codex agent. Must be an OpenAI model (e.g., `gpt-5.5`, `o3`, `gpt-4o`)
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+ - **REVIEWER_BACKEND = `codex`** — Default: Codex reviewer agent at xhigh reasoning. Override with `--reviewer: oracle-pro` only when the user explicitly requests Oracle; if Oracle is unavailable, warn and fall back to Codex xhigh. **Same-family note:** this default reviewer is a second Codex/GPT agent — valid for Type-A completeness/drive review, but not a cross-family Type-B verdict; install a `skills-codex-claude-review` / `skills-codex-gemini-review` overlay for a cross-family acquittal (see `shared-references/reviewer-routing.md`).
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+ - **HUMAN_CHECKPOINT = false** — When `true`, pause after each round's review (Phase B) and present the score + weaknesses to the user. Wait for user input before proceeding to Phase C. The user can: approve the suggested fixes, provide custom modification instructions, skip specific fixes, or stop the loop early. When `false` (default), the loop runs fully autonomously.
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+ - **COMPACT = false** — When `true`, (1) read `EXPERIMENT_LOG.md` and `findings.md` instead of parsing full logs on session recovery, (2) append key findings to `findings.md` after each round.
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+ - **REVIEWER_DIFFICULTY = medium** — Controls adversarial depth: `medium` uses normal Codex xhigh review through `spawn_agent` / `send_input`; `hard` adds Reviewer Memory and Debate Protocol; `nightmare` adds direct repository-reading adversarial verification by an independent reviewer.
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+ - **RENDER_HTML = true** — When `true` (default), auto-render `review-stage/AUTO_REVIEW.md` to HTML on loop termination via `/render-html`. Uses `--no-review` (the loop itself IS the cross-model review; the HTML render is a structural conversion). Set `false` to skip, or pass `— render html: false`.
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+
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+ > 💡 Override: `/auto-review-loop "topic" — compact: true, human checkpoint: true, difficulty: hard`
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+
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+ ## Claude-Aligned Reviewer Memory and Debate
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+
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+ For `difficulty: hard` and `difficulty: nightmare`, maintain `review-stage/REVIEWER_MEMORY.md`.
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+
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+ - Before each reviewer call, prepend the full `REVIEWER_MEMORY.md` contents under `## Your Reviewer Memory (persistent across rounds)`.
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+ - Tell the reviewer to check whether prior suspicions were genuinely addressed or merely sidestepped.
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+ - Require a `Memory update` section in the reviewer response.
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+ - After Phase B, copy the `Memory update` into `REVIEWER_MEMORY.md` before writing `REVIEW_STATE.json`.
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+ - In `nightmare`, launch an additional fresh adversarial reviewer with direct repository/file-reading instructions. It should read `NARRATIVE_REPORT.md` or `review-stage/AUTO_REVIEW.md` for the author's claims, then verify those claims against code, logs, result files, and paper drafts instead of trusting executor summaries.
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+
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+ ## Instructions
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+
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+ In hard and nightmare modes, the reviewer must actively look for omissions, unsupported claims, cherry-picked evidence, metric mistakes, and weaknesses the executor may have downplayed.
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+
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+ For `difficulty: hard` and `nightmare`, use the **Debate Protocol** after a critical review:
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+
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+ 1. Codex writes a concise rebuttal with evidence, not spin.
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+ 2. Send the rebuttal to the same reviewer via `send_input`.
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+ 3. The reviewer rules which objections are resolved, unresolved, or newly discovered.
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+ 4. Only mark a concern resolved when the reviewer accepts the rebuttal.
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+
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+ ## State Persistence (Compact Recovery)
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+
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+ Long-running loops may hit the context window limit, triggering automatic compaction. To survive this, persist state to `review-stage/REVIEW_STATE.json` after each round:
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+
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+ ```json
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+ {
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+ "round": 2,
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+ "agent_id": "019cd392-...",
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+ "status": "in_progress",
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+ "last_score": 5.0,
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+ "last_verdict": "not ready",
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+ "pending_experiments": ["screen_name_1"],
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+ "timestamp": "2026-03-13T21:00:00"
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+ }
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+ ```
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+
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+ **Write this file at the end of every Phase E** (after documenting the round). Overwrite each time — only the latest state matters.
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+
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+ **On completion** (positive assessment or max rounds), set `"status": "completed"` so future invocations don't accidentally resume a finished loop.
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+
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+ ## Workflow
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+
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+ ### Initialization
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+
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+ 1. **Check for `review-stage/REVIEW_STATE.json`** *(fall back to `./REVIEW_STATE.json` if not found — legacy path)*:
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+ - If neither path exists: **fresh start** (normal case, identical to behavior before this feature existed)
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+ - If it exists AND `status` is `"completed"`: **fresh start** (previous loop finished normally)
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+ - If it exists AND `status` is `"in_progress"` AND `timestamp` is older than 24 hours: **fresh start** (stale state from a killed/abandoned run — delete the file and start over)
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+ - If it exists AND `status` is `"in_progress"` AND `timestamp` is within 24 hours: **resume**
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+ - Read the state file to recover `round`, `agent_id`, `last_score`, `pending_experiments`
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+ - Read `review-stage/AUTO_REVIEW.md` to restore full context of prior rounds *(fall back to `./AUTO_REVIEW.md`)*
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+ - If `pending_experiments` is non-empty, check if they have completed (e.g., check screen sessions)
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+ - Resume from the next round (round = saved round + 1)
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+ - Log: "Recovered from context compaction. Resuming at Round N."
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+ 2. Read project narrative documents, memory files, and any prior review documents. When `COMPACT = true` and compact files exist, prefer `findings.md` + `EXPERIMENT_LOG.md` over full raw logs.
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+ 3. Read recent experiment results (check output directories, logs)
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+ 4. Identify current weaknesses and open TODOs from prior reviews
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+ 5. Initialize round counter = 1 (unless recovered from state file)
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+ 6. Create/update `review-stage/AUTO_REVIEW.md` with header and timestamp
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+
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+ ### Loop (repeat up to MAX_ROUNDS)
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+
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+ #### Phase A: Review
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+
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+ **Route by REVIEWER_DIFFICULTY:**
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+
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+ ##### Medium (default) — Codex Review
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+
96
+ Send comprehensive context to the external reviewer:
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+
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+ ```
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+ spawn_agent:
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+ reasoning_effort: xhigh
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+ message: |
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+ [Round N/MAX_ROUNDS of autonomous review loop]
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+
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+ Review the work directly from its artifacts — executor notes are not
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+ evidence, so read the files yourself rather than trusting my framing:
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+ - Claims / paper draft: <path>
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+ - Methods / code under review: <path(s)>
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+ - Raw results (verbatim files, not a summary): <path(s)>
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+ - Changed since last round: <changed-file paths> — read the diff, not my description
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+
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+ Please act as a senior ML reviewer (NeurIPS/ICML level).
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+
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+ 1. Score this work 1-10 for a top venue
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+ 2. List remaining critical weaknesses (ranked by severity)
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+ 3. For each weakness, specify the MINIMUM fix (experiment, analysis, or reframing)
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+ 4. State clearly: is this READY for submission? Yes/No/Almost
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+
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+ Be brutally honest. If the work is ready, say so clearly.
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+ ```
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+
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+ If this is round 2+, use `send_input` with the saved agent id to maintain continuity.
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+
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+ ##### Hard — Codex Review + Reviewer Memory
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+
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+ Use the same `spawn_agent` / `send_input` route as medium, but prepend the full `review-stage/REVIEWER_MEMORY.md` contents under `## Your Reviewer Memory (persistent across rounds)` and require a `Memory update` section in the reviewer response.
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+
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+ ##### Nightmare — Independent Repository Review
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+
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+ Use everything in hard mode, then ask an additional fresh adversarial reviewer to verify claims against repository files, logs, result files, and paper drafts instead of trusting executor summaries. Preserve the fresh review as a separate raw response and trace.
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+
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+ #### Phase B: Parse Assessment
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+
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+ **CRITICAL: Save the FULL raw response** from the external reviewer verbatim (store in a variable for Phase E). Do NOT discard or summarize — the raw text is the primary record.
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+
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+ Then extract structured fields:
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+ - **Score** (numeric 1-10)
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+ - **Verdict** ("ready" / "almost" / "not ready")
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+ - **Action items** (ranked list of fixes)
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+
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+ **STOP CONDITION**: If score >= 6 AND verdict ∈ {"ready", "almost"} (exact match — "not ready" does NOT qualify) → stop loop, document final state.
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+
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+ #### Phase B.5: Reviewer Memory Update (hard + nightmare only)
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+
144
+ Skip entirely if `REVIEWER_DIFFICULTY = medium`.
145
+
146
+ After parsing the assessment, update `review-stage/REVIEWER_MEMORY.md`:
147
+
148
+ ## Your Reviewer Memory (persistent across rounds)
149
+
150
+ Pass this file back to the reviewer in the next round so it can track its own suspicions.
151
+
152
+ ```markdown
153
+ # Reviewer Memory
154
+
155
+ ## Round 1 — Score: X/10
156
+ - **Suspicion**: [what the reviewer flagged]
157
+ - **Unresolved**: [concerns not yet addressed]
158
+ - **Patterns**: [recurring issues the reviewer noticed]
159
+
160
+ ## Round 2 — Score: X/10
161
+ - **Previous suspicions addressed?**: [yes/no for each, with reviewer judgment]
162
+ - **New suspicions**: [...]
163
+ - **Unresolved**: [carried forward + new]
164
+ ```
165
+
166
+ Rules:
167
+ - Append each round; never delete prior rounds.
168
+ - If the reviewer response includes a `Memory update` section, copy it verbatim.
169
+ - This file is passed back to the reviewer in the next round's Phase A.
170
+
171
+ #### Phase B.6: Debate Protocol (hard + nightmare only)
172
+
173
+ Skip entirely if `REVIEWER_DIFFICULTY = medium`.
174
+
175
+ After parsing the review, Codex writes a structured rebuttal for up to three high-impact weaknesses:
176
+
177
+ ```markdown
178
+ ### Rebuttal to Weakness #1: [title]
179
+ - **Accept / Partially Accept / Reject**
180
+ - **Argument**: [why this criticism is valid, invalid, already addressed, or out of scope]
181
+ - **Evidence**: [specific code, result file, log, prior-round fix, or paper section]
182
+ ```
183
+
184
+ Send the rebuttal to the same reviewer via `send_input`:
185
+
186
+ ```text
187
+ send_input:
188
+ target: [saved reviewer id]
189
+ message: |
190
+ Please rule on the author's rebuttal below.
191
+ For each contested weakness, decide: accepted / partially accepted / rejected.
192
+ If rejected, state the minimum evidence or change required.
193
+
194
+ [paste rebuttal + evidence]
195
+ ```
196
+
197
+ Record a `### Debate Transcript (hard + nightmare only)` section in `review-stage/AUTO_REVIEW.md`. Only mark a weakness resolved if the reviewer accepts the rebuttal.
198
+
199
+ ### Debate Transcript (hard + nightmare only)
200
+
201
+ In the round log, preserve the rebuttal, reviewer ruling, accepted objections, rejected objections, and any required follow-up evidence.
202
+
203
+ #### Human Checkpoint (if enabled)
204
+
205
+ **Skip this step entirely if `HUMAN_CHECKPOINT = false`.**
206
+
207
+ When `HUMAN_CHECKPOINT = true`, present the review results and wait for user input:
208
+
209
+ ```
210
+ 📋 Round N/MAX_ROUNDS review complete.
211
+
212
+ Score: X/10 — [verdict]
213
+ Top weaknesses:
214
+ 1. [weakness 1]
215
+ 2. [weakness 2]
216
+ 3. [weakness 3]
217
+
218
+ Suggested fixes:
219
+ 1. [fix 1]
220
+ 2. [fix 2]
221
+ 3. [fix 3]
222
+
223
+ Options:
224
+ - Reply "go" or "continue" → implement all suggested fixes
225
+ - Reply with custom instructions → implement your modifications instead
226
+ - Reply "skip 2" → skip fix #2, implement the rest
227
+ - Reply "stop" → end the loop, document current state
228
+ ```
229
+
230
+ Wait for the user's response. Parse their input:
231
+ - **Approval** ("go", "continue", "ok", "proceed"): proceed to Phase C with all suggested fixes
232
+ - **Custom instructions** (any other text): treat as additional/replacement guidance for Phase C. Merge with reviewer suggestions where appropriate
233
+ - **Skip specific fixes** ("skip 1,3"): remove those fixes from the action list
234
+ - **Stop** ("stop", "enough", "done"): terminate the loop, jump to Termination
235
+
236
+ #### Feishu Notification (if configured)
237
+
238
+ After parsing the score, check if `~/.codex/feishu.json` exists and mode is not `"off"`:
239
+ - Send a `review_scored` notification: "Round N: X/10 — [verdict]" with top 3 weaknesses
240
+ - If **interactive** mode and verdict is "almost": send as checkpoint, wait for user reply on whether to continue or stop
241
+ - If config absent or mode off: skip entirely (no-op)
242
+
243
+ #### Phase C: Implement Fixes (if not stopping)
244
+
245
+ For each action item (highest priority first):
246
+
247
+ 1. **Code changes**: Write/modify experiment scripts, model code, analysis scripts
248
+ 2. **Run experiments**: Deploy to GPU server via SSH + screen/tmux
249
+ 3. **Analysis**: Run evaluation, collect results, update figures/tables
250
+ 4. **Documentation**: Update project notes and review document
251
+
252
+ Prioritization rules:
253
+ - Skip fixes requiring excessive compute (flag for manual follow-up)
254
+ - Skip fixes requiring external data/models not available
255
+ - Prefer reframing/analysis over new experiments when both address the concern
256
+ - Always implement metric additions (cheap, high impact)
257
+
258
+ #### Phase D: Wait for Results
259
+
260
+ If experiments were launched:
261
+ - Monitor remote sessions for completion
262
+ - Collect results from output files and logs
263
+ - **Training quality check** — if W&B is configured, invoke `/training-check` to verify training was healthy (no NaN, no divergence, no plateau). If W&B is not available, skip silently.
264
+
265
+ #### Phase E: Document Round
266
+
267
+ Append to `review-stage/AUTO_REVIEW.md`:
268
+
269
+ ```markdown
270
+ ## Round N (timestamp)
271
+
272
+ ### Assessment (Summary)
273
+ - Score: X/10
274
+ - Verdict: [ready/almost/not ready]
275
+ - Key criticisms: [bullet list]
276
+
277
+ ### Reviewer Raw Response
278
+
279
+ <details>
280
+ <summary>Click to expand full reviewer response</summary>
281
+
282
+ [Paste the COMPLETE raw response from the external reviewer here — verbatim, unedited.
283
+ This is the authoritative record. Do NOT truncate or paraphrase.]
284
+
285
+ </details>
286
+
287
+ ### Actions Taken
288
+ - [what was implemented/changed]
289
+
290
+ ### Results
291
+ - [experiment outcomes, if any]
292
+
293
+ ### Status
294
+ - [continuing to round N+1 / stopping]
295
+ ```
296
+
297
+ **Write `review-stage/REVIEW_STATE.json`** with current round, agent id, score, verdict, and any pending experiments.
298
+
299
+ **Append to `findings.md`** (when `COMPACT = true`): one-line entry per key finding this round.
300
+
301
+ ```markdown
302
+ - [Round N] [positive/negative/unexpected]: [one-sentence finding] (metric: X.XX → Y.YY)
303
+ ```
304
+
305
+ Increment round counter → back to Phase A.
306
+
307
+ #### Review Tracing
308
+
309
+ ## Review Tracing
310
+
311
+ After every `spawn_agent`, `send_input`, `oracle-pro`, or nightmare adversarial verification call, save a trace following `../shared-references/review-tracing.md`. Include prompt summary, reviewer route, saved agent id, raw response path, score/verdict, accepted fixes, rejected rebuttals, and the `Reviewer Memory` update if present.
312
+
313
+ ### Termination
314
+
315
+ When loop ends (positive assessment or max rounds):
316
+
317
+ 1. Update `review-stage/REVIEW_STATE.json` with `"status": "completed"`
318
+ 2. Write final summary to `review-stage/AUTO_REVIEW.md`
319
+ 3. Update project notes with conclusions
320
+ 4. **Write method/pipeline description** to `review-stage/AUTO_REVIEW.md` under a `## Method Description` section — a concise 1-2 paragraph summary of the final method, architecture, and data flow. This serves as direct input for `/paper-illustration`.
321
+ 5. **Generate claims from results** — invoke `/result-to-claim` to convert experiment results from `review-stage/AUTO_REVIEW.md` into structured paper claims. Output: `CLAIMS_FROM_RESULTS.md`. If `/result-to-claim` is unavailable, skip silently.
322
+ 6. If stopped at max rounds without positive assessment:
323
+ - List remaining blockers
324
+ - Estimate effort needed for each
325
+ - Suggest whether to continue manually or pivot
326
+ 7. **Feishu notification** (if configured): Send `pipeline_done` with final score progression table
327
+ 8. **Render HTML view** (if `RENDER_HTML = true`, default): invoke `/render-html` on the cumulative review log:
328
+ ```
329
+ /render-html "review-stage/AUTO_REVIEW.md" --no-review --state review-stage/REVIEW_STATE.json
330
+ ```
331
+ Pass `--state` explicitly when `REVIEW_STATE.json` exists (the helper does not auto-discover the sidecar). HTML lands at `review-stage/AUTO_REVIEW.html` with embedded source SHA256. **Non-blocking**: if `/render-html` fails, log the error and continue — the HTML is a convenience, not a termination prerequisite.
332
+
333
+ ## Output Protocols
334
+
335
+ > Follow these shared protocols for all output files:
336
+ > - **[Output Versioning Protocol](../../shared-references/output-versioning.md)** — write timestamped file first, then copy to fixed name
337
+ > - **[Output Manifest Protocol](../../shared-references/output-manifest.md)** — log every output to MANIFEST.md
338
+ > - **[Output Language Protocol](../../shared-references/output-language.md)** — respect the project's language setting
339
+
340
+ ## Key Rules
341
+
342
+ - **Large file handling**: If the Write tool fails due to file size, immediately retry using Bash (`cat << 'EOF' > file`) to write in chunks. Do NOT ask the user for permission — just do it silently.
343
+
344
+ - ALWAYS use `reasoning_effort: xhigh` for maximum reasoning depth
345
+ - Save agent id from first call, use `send_input` for subsequent rounds
346
+ - Be honest — include negative results and failed experiments
347
+ - Do NOT hide weaknesses to game a positive score
348
+ - Implement fixes BEFORE re-reviewing (don't just promise to fix)
349
+ - If an experiment takes > 30 minutes, launch it and continue with other fixes while waiting
350
+ - Document EVERYTHING — the review log should be self-contained
351
+ - Update project notes after each round, not just at the end
352
+
353
+ ## Prompt Template for Round 2+
354
+
355
+ ```
356
+ send_input:
357
+ id: [saved from round 1]
358
+ reasoning_effort: xhigh
359
+ message: |
360
+ [Round N update]
361
+
362
+ Since your last review these files changed — read them yourself; do not
363
+ take my word for what changed or whether it worked:
364
+ - Changed files: <paths>
365
+ - Raw diff: <path, or the `git diff` range>
366
+ - Updated raw results: <result-file paths> (verbatim files, not a pasted table)
367
+
368
+ Please re-score and re-assess. Are the remaining concerns addressed?
369
+ Same format: Score, Verdict, Remaining Weaknesses, Minimum Fixes.
370
+ ```
@@ -0,0 +1,247 @@
1
+ ---
2
+ name: "auto-review-loop-llm"
3
+ description: "Autonomous research review loop using any OpenAI-compatible LLM API. Configure via llm-chat MCP server or environment variables. Trigger with \"auto review loop llm\" or \"llm review\"."
4
+ ---
5
+
6
+ # Auto Review Loop (Generic LLM): Autonomous Research Improvement
7
+
8
+ Autonomously iterate: review → implement fixes → re-review, until the external reviewer gives a positive assessment or MAX_ROUNDS is reached.
9
+
10
+ ## Context: $ARGUMENTS
11
+
12
+ ## Constants
13
+
14
+ - MAX_ROUNDS = 4
15
+ - POSITIVE_THRESHOLD: score >= 6/10 AND verdict ∈ {"ready", "almost"} — both must hold, matching the operative STOP CONDITION below. Verdict vocabulary is {"ready", "almost", "not ready"}. (Earlier wording used "or" + a stale verdict set; the AND form is authoritative.)
16
+ - REVIEW_DOC: `review-stage/AUTO_REVIEW.md` (cumulative log) *(fall back to `./AUTO_REVIEW.md` for legacy projects)*
17
+
18
+ ## LLM Configuration
19
+
20
+ This skill uses **any OpenAI-compatible API** for external review via the `llm-chat` MCP server.
21
+
22
+ ### Configuration via MCP Server (Recommended)
23
+
24
+ Add to `~/.codex/settings.json`:
25
+
26
+ ```json
27
+ {
28
+ "mcpServers": {
29
+ "llm-chat": {
30
+ "command": "/usr/bin/python3",
31
+ "args": ["/Users/yourname/.codex/mcp-servers/llm-chat/server.py"],
32
+ "env": {
33
+ "LLM_API_KEY": "your-api-key",
34
+ "LLM_BASE_URL": "https://api.deepseek.com/v1",
35
+ "LLM_MODEL": "deepseek-chat"
36
+ }
37
+ }
38
+ }
39
+ }
40
+ ```
41
+
42
+ ### Supported Providers
43
+
44
+ | Provider | LLM_BASE_URL | LLM_MODEL |
45
+ |----------|--------------|-----------|
46
+ | **OpenAI** | `https://api.openai.com/v1` | `gpt-4o`, `o3` |
47
+ | **DeepSeek** | `https://api.deepseek.com/v1` | `deepseek-chat`, `deepseek-reasoner` |
48
+ | **MiniMax** | `https://api.minimax.io/v1` | `MiniMax-M3` |
49
+ | **Kimi (Moonshot)** | `https://api.moonshot.cn/v1` | `moonshot-v1-8k`, `moonshot-v1-32k` |
50
+ | **ZhiPu (GLM)** | `https://open.bigmodel.cn/api/paas/v4` | `glm-4`, `glm-4-plus` |
51
+ | **SiliconFlow** | `https://api.siliconflow.cn/v1` | `Qwen/Qwen2.5-72B-Instruct` |
52
+ | **阿里云百炼** | `https://dashscope.aliyuncs.com/compatible-mode/v1` | `qwen-max` |
53
+ | **零一万物** | `https://api.lingyiwanwu.com/v1` | `yi-large` |
54
+
55
+ ## API Call Method
56
+
57
+ **Primary: MCP Tool**
58
+
59
+ ```
60
+ mcp__llm-chat__chat:
61
+ message: |
62
+ [Review prompt content]
63
+ model: "deepseek-chat"
64
+ system: "You are a senior ML reviewer..."
65
+ ```
66
+
67
+ **Fallback: curl**
68
+
69
+ ```bash
70
+ curl -s "${LLM_BASE_URL}/chat/completions" \
71
+ -H "Content-Type: application/json" \
72
+ -H "Authorization: Bearer ${LLM_API_KEY}" \
73
+ -d '{
74
+ "model": "${LLM_MODEL}",
75
+ "messages": [
76
+ {"role": "system", "content": "You are a senior ML reviewer..."},
77
+ {"role": "user", "content": "[review prompt]"}
78
+ ],
79
+ "max_tokens": 4096
80
+ }'
81
+ ```
82
+
83
+ ## State Persistence (Compact Recovery)
84
+
85
+ Persist state to `review-stage/REVIEW_STATE.json` after each round:
86
+
87
+ ```json
88
+ {
89
+ "round": 2,
90
+ "status": "in_progress",
91
+ "last_score": 5.0,
92
+ "last_verdict": "not ready",
93
+ "pending_experiments": [],
94
+ "timestamp": "2026-03-15T10:00:00"
95
+ }
96
+ ```
97
+
98
+ **Write this file at the end of every Phase E** (after documenting the round).
99
+
100
+ **On completion**, set `"status": "completed"`.
101
+
102
+ ## Workflow
103
+
104
+ ### Initialization
105
+
106
+ 1. **Check `review-stage/REVIEW_STATE.json`** for recovery *(fall back to `./REVIEW_STATE.json` if not found — legacy path)*
107
+ 2. Read project context and prior reviews
108
+ 3. Initialize round counter
109
+
110
+ ### Loop (up to MAX_ROUNDS)
111
+
112
+ #### Phase A: Review
113
+
114
+ **If MCP available:**
115
+ ```
116
+ mcp__llm-chat__chat:
117
+ system: "You are a senior ML reviewer (NeurIPS/ICML level)."
118
+ message: |
119
+ [Round N/MAX_ROUNDS of autonomous review loop]
120
+
121
+ [Full research context: claims, methods, results, known weaknesses]
122
+ [Changes since last round, if any]
123
+
124
+ 1. Score this work 1-10 for a top venue
125
+ 2. List remaining critical weaknesses (ranked by severity)
126
+ 3. For each weakness, specify the MINIMUM fix
127
+ 4. State clearly: is this READY for submission? Yes/No/Almost
128
+
129
+ Be brutally honest. If the work is ready, say so clearly.
130
+ ```
131
+
132
+ **If MCP NOT available:**
133
+ ```bash
134
+ curl -s "${LLM_BASE_URL}/chat/completions" \
135
+ -H "Content-Type: application/json" \
136
+ -H "Authorization: Bearer ${LLM_API_KEY}" \
137
+ -d '{
138
+ "model": "${LLM_MODEL}",
139
+ "messages": [
140
+ {"role": "system", "content": "You are a senior ML reviewer (NeurIPS/ICML level)."},
141
+ {"role": "user", "content": "[Full review prompt]"}
142
+ ],
143
+ "max_tokens": 4096
144
+ }'
145
+ ```
146
+
147
+ #### Phase B: Parse Assessment
148
+
149
+ **CRITICAL: Save the FULL raw response** verbatim. Then extract:
150
+ - **Score** (numeric 1-10)
151
+ - **Verdict** ("ready" / "almost" / "not ready")
152
+ - **Action items** (ranked list of fixes)
153
+
154
+ **STOP**: If score >= 6 AND verdict ∈ {"ready", "almost"} (exact — "not ready" does NOT qualify)
155
+
156
+ #### Phase C: Implement Fixes
157
+
158
+ Priority: metric additions > reframing > new experiments
159
+
160
+ #### Phase D: Wait for Results
161
+
162
+ Monitor remote experiments
163
+
164
+ #### Phase E: Document Round
165
+
166
+ Append to `review-stage/AUTO_REVIEW.md`:
167
+
168
+ ```markdown
169
+ ## Round N (timestamp)
170
+
171
+ ### Assessment (Summary)
172
+ - Score: X/10
173
+ - Verdict: [ready/almost/not ready]
174
+ - Key criticisms: [bullet list]
175
+
176
+ ### Reviewer Raw Response
177
+
178
+ <details>
179
+ <summary>Click to expand full reviewer response</summary>
180
+
181
+ [Paste the COMPLETE raw response here — verbatim, unedited.]
182
+
183
+ </details>
184
+
185
+ ### Actions Taken
186
+ - [what was implemented/changed]
187
+
188
+ ### Results
189
+ - [experiment outcomes, if any]
190
+
191
+ ### Status
192
+ - [continuing to round N+1 / stopping]
193
+ ```
194
+
195
+ **Write `review-stage/REVIEW_STATE.json`** with current state.
196
+
197
+ ### Termination
198
+
199
+ 1. Set `review-stage/REVIEW_STATE.json` status to "completed"
200
+ 2. Write final summary
201
+
202
+ ## Key Rules
203
+
204
+ - **Large file handling**: If the Write tool fails due to file size, immediately retry using Bash (`cat << 'EOF' > file`) to write in chunks. Do NOT ask the user for permission — just do it silently.
205
+
206
+ - Be honest about weaknesses
207
+ - Implement fixes BEFORE re-reviewing
208
+ - Document everything
209
+ - Include previous context in round 2+ prompts
210
+ - Prefer MCP tool over curl when available
211
+
212
+ ## Prompt Template for Round 2+
213
+
214
+ ```
215
+ mcp__llm-chat__chat:
216
+ system: "You are a senior ML reviewer (NeurIPS/ICML level)."
217
+ message: |
218
+ [Round N/MAX_ROUNDS of autonomous review loop]
219
+
220
+ ## Previous Review Summary (Round N-1)
221
+ - Previous Score: X/10
222
+ - Previous Verdict: [ready/almost/not ready]
223
+ - Previous Key Weaknesses: [list]
224
+
225
+ ## Changes Since Last Review
226
+ 1. [Action 1]: [result]
227
+ 2. [Action 2]: [result]
228
+
229
+ ## Updated Results
230
+ [paste updated metrics/tables]
231
+
232
+ Please re-score and re-assess:
233
+ 1. Score this work 1-10 for a top venue
234
+ 2. List remaining critical weaknesses (ranked by severity)
235
+ 3. For each weakness, specify the MINIMUM fix
236
+ 4. State clearly: is this READY for submission? Yes/No/Almost
237
+
238
+ Be brutally honest. If the work is ready, say so clearly.
239
+ ```
240
+
241
+
242
+ ## Output Protocols
243
+
244
+ > Follow these shared protocols for all output files:
245
+ > - **[Output Versioning Protocol](../../shared-references/output-versioning.md)** — write timestamped file first, then copy to fixed name
246
+ > - **[Output Manifest Protocol](../../shared-references/output-manifest.md)** — log every output to MANIFEST.md
247
+ > - **[Output Language Protocol](../../shared-references/output-language.md)** — respect the project's language setting