@research-copilot/plugin 1.1.17 โ†’ 1.1.19

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 (800) hide show
  1. package/README.md +18 -9
  2. package/dist/.claude-plugin/plugin.json +1 -1
  3. package/dist/.codex-plugin/plugin.toml +1 -1
  4. package/dist/.cursor-plugin/plugin.json +1 -1
  5. package/dist/.gemini-plugin/plugin.json +1 -1
  6. package/dist/.opencode-plugin/plugin.json +1 -1
  7. package/dist/.windsurf-plugin/plugin.json +1 -1
  8. package/dist/skills/ablation-planner/SKILL.md +126 -0
  9. package/dist/skills/alphaxiv/SKILL.md +186 -0
  10. package/dist/skills/analyze-results/SKILL.md +45 -0
  11. package/dist/skills/arxiv/SKILL.md +210 -0
  12. package/dist/skills/auto-paper-improvement-loop/SKILL.md +574 -0
  13. package/dist/skills/auto-review-loop/SKILL.md +370 -0
  14. package/dist/skills/auto-review-loop-llm/SKILL.md +247 -0
  15. package/dist/skills/auto-review-loop-minimax/SKILL.md +290 -0
  16. package/dist/skills/benchmark-paper-template/SKILL.md +142 -0
  17. package/dist/skills/benchmark-paper-template/references/benchmark-design.md +180 -0
  18. package/dist/skills/benchmark-paper-template/references/checklist.md +113 -0
  19. package/dist/skills/benchmark-paper-template/references/construction-pipeline.md +127 -0
  20. package/dist/skills/benchmark-paper-template/references/experiments.md +159 -0
  21. package/dist/skills/benchmark-paper-template/references/gap-analysis.md +86 -0
  22. package/dist/skills/benchmark-paper-template/references/instantiation-template.md +194 -0
  23. package/dist/skills/benchmark-paper-template/references/orchestrator-notes.md +96 -0
  24. package/dist/skills/benchmark-paper-template/references/paper-structure.md +209 -0
  25. package/dist/skills/citation-audit/SKILL.md +494 -0
  26. package/dist/skills/claims-drafting/SKILL.md +239 -0
  27. package/dist/skills/comm-lit-review/SKILL.md +299 -0
  28. package/dist/skills/comm-lit-review/references/domain-taxonomy.md +57 -0
  29. package/dist/skills/comm-lit-review/references/output-template.md +37 -0
  30. package/dist/skills/comm-lit-review/references/source-policy.md +99 -0
  31. package/dist/skills/comm-lit-review/references/venue-tiering.md +112 -0
  32. package/dist/skills/composer/SKILL.md +840 -0
  33. package/dist/skills/composer/references/section_guides.md +675 -0
  34. package/dist/skills/composer/references/writing_standards.md +629 -0
  35. package/dist/skills/composer/scripts/chapter_quality_check.py +470 -0
  36. package/dist/skills/composer/scripts/final_evaluation.py +550 -0
  37. package/dist/skills/deepxiv/SKILL.md +142 -0
  38. package/dist/skills/dse-loop/SKILL.md +277 -0
  39. package/dist/skills/embodiment-description/SKILL.md +129 -0
  40. package/dist/skills/exa-search/SKILL.md +192 -0
  41. package/dist/skills/experiment-audit/SKILL.md +262 -0
  42. package/dist/skills/experiment-bridge/SKILL.md +316 -0
  43. package/dist/skills/experiment-plan/SKILL.md +249 -0
  44. package/dist/skills/experiment-queue/SKILL.md +380 -0
  45. package/dist/skills/experiment-queue/scripts/build_manifest.py +142 -0
  46. package/dist/skills/experiment-queue/scripts/queue_manager.py +426 -0
  47. package/dist/skills/feishu-notify/SKILL.md +155 -0
  48. package/dist/skills/figure-description/SKILL.md +138 -0
  49. package/dist/skills/figure-designer/SKILL.md +207 -0
  50. package/dist/skills/figure-designer/references/design-rules.md +99 -0
  51. package/dist/skills/figure-designer/references/experimental-results.md +127 -0
  52. package/dist/skills/figure-designer/references/motivated-example.md +138 -0
  53. package/dist/skills/figure-designer/references/solution-overview.md +145 -0
  54. package/dist/skills/figure-designer/references/tools.md +124 -0
  55. package/dist/skills/figure-spec/SKILL.md +252 -0
  56. package/dist/skills/figure-spec/scripts/figure_renderer.py +799 -0
  57. package/dist/skills/formula-derivation/SKILL.md +280 -0
  58. package/dist/skills/gemini-search/SKILL.md +205 -0
  59. package/dist/skills/grant-proposal/SKILL.md +625 -0
  60. package/dist/skills/humanizer/AGENTS.md +25 -0
  61. package/dist/skills/humanizer/SKILL.md +621 -0
  62. package/dist/skills/idea-creator/SKILL.md +311 -0
  63. package/dist/skills/idea-discovery/SKILL.md +340 -0
  64. package/dist/skills/idea-discovery-robot/SKILL.md +362 -0
  65. package/dist/skills/idea-evaluator/SKILL.md +265 -0
  66. package/dist/skills/idea-evaluator/references/fatal-flaws.md +192 -0
  67. package/dist/skills/idea-evaluator/references/five-dimensions.md +251 -0
  68. package/dist/skills/idea-evaluator/references/lifecycle-capability-matching.md +177 -0
  69. package/dist/skills/idea-evaluator/references/paradigm-elephant.md +112 -0
  70. package/dist/skills/idea-evaluator/references/paradigm-examples.md +107 -0
  71. package/dist/skills/idea-evaluator/references/paradigm-first-principles.md +115 -0
  72. package/dist/skills/idea-evaluator/references/paradigm-hamming.md +137 -0
  73. package/dist/skills/idea-evaluator/references/paradigm-shift-probe.md +160 -0
  74. package/dist/skills/idea-evaluator/references/paradigm-technology-cycle.md +116 -0
  75. package/dist/skills/idea-evaluator/references/worked-examples.md +206 -0
  76. package/dist/skills/interview-cheatsheet/SKILL.md +245 -0
  77. package/dist/skills/intro-drafter/SKILL.md +250 -0
  78. package/dist/skills/intro-drafter/references/contribution-patterns.md +116 -0
  79. package/dist/skills/intro-drafter/references/flowchart.md +204 -0
  80. package/dist/skills/intro-drafter/references/paper-types.md +155 -0
  81. package/dist/skills/intro-drafter/references/running-example.md +133 -0
  82. package/dist/skills/intro-drafter/references/worked-examples.md +161 -0
  83. package/dist/skills/invention-structuring/SKILL.md +188 -0
  84. package/dist/skills/jurisdiction-format/SKILL.md +192 -0
  85. package/dist/skills/kill-argument/SKILL.md +384 -0
  86. package/dist/skills/llm-wiki/.mise.toml +2 -0
  87. package/dist/skills/llm-wiki/.nvmrc +1 -0
  88. package/dist/skills/llm-wiki/AGENTS.md +132 -0
  89. package/dist/skills/llm-wiki/CHANGELOG.md +459 -0
  90. package/dist/skills/llm-wiki/CLAUDE.md +109 -0
  91. package/dist/skills/llm-wiki/HERMES.md +44 -0
  92. package/dist/skills/llm-wiki/SKILL.md +1133 -0
  93. package/dist/skills/llm-wiki/assets/graph-demo.gif +0 -0
  94. package/dist/skills/llm-wiki/assets/graph-preview.png +0 -0
  95. package/dist/skills/llm-wiki/deps/LICENSE-d3.txt +13 -0
  96. package/dist/skills/llm-wiki/deps/LICENSE-marked.txt +44 -0
  97. package/dist/skills/llm-wiki/deps/LICENSE-purify.txt +568 -0
  98. package/{LICENSE โ†’ dist/skills/llm-wiki/deps/LICENSE-roughjs.txt} +1 -1
  99. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/SKILL.md +261 -0
  100. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/references/config/first-time-setup.md +106 -0
  101. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/cdp.ts +179 -0
  102. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/constants.ts +13 -0
  103. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/defuddle-converter.ts +58 -0
  104. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/html-to-markdown.ts +135 -0
  105. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/legacy-converter.ts +629 -0
  106. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/main.ts +314 -0
  107. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/markdown-conversion-shared.ts +305 -0
  108. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/media-localizer.ts +317 -0
  109. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/package.json +14 -0
  110. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/paths.ts +29 -0
  111. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/vendor/baoyu-chrome-cdp/package.json +9 -0
  112. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/vendor/baoyu-chrome-cdp/src/index.test.ts +307 -0
  113. package/dist/skills/llm-wiki/deps/baoyu-url-to-markdown/scripts/vendor/baoyu-chrome-cdp/src/index.ts +523 -0
  114. package/dist/skills/llm-wiki/deps/d3.min.js +2 -0
  115. package/dist/skills/llm-wiki/deps/marked.min.js +6 -0
  116. package/dist/skills/llm-wiki/deps/purify.min.js +3 -0
  117. package/dist/skills/llm-wiki/deps/rough.min.js +7 -0
  118. package/dist/skills/llm-wiki/deps/youtube-transcript/SKILL.md +47 -0
  119. package/dist/skills/llm-wiki/deps/youtube-transcript/scripts/get_transcript.py +72 -0
  120. package/dist/skills/llm-wiki/docs/design/oriental-atlas/DESIGN.md +183 -0
  121. package/dist/skills/llm-wiki/docs/design/oriental-atlas/design-brief.md +170 -0
  122. package/dist/skills/llm-wiki/docs/design/oriental-atlas/oriental-editorial-atlas.html +1908 -0
  123. package/dist/skills/llm-wiki/docs/design/oriental-atlas/reviews/result-review.md +68 -0
  124. package/dist/skills/llm-wiki/docs/plans/2026-06-15-omp-tool-status-events-phased-plan.md +655 -0
  125. package/dist/skills/llm-wiki/docs/plans/2026-06-15-omp-tool-status-events-progress.json +913 -0
  126. package/dist/skills/llm-wiki/docs/spark/2026-06-15-omp-tool-status-events-design.md +174 -0
  127. package/dist/skills/llm-wiki/install.ps1 +87 -0
  128. package/dist/skills/llm-wiki/install.sh +722 -0
  129. package/dist/skills/llm-wiki/package-lock.json +10309 -0
  130. package/dist/skills/llm-wiki/package.json +24 -0
  131. package/dist/skills/llm-wiki/packages/graph-engine/package.json +33 -0
  132. package/dist/skills/llm-wiki/packages/graph-engine/src/anim/.gitkeep +1 -0
  133. package/dist/skills/llm-wiki/packages/graph-engine/src/anim/index.ts +179 -0
  134. package/dist/skills/llm-wiki/packages/graph-engine/src/diff.ts +121 -0
  135. package/dist/skills/llm-wiki/packages/graph-engine/src/graph-node.ts +37 -0
  136. package/dist/skills/llm-wiki/packages/graph-engine/src/index.ts +140 -0
  137. package/dist/skills/llm-wiki/packages/graph-engine/src/model/atlas.ts +18 -0
  138. package/dist/skills/llm-wiki/packages/graph-engine/src/model/index.ts +6 -0
  139. package/dist/skills/llm-wiki/packages/graph-engine/src/model/labels.ts +11 -0
  140. package/dist/skills/llm-wiki/packages/graph-engine/src/model/learning.ts +8 -0
  141. package/dist/skills/llm-wiki/packages/graph-engine/src/model/legacy-helpers.ts +1373 -0
  142. package/dist/skills/llm-wiki/packages/graph-engine/src/model/queue.ts +7 -0
  143. package/dist/skills/llm-wiki/packages/graph-engine/src/model/storage.ts +4 -0
  144. package/dist/skills/llm-wiki/packages/graph-engine/src/model/visibility.ts +9 -0
  145. package/dist/skills/llm-wiki/packages/graph-engine/src/render/.gitkeep +1 -0
  146. package/dist/skills/llm-wiki/packages/graph-engine/src/render/index.ts +59 -0
  147. package/dist/skills/llm-wiki/packages/graph-engine/src/render/legend.ts +25 -0
  148. package/dist/skills/llm-wiki/packages/graph-engine/src/render/model.ts +593 -0
  149. package/dist/skills/llm-wiki/packages/graph-engine/src/render/preview.ts +65 -0
  150. package/dist/skills/llm-wiki/packages/graph-engine/src/render/search.ts +48 -0
  151. package/dist/skills/llm-wiki/packages/graph-engine/src/render/static-renderer.ts +2783 -0
  152. package/dist/skills/llm-wiki/packages/graph-engine/src/render/toolbar.ts +40 -0
  153. package/dist/skills/llm-wiki/packages/graph-engine/src/render/viewport.ts +272 -0
  154. package/dist/skills/llm-wiki/packages/graph-engine/src/select/.gitkeep +1 -0
  155. package/dist/skills/llm-wiki/packages/graph-engine/src/select/index.ts +189 -0
  156. package/dist/skills/llm-wiki/packages/graph-engine/src/sim/index.ts +298 -0
  157. package/dist/skills/llm-wiki/packages/graph-engine/src/sim/pins.ts +96 -0
  158. package/dist/skills/llm-wiki/packages/graph-engine/src/themes/.gitkeep +1 -0
  159. package/dist/skills/llm-wiki/packages/graph-engine/src/themes/index.ts +8 -0
  160. package/dist/skills/llm-wiki/packages/graph-engine/src/themes/tokens.ts +107 -0
  161. package/dist/skills/llm-wiki/packages/graph-engine/src/types.ts +313 -0
  162. package/dist/skills/llm-wiki/packages/graph-engine/test/anim.test.ts +100 -0
  163. package/dist/skills/llm-wiki/packages/graph-engine/test/diff.test.ts +133 -0
  164. package/dist/skills/llm-wiki/packages/graph-engine/test/helpers.test.ts +275 -0
  165. package/dist/skills/llm-wiki/packages/graph-engine/test/learning.test.ts +259 -0
  166. package/dist/skills/llm-wiki/packages/graph-engine/test/preview.test.ts +56 -0
  167. package/dist/skills/llm-wiki/packages/graph-engine/test/queue.test.ts +114 -0
  168. package/dist/skills/llm-wiki/packages/graph-engine/test/render-model.test.ts +322 -0
  169. package/dist/skills/llm-wiki/packages/graph-engine/test/runtime-state.test.ts +281 -0
  170. package/dist/skills/llm-wiki/packages/graph-engine/test/search-and-legend.test.ts +111 -0
  171. package/dist/skills/llm-wiki/packages/graph-engine/test/select.test.ts +168 -0
  172. package/dist/skills/llm-wiki/packages/graph-engine/test/sim.test.ts +123 -0
  173. package/dist/skills/llm-wiki/packages/graph-engine/test/themes.test.ts +62 -0
  174. package/dist/skills/llm-wiki/packages/graph-engine/test/toolbar.test.ts +64 -0
  175. package/dist/skills/llm-wiki/packages/graph-engine/test/viewport.test.ts +167 -0
  176. package/dist/skills/llm-wiki/packages/graph-engine/tsconfig.json +17 -0
  177. package/dist/skills/llm-wiki/packages/graph-engine/vite.config.ts +15 -0
  178. package/dist/skills/llm-wiki/platforms/claude/CLAUDE.md +37 -0
  179. package/dist/skills/llm-wiki/platforms/claude/companions/llm-wiki-upgrade/SKILL.md +95 -0
  180. package/dist/skills/llm-wiki/platforms/codex/AGENTS.md +23 -0
  181. package/dist/skills/llm-wiki/scripts/adapter-state.sh +424 -0
  182. package/dist/skills/llm-wiki/scripts/build-graph-data.sh +395 -0
  183. package/dist/skills/llm-wiki/scripts/build-graph-html.sh +453 -0
  184. package/dist/skills/llm-wiki/scripts/cache.sh +352 -0
  185. package/dist/skills/llm-wiki/scripts/create-source-page.sh +100 -0
  186. package/dist/skills/llm-wiki/scripts/delete-helper.sh +68 -0
  187. package/dist/skills/llm-wiki/scripts/graph-analysis.js +732 -0
  188. package/dist/skills/llm-wiki/scripts/hook-session-start.sh +46 -0
  189. package/dist/skills/llm-wiki/scripts/init-wiki.sh +95 -0
  190. package/dist/skills/llm-wiki/scripts/lib/source-signal-eligibility.js +158 -0
  191. package/dist/skills/llm-wiki/scripts/lint-fix.sh +114 -0
  192. package/dist/skills/llm-wiki/scripts/lint-runner.sh +217 -0
  193. package/dist/skills/llm-wiki/scripts/runtime-context.sh +77 -0
  194. package/dist/skills/llm-wiki/scripts/shared-config.sh +83 -0
  195. package/dist/skills/llm-wiki/scripts/source-record-contract.tsv +10 -0
  196. package/dist/skills/llm-wiki/scripts/source-registry.sh +349 -0
  197. package/dist/skills/llm-wiki/scripts/source-registry.tsv +10 -0
  198. package/dist/skills/llm-wiki/scripts/source-signal-coverage.js +83 -0
  199. package/dist/skills/llm-wiki/scripts/validate-step1.sh +144 -0
  200. package/dist/skills/llm-wiki/scripts/wiki-compat.sh +267 -0
  201. package/dist/skills/llm-wiki/setup.sh +8 -0
  202. package/dist/skills/llm-wiki/templates/entity-template.md +30 -0
  203. package/dist/skills/llm-wiki/templates/graph-styles/wash/footer.html +27 -0
  204. package/dist/skills/llm-wiki/templates/graph-styles/wash/graph-wash-helpers.js +1326 -0
  205. package/dist/skills/llm-wiki/templates/graph-styles/wash/graph-wash.js +1009 -0
  206. package/dist/skills/llm-wiki/templates/graph-styles/wash/header.html +2002 -0
  207. package/dist/skills/llm-wiki/templates/index-en-template.md +51 -0
  208. package/dist/skills/llm-wiki/templates/index-template.md +51 -0
  209. package/dist/skills/llm-wiki/templates/log-en-template.md +11 -0
  210. package/dist/skills/llm-wiki/templates/log-template.md +11 -0
  211. package/dist/skills/llm-wiki/templates/overview-en-template.md +41 -0
  212. package/dist/skills/llm-wiki/templates/overview-template.md +41 -0
  213. package/dist/skills/llm-wiki/templates/purpose-en-template.md +16 -0
  214. package/dist/skills/llm-wiki/templates/purpose-template.md +16 -0
  215. package/dist/skills/llm-wiki/templates/query-template.md +19 -0
  216. package/dist/skills/llm-wiki/templates/schema-template.md +185 -0
  217. package/dist/skills/llm-wiki/templates/source-template.md +51 -0
  218. package/dist/skills/llm-wiki/templates/synthesis-template.md +25 -0
  219. package/dist/skills/llm-wiki/templates/topic-template.md +35 -0
  220. package/dist/skills/llm-wiki/tests/adapter-state.sh +338 -0
  221. package/dist/skills/llm-wiki/tests/browser/graph-density-preview.mjs +53 -0
  222. package/dist/skills/llm-wiki/tests/browser/graph-html-insights.mjs +41 -0
  223. package/dist/skills/llm-wiki/tests/browser/graph-node-slim.mjs +71 -0
  224. package/dist/skills/llm-wiki/tests/browser/graph-stage-4-5.mjs +717 -0
  225. package/dist/skills/llm-wiki/tests/expected/graph-data-empty.json +60 -0
  226. package/dist/skills/llm-wiki/tests/expected/graph-data-sample.json +396 -0
  227. package/dist/skills/llm-wiki/tests/expected/graph-interactive-basic.html +1736 -0
  228. package/dist/skills/llm-wiki/tests/expected/lint-output.txt +44 -0
  229. package/dist/skills/llm-wiki/tests/fixtures/coverage-sample-wiki/index.md +1 -0
  230. package/dist/skills/llm-wiki/tests/fixtures/coverage-sample-wiki/wiki/entities/Alpha.md +10 -0
  231. package/dist/skills/llm-wiki/tests/fixtures/coverage-sample-wiki/wiki/entities/Beta.md +7 -0
  232. package/dist/skills/llm-wiki/tests/fixtures/coverage-sample-wiki/wiki/entities/Delta.md +8 -0
  233. package/dist/skills/llm-wiki/tests/fixtures/coverage-sample-wiki/wiki/entities/Gamma.md +8 -0
  234. package/dist/skills/llm-wiki/tests/fixtures/coverage-sample-wiki/wiki/queries/20260422-abc.md +10 -0
  235. package/dist/skills/llm-wiki/tests/fixtures/coverage-sample-wiki/wiki/synthesis/Crystal.md +8 -0
  236. package/dist/skills/llm-wiki/tests/fixtures/coverage-sample-wiki/wiki/topics/Overview.md +9 -0
  237. package/dist/skills/llm-wiki/tests/fixtures/graph-data-empty-wiki/wiki/entities/.gitkeep +0 -0
  238. package/dist/skills/llm-wiki/tests/fixtures/graph-data-sample-wiki/purpose.md +3 -0
  239. package/dist/skills/llm-wiki/tests/fixtures/graph-data-sample-wiki/wiki/entities/Attention.md +7 -0
  240. package/dist/skills/llm-wiki/tests/fixtures/graph-data-sample-wiki/wiki/entities/Decoder.md +7 -0
  241. package/dist/skills/llm-wiki/tests/fixtures/graph-data-sample-wiki/wiki/entities/Encoder.md +7 -0
  242. package/dist/skills/llm-wiki/tests/fixtures/graph-data-sample-wiki/wiki/entities/GPT.md +7 -0
  243. package/dist/skills/llm-wiki/tests/fixtures/graph-data-sample-wiki/wiki/entities/Transformer.md +13 -0
  244. package/dist/skills/llm-wiki/tests/fixtures/graph-data-sample-wiki/wiki/sources/paper.md +9 -0
  245. package/dist/skills/llm-wiki/tests/fixtures/graph-data-sample-wiki/wiki/topics/arch.md +12 -0
  246. package/dist/skills/llm-wiki/tests/fixtures/graph-data-sample-wiki/wiki/topics/finetune.md +9 -0
  247. package/dist/skills/llm-wiki/tests/fixtures/graph-interactive-basic/wiki/graph-data.json +40 -0
  248. package/dist/skills/llm-wiki/tests/fixtures/graph-interactive-dense/wiki/graph-data.json +3965 -0
  249. package/dist/skills/llm-wiki/tests/fixtures/graph-interactive-multicomm/wiki/graph-data.json +212 -0
  250. package/dist/skills/llm-wiki/tests/fixtures/lint-sample-wiki/index.md +14 -0
  251. package/dist/skills/llm-wiki/tests/fixtures/lint-sample-wiki/wiki/entities/C++.md +6 -0
  252. package/dist/skills/llm-wiki/tests/fixtures/lint-sample-wiki/wiki/entities/Lonely.md +4 -0
  253. package/dist/skills/llm-wiki/tests/fixtures/lint-sample-wiki/wiki/entities/Other.md +8 -0
  254. package/dist/skills/llm-wiki/tests/fixtures/lint-sample-wiki/wiki/entities/Real.md +7 -0
  255. package/dist/skills/llm-wiki/tests/fixtures/lint-sample-wiki/wiki/sources/2026-01-01-test-source.md +15 -0
  256. package/dist/skills/llm-wiki/tests/fixtures/lint-sample-wiki/wiki/sources/2026-02-01-inline-img.md +12 -0
  257. package/dist/skills/llm-wiki/tests/fixtures/lint-sample-wiki/wiki/topics/AIbasic.md +3 -0
  258. package/dist/skills/llm-wiki/tests/graph-analysis-helper.regression-1.sh +237 -0
  259. package/dist/skills/llm-wiki/tests/graph-browser-stage-4-5.regression-1.sh +157 -0
  260. package/dist/skills/llm-wiki/tests/graph-build-failures.regression-1.sh +91 -0
  261. package/dist/skills/llm-wiki/tests/graph-data-confidence-merge.regression-1.sh +309 -0
  262. package/dist/skills/llm-wiki/tests/graph-data-source-paths.regression-1.sh +49 -0
  263. package/dist/skills/llm-wiki/tests/graph-html-a11y.regression-1.sh +47 -0
  264. package/dist/skills/llm-wiki/tests/graph-html-brand-link.regression-1.sh +47 -0
  265. package/dist/skills/llm-wiki/tests/graph-html-density.regression-1.sh +228 -0
  266. package/dist/skills/llm-wiki/tests/graph-html-drawer-neighbors.regression-1.sh +47 -0
  267. package/dist/skills/llm-wiki/tests/graph-html-insights.regression-1.sh +80 -0
  268. package/dist/skills/llm-wiki/tests/graph-html-long-label.regression-1.sh +92 -0
  269. package/dist/skills/llm-wiki/tests/graph-html-minimap.regression-1.sh +51 -0
  270. package/dist/skills/llm-wiki/tests/graph-html-mobile.regression-1.sh +48 -0
  271. package/dist/skills/llm-wiki/tests/graph-html-oriental-atlas-contract.regression-1.sh +94 -0
  272. package/dist/skills/llm-wiki/tests/graph-html-oriental-design-contract.regression-1.sh +82 -0
  273. package/dist/skills/llm-wiki/tests/graph-html-search.regression-1.sh +52 -0
  274. package/dist/skills/llm-wiki/tests/graph-html-styles.regression-1.sh +66 -0
  275. package/dist/skills/llm-wiki/tests/graph-html-toolbar.regression-1.sh +62 -0
  276. package/dist/skills/llm-wiki/tests/js/graph-wash-bootstrap.test.js +110 -0
  277. package/dist/skills/llm-wiki/tests/js/graph-wash-helpers.test.js +296 -0
  278. package/dist/skills/llm-wiki/tests/js/graph-wash-learning.test.js +260 -0
  279. package/dist/skills/llm-wiki/tests/js/graph-wash-queue.test.js +115 -0
  280. package/dist/skills/llm-wiki/tests/js/graph-wash-runtime-state.test.js +282 -0
  281. package/dist/skills/llm-wiki/tests/js/source-signal-coverage.test.js +48 -0
  282. package/dist/skills/llm-wiki/tests/js/source-signal-eligibility.test.js +202 -0
  283. package/dist/skills/llm-wiki/tests/lib/graph-html-engine-helpers.sh +110 -0
  284. package/dist/skills/llm-wiki/tests/lint-output.regression-1.sh +32 -0
  285. package/dist/skills/llm-wiki/tests/regression.sh +1754 -0
  286. package/dist/skills/llm-wiki/workbench/.claude/skills/.gitkeep +0 -0
  287. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/SKILL.md +590 -0
  288. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/__init__.py +1 -0
  289. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/accept_changes.py +135 -0
  290. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/comment.py +318 -0
  291. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/helpers/__init__.py +0 -0
  292. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/helpers/merge_runs.py +199 -0
  293. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/helpers/simplify_redlines.py +197 -0
  294. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/pack.py +159 -0
  295. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  296. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  297. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  298. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  299. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  300. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  301. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  302. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  303. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  304. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  305. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  306. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  307. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  308. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  309. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  310. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  311. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  312. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  313. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  314. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  315. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  316. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  317. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  318. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  319. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  320. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  321. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  322. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  323. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  324. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  325. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  326. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/mce/mc.xsd +75 -0
  327. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
  328. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
  329. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
  330. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
  331. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
  332. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  333. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
  334. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/soffice.py +183 -0
  335. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/unpack.py +132 -0
  336. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/validate.py +111 -0
  337. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/validators/__init__.py +15 -0
  338. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/validators/base.py +847 -0
  339. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/validators/docx.py +446 -0
  340. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/validators/pptx.py +275 -0
  341. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/office/validators/redlining.py +247 -0
  342. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/templates/comments.xml +3 -0
  343. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/templates/commentsExtended.xml +3 -0
  344. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  345. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/templates/commentsIds.xml +3 -0
  346. package/dist/skills/llm-wiki/workbench/.claude/skills/docx/scripts/templates/people.xml +3 -0
  347. package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/SKILL.md +314 -0
  348. package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/forms.md +294 -0
  349. package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/reference.md +612 -0
  350. package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/scripts/check_bounding_boxes.py +65 -0
  351. package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/scripts/check_fillable_fields.py +11 -0
  352. package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/scripts/convert_pdf_to_images.py +33 -0
  353. package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/scripts/create_validation_image.py +37 -0
  354. package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/scripts/extract_form_field_info.py +122 -0
  355. package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/scripts/extract_form_structure.py +115 -0
  356. package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/scripts/fill_fillable_fields.py +98 -0
  357. package/dist/skills/llm-wiki/workbench/.claude/skills/pdf/scripts/fill_pdf_form_with_annotations.py +107 -0
  358. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/SKILL.md +232 -0
  359. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/editing.md +205 -0
  360. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/pptxgenjs.md +420 -0
  361. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/__init__.py +0 -0
  362. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/add_slide.py +195 -0
  363. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/clean.py +286 -0
  364. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/helpers/__init__.py +0 -0
  365. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/helpers/merge_runs.py +199 -0
  366. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/helpers/simplify_redlines.py +197 -0
  367. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/pack.py +159 -0
  368. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  369. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  370. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  371. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  372. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  373. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  374. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  375. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  376. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  377. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  378. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  379. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  380. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  381. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  382. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  383. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  384. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  385. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  386. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  387. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  388. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  389. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  390. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  391. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  392. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  393. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  394. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  395. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  396. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  397. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  398. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  399. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/mce/mc.xsd +75 -0
  400. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
  401. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
  402. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
  403. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
  404. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
  405. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  406. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
  407. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/soffice.py +183 -0
  408. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/unpack.py +132 -0
  409. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/validate.py +111 -0
  410. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/validators/__init__.py +15 -0
  411. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/validators/base.py +847 -0
  412. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/validators/docx.py +446 -0
  413. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/validators/pptx.py +275 -0
  414. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/office/validators/redlining.py +247 -0
  415. package/dist/skills/llm-wiki/workbench/.claude/skills/pptx/scripts/thumbnail.py +289 -0
  416. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/SKILL.md +292 -0
  417. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/helpers/__init__.py +0 -0
  418. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/helpers/merge_runs.py +199 -0
  419. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/helpers/simplify_redlines.py +197 -0
  420. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/pack.py +159 -0
  421. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  422. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  423. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  424. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  425. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  426. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  427. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  428. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  429. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  430. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  431. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  432. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  433. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  434. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  435. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  436. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  437. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  438. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  439. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  440. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  441. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  442. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  443. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  444. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  445. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  446. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  447. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  448. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  449. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  450. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  451. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  452. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/mce/mc.xsd +75 -0
  453. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
  454. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
  455. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
  456. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
  457. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
  458. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  459. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
  460. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/soffice.py +183 -0
  461. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/unpack.py +132 -0
  462. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/validate.py +111 -0
  463. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/validators/__init__.py +15 -0
  464. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/validators/base.py +847 -0
  465. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/validators/docx.py +446 -0
  466. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/validators/pptx.py +275 -0
  467. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/office/validators/redlining.py +247 -0
  468. package/dist/skills/llm-wiki/workbench/.claude/skills/xlsx/scripts/recalc.py +184 -0
  469. package/dist/skills/llm-wiki/workbench/AGENTS.md +110 -0
  470. package/dist/skills/llm-wiki/workbench/CLAUDE.md +54 -0
  471. package/dist/skills/llm-wiki/workbench/PRODUCT.md +1268 -0
  472. package/dist/skills/llm-wiki/workbench/docs/current-kb-retrieval-design.md +587 -0
  473. package/dist/skills/llm-wiki/workbench/docs/graph-evolution-1-design.md +210 -0
  474. package/dist/skills/llm-wiki/workbench/docs/stage-2-design.md +1139 -0
  475. package/dist/skills/llm-wiki/workbench/docs/stage-3-design.md +1269 -0
  476. package/dist/skills/llm-wiki/workbench/docs/stage-3.5-design.md +1164 -0
  477. package/dist/skills/llm-wiki/workbench/docs/stage-4-design.md +504 -0
  478. package/dist/skills/llm-wiki/workbench/docs/stage-4.5-design.md +195 -0
  479. package/dist/skills/llm-wiki/workbench/docs/superpowers/specs/2026-05-28-resizable-preview-layout-design.md +165 -0
  480. package/dist/skills/llm-wiki/workbench/docs/superpowers/specs/2026-05-28-settings-panel-scroll-fix.md +50 -0
  481. package/dist/skills/llm-wiki/workbench/server/package.json +29 -0
  482. package/dist/skills/llm-wiki/workbench/server/src/agent.ts +457 -0
  483. package/dist/skills/llm-wiki/workbench/server/src/artifacts.ts +248 -0
  484. package/dist/skills/llm-wiki/workbench/server/src/auth.ts +164 -0
  485. package/dist/skills/llm-wiki/workbench/server/src/config.ts +130 -0
  486. package/dist/skills/llm-wiki/workbench/server/src/conversations.test.ts +121 -0
  487. package/dist/skills/llm-wiki/workbench/server/src/conversations.ts +255 -0
  488. package/dist/skills/llm-wiki/workbench/server/src/digest/batch.ts +189 -0
  489. package/dist/skills/llm-wiki/workbench/server/src/digest/concurrency.test.ts +36 -0
  490. package/dist/skills/llm-wiki/workbench/server/src/digest/concurrency.ts +31 -0
  491. package/dist/skills/llm-wiki/workbench/server/src/digest/subagent.ts +91 -0
  492. package/dist/skills/llm-wiki/workbench/server/src/extensions/artifacts.ts +81 -0
  493. package/dist/skills/llm-wiki/workbench/server/src/extensions/knowledge-base.ts +263 -0
  494. package/dist/skills/llm-wiki/workbench/server/src/extensions/new-wiki.ts +42 -0
  495. package/dist/skills/llm-wiki/workbench/server/src/extensions/synthesis.ts +172 -0
  496. package/dist/skills/llm-wiki/workbench/server/src/graph-watcher.test.ts +196 -0
  497. package/dist/skills/llm-wiki/workbench/server/src/graph.test.ts +84 -0
  498. package/dist/skills/llm-wiki/workbench/server/src/graph.ts +379 -0
  499. package/dist/skills/llm-wiki/workbench/server/src/index.ts +1148 -0
  500. package/dist/skills/llm-wiki/workbench/server/src/knowledge-bases.test.ts +30 -0
  501. package/dist/skills/llm-wiki/workbench/server/src/knowledge-bases.ts +321 -0
  502. package/dist/skills/llm-wiki/workbench/server/src/pages.test.ts +16 -0
  503. package/dist/skills/llm-wiki/workbench/server/src/pages.ts +158 -0
  504. package/dist/skills/llm-wiki/workbench/server/src/retrieval.test.ts +151 -0
  505. package/dist/skills/llm-wiki/workbench/server/src/retrieval.ts +427 -0
  506. package/dist/skills/llm-wiki/workbench/server/src/tool-status-events.test.ts +363 -0
  507. package/dist/skills/llm-wiki/workbench/server/src/tool-status-events.ts +616 -0
  508. package/dist/skills/llm-wiki/workbench/server/src/wiki-init.test.ts +19 -0
  509. package/dist/skills/llm-wiki/workbench/server/src/wiki-init.ts +188 -0
  510. package/dist/skills/llm-wiki/workbench/server/tsconfig.json +10 -0
  511. package/dist/skills/llm-wiki/workbench/tsconfig.json +20 -0
  512. package/dist/skills/llm-wiki/workbench/web/components.json +21 -0
  513. package/dist/skills/llm-wiki/workbench/web/eslint.config.js +22 -0
  514. package/dist/skills/llm-wiki/workbench/web/index.html +13 -0
  515. package/dist/skills/llm-wiki/workbench/web/package.json +48 -0
  516. package/dist/skills/llm-wiki/workbench/web/src/App.tsx +749 -0
  517. package/dist/skills/llm-wiki/workbench/web/src/components/AddExternalDialog.tsx +373 -0
  518. package/dist/skills/llm-wiki/workbench/web/src/components/ArtifactView.tsx +15 -0
  519. package/dist/skills/llm-wiki/workbench/web/src/components/BatchDigestPanel.tsx +106 -0
  520. package/dist/skills/llm-wiki/workbench/web/src/components/ChatPanel.tsx +821 -0
  521. package/dist/skills/llm-wiki/workbench/web/src/components/CommandMenu.tsx +65 -0
  522. package/dist/skills/llm-wiki/workbench/web/src/components/ExportButtons.tsx +54 -0
  523. package/dist/skills/llm-wiki/workbench/web/src/components/GraphPanel.tsx +516 -0
  524. package/dist/skills/llm-wiki/workbench/web/src/components/GraphReader.tsx +48 -0
  525. package/dist/skills/llm-wiki/workbench/web/src/components/GraphSelection.tsx +100 -0
  526. package/dist/skills/llm-wiki/workbench/web/src/components/MarkdownView.tsx +56 -0
  527. package/dist/skills/llm-wiki/workbench/web/src/components/NewWikiDialog.tsx +101 -0
  528. package/dist/skills/llm-wiki/workbench/web/src/components/RefMenu.tsx +40 -0
  529. package/dist/skills/llm-wiki/workbench/web/src/components/RightDrawer.tsx +227 -0
  530. package/dist/skills/llm-wiki/workbench/web/src/components/SettingsPanel.tsx +331 -0
  531. package/dist/skills/llm-wiki/workbench/web/src/components/Sidebar.tsx +436 -0
  532. package/dist/skills/llm-wiki/workbench/web/src/components/ToolHistorySummary.tsx +123 -0
  533. package/dist/skills/llm-wiki/workbench/web/src/components/ToolStatusRunway.tsx +90 -0
  534. package/dist/skills/llm-wiki/workbench/web/src/components/renderers/DownloadOnlyRenderer.tsx +88 -0
  535. package/dist/skills/llm-wiki/workbench/web/src/components/renderers/HtmlRenderer.tsx +92 -0
  536. package/dist/skills/llm-wiki/workbench/web/src/components/ui/button.tsx +52 -0
  537. package/dist/skills/llm-wiki/workbench/web/src/components/ui/command.tsx +50 -0
  538. package/dist/skills/llm-wiki/workbench/web/src/components/ui/dialog.tsx +156 -0
  539. package/dist/skills/llm-wiki/workbench/web/src/components/ui/input.tsx +21 -0
  540. package/dist/skills/llm-wiki/workbench/web/src/components/ui/tooltip.tsx +57 -0
  541. package/dist/skills/llm-wiki/workbench/web/src/index.css +1737 -0
  542. package/dist/skills/llm-wiki/workbench/web/src/lib/api.ts +648 -0
  543. package/dist/skills/llm-wiki/workbench/web/src/lib/drawer-state.ts +79 -0
  544. package/dist/skills/llm-wiki/workbench/web/src/lib/graph-reader.ts +25 -0
  545. package/dist/skills/llm-wiki/workbench/web/src/lib/graph-selection-drawer.ts +35 -0
  546. package/dist/skills/llm-wiki/workbench/web/src/lib/graph-selection.ts +96 -0
  547. package/dist/skills/llm-wiki/workbench/web/src/lib/legacy-tool-status.ts +113 -0
  548. package/dist/skills/llm-wiki/workbench/web/src/lib/sse.ts +72 -0
  549. package/dist/skills/llm-wiki/workbench/web/src/lib/tool-status-format.ts +170 -0
  550. package/dist/skills/llm-wiki/workbench/web/src/lib/tool-status-model.ts +392 -0
  551. package/dist/skills/llm-wiki/workbench/web/src/lib/utils.ts +10 -0
  552. package/dist/skills/llm-wiki/workbench/web/src/lib/wiki-links.ts +32 -0
  553. package/dist/skills/llm-wiki/workbench/web/src/main.tsx +10 -0
  554. package/dist/skills/llm-wiki/workbench/web/test/api.test.ts +61 -0
  555. package/dist/skills/llm-wiki/workbench/web/test/chat-panel-tool-status.test.tsx +26 -0
  556. package/dist/skills/llm-wiki/workbench/web/test/graph-drawer-state.test.ts +78 -0
  557. package/dist/skills/llm-wiki/workbench/web/test/graph-reader-request.test.ts +32 -0
  558. package/dist/skills/llm-wiki/workbench/web/test/graph-reader.test.ts +62 -0
  559. package/dist/skills/llm-wiki/workbench/web/test/graph-selection-drawer.test.ts +56 -0
  560. package/dist/skills/llm-wiki/workbench/web/test/graph-selection.test.ts +83 -0
  561. package/dist/skills/llm-wiki/workbench/web/test/tool-history-summary.test.tsx +124 -0
  562. package/dist/skills/llm-wiki/workbench/web/test/tool-status-format.test.ts +107 -0
  563. package/dist/skills/llm-wiki/workbench/web/test/tool-status-model.test.ts +324 -0
  564. package/dist/skills/llm-wiki/workbench/web/test/tool-status-runway.test.ts +134 -0
  565. package/dist/skills/llm-wiki/workbench/web/test/wiki-links.test.ts +23 -0
  566. package/dist/skills/llm-wiki/workbench/web/tsconfig.app.json +30 -0
  567. package/dist/skills/llm-wiki/workbench/web/tsconfig.json +7 -0
  568. package/dist/skills/llm-wiki/workbench/web/tsconfig.node.json +24 -0
  569. package/dist/skills/llm-wiki/workbench/web/vite.config.ts +26 -0
  570. package/dist/skills/mean-reviewer/SECURITY.md +23 -0
  571. package/dist/skills/mean-reviewer/SKILL.md +203 -0
  572. package/dist/skills/mean-reviewer/examples/13446_1000_Layer_Networks_for_.pdf +0 -0
  573. package/dist/skills/mean-reviewer/examples/13446_mean_reviewer.md +116 -0
  574. package/dist/skills/mean-reviewer/examples/13446_mean_reviewer_author_rebuttal_simulated.md +282 -0
  575. package/dist/skills/mean-reviewer/examples/13446_mean_reviewer_reply.md +91 -0
  576. package/dist/skills/mean-reviewer/examples/13446_official_review.json +973 -0
  577. package/dist/skills/mean-reviewer/examples/ChatGPT_AC_Roleplay.jpeg +0 -0
  578. package/dist/skills/medical-imaging-review/SKILL.md +295 -0
  579. package/dist/skills/medical-imaging-review/references/CITATION_INTEGRITY.md +233 -0
  580. package/dist/skills/medical-imaging-review/references/DOMAINS.md +302 -0
  581. package/dist/skills/medical-imaging-review/references/HALLUCINATION_PATTERNS.md +211 -0
  582. package/dist/skills/medical-imaging-review/references/MCP_SETUP.md +216 -0
  583. package/dist/skills/medical-imaging-review/references/PARADIGM.md +221 -0
  584. package/dist/skills/medical-imaging-review/references/QUALITY_CHECKLIST.md +169 -0
  585. package/dist/skills/medical-imaging-review/references/TEMPLATES.md +291 -0
  586. package/dist/skills/medical-imaging-review/references/WORKFLOW.md +289 -0
  587. package/dist/skills/mermaid-diagram/SKILL.md +379 -0
  588. package/dist/skills/meta-apply/SKILL.md +137 -0
  589. package/dist/skills/meta-optimize/SKILL.md +253 -0
  590. package/dist/skills/monitor-experiment/SKILL.md +98 -0
  591. package/dist/skills/novelty-check/SKILL.md +89 -0
  592. package/dist/skills/openalex/SKILL.md +228 -0
  593. package/dist/skills/overleaf-sync/SKILL.md +220 -0
  594. package/dist/skills/paper-claim-audit/SKILL.md +340 -0
  595. package/dist/skills/paper-compile/SKILL.md +253 -0
  596. package/dist/skills/paper-figure/SKILL.md +279 -0
  597. package/dist/skills/paper-illustration/SKILL.md +690 -0
  598. package/dist/skills/paper-illustration-image2/SKILL.md +383 -0
  599. package/dist/skills/paper-illustration-image2/scripts/paper_illustration_image2.py +255 -0
  600. package/dist/skills/paper-plan/SKILL.md +278 -0
  601. package/dist/skills/paper-poster/SKILL.md +19 -0
  602. package/dist/skills/paper-poster-html/DESIGN_FINAL.md +176 -0
  603. package/dist/skills/paper-poster-html/IMPLEMENTATION_CONVENTIONS.md +161 -0
  604. package/dist/skills/paper-poster-html/LICENSES/posterly-MIT.txt +21 -0
  605. package/dist/skills/paper-poster-html/NOTICE.md +57 -0
  606. package/dist/skills/paper-poster-html/SKILL.md +357 -0
  607. package/dist/skills/paper-poster-html/scripts/_posterly/__init__.py +0 -0
  608. package/dist/skills/paper-poster-html/scripts/_posterly/canvas.py +200 -0
  609. package/dist/skills/paper-poster-html/scripts/_posterly/measure.py +588 -0
  610. package/dist/skills/paper-poster-html/scripts/_posterly/polish.py +498 -0
  611. package/dist/skills/paper-poster-html/scripts/_posterly/preflight.py +489 -0
  612. package/dist/skills/paper-poster-html/scripts/_posterly/render.py +215 -0
  613. package/dist/skills/paper-poster-html/scripts/_posterly/textutil.py +16 -0
  614. package/dist/skills/paper-poster-html/scripts/_posterly/verify_final.py +171 -0
  615. package/dist/skills/paper-poster-html/scripts/asset_check.py +897 -0
  616. package/dist/skills/paper-poster-html/scripts/extract_pdf_figures.py +666 -0
  617. package/dist/skills/paper-poster-html/scripts/poster_check.py +251 -0
  618. package/dist/skills/paper-poster-html/scripts/preprocess_figures.py +238 -0
  619. package/dist/skills/paper-poster-html/scripts/render_preview.py +217 -0
  620. package/dist/skills/paper-poster-html/scripts/run_gates.py +556 -0
  621. package/dist/skills/paper-poster-html/scripts/style_check.py +1324 -0
  622. package/dist/skills/paper-poster-html/templates/COMPONENTS.md +462 -0
  623. package/dist/skills/paper-poster-html/templates/landscape_4col.html +1032 -0
  624. package/dist/skills/paper-poster-html/templates/landscape_hero.html +1046 -0
  625. package/dist/skills/paper-poster-html/templates/portrait_2col.html +947 -0
  626. package/dist/skills/paper-poster-html/templates/tokens/acl.json +9 -0
  627. package/dist/skills/paper-poster-html/templates/tokens/cvpr.json +9 -0
  628. package/dist/skills/paper-poster-html/templates/tokens/generic.json +9 -0
  629. package/dist/skills/paper-poster-html/templates/tokens/iclr.json +9 -0
  630. package/dist/skills/paper-poster-html/templates/tokens/icml.json +9 -0
  631. package/dist/skills/paper-poster-html/templates/tokens/neurips.json +9 -0
  632. package/dist/skills/paper-slide-deck/SKILL.md +464 -0
  633. package/dist/skills/paper-slide-deck/references/analysis-framework.md +392 -0
  634. package/dist/skills/paper-slide-deck/references/base-prompt.md +70 -0
  635. package/dist/skills/paper-slide-deck/references/content-rules.md +95 -0
  636. package/dist/skills/paper-slide-deck/references/figure-container-template.md +177 -0
  637. package/dist/skills/paper-slide-deck/references/modification-guide.md +85 -0
  638. package/dist/skills/paper-slide-deck/references/outline-template.md +437 -0
  639. package/dist/skills/paper-slide-deck/references/styles/academic-paper.md +109 -0
  640. package/dist/skills/paper-slide-deck/references/styles/blueprint.md +67 -0
  641. package/dist/skills/paper-slide-deck/references/styles/bold-editorial.md +70 -0
  642. package/dist/skills/paper-slide-deck/references/styles/chalkboard.md +68 -0
  643. package/dist/skills/paper-slide-deck/references/styles/corporate.md +69 -0
  644. package/dist/skills/paper-slide-deck/references/styles/dark-atmospheric.md +69 -0
  645. package/dist/skills/paper-slide-deck/references/styles/editorial-infographic.md +73 -0
  646. package/dist/skills/paper-slide-deck/references/styles/fantasy-animation.md +69 -0
  647. package/dist/skills/paper-slide-deck/references/styles/intuition-machine.md +72 -0
  648. package/dist/skills/paper-slide-deck/references/styles/minimal.md +64 -0
  649. package/dist/skills/paper-slide-deck/references/styles/notion.md +69 -0
  650. package/dist/skills/paper-slide-deck/references/styles/pixel-art.md +67 -0
  651. package/dist/skills/paper-slide-deck/references/styles/scientific.md +73 -0
  652. package/dist/skills/paper-slide-deck/references/styles/sketch-notes.md +66 -0
  653. package/dist/skills/paper-slide-deck/references/styles/vector-illustration.md +72 -0
  654. package/dist/skills/paper-slide-deck/references/styles/vintage.md +73 -0
  655. package/dist/skills/paper-slide-deck/references/styles/watercolor.md +68 -0
  656. package/dist/skills/paper-slide-deck/scripts/apply-template.ts +282 -0
  657. package/dist/skills/paper-slide-deck/scripts/detect-figures.ts +283 -0
  658. package/dist/skills/paper-slide-deck/scripts/extract-figure.ts +140 -0
  659. package/dist/skills/paper-slide-deck/scripts/generate-slides.py +182 -0
  660. package/dist/skills/paper-slide-deck/scripts/merge-to-pdf.ts +116 -0
  661. package/dist/skills/paper-slide-deck/scripts/merge-to-pptx.ts +137 -0
  662. package/dist/skills/paper-slide-deck/scripts/package-lock.json +899 -0
  663. package/dist/skills/paper-slide-deck/scripts/package.json +8 -0
  664. package/dist/skills/paper-slides/SKILL.md +571 -0
  665. package/dist/skills/paper-talk/SKILL.md +381 -0
  666. package/dist/skills/paper-write/SKILL.md +411 -0
  667. package/dist/skills/paper-write/templates/IEEEtran.bst +2409 -0
  668. package/dist/skills/paper-write/templates/IEEEtran.cls +6347 -0
  669. package/dist/skills/paper-write/templates/aaai2026.bst +1493 -0
  670. package/dist/skills/paper-write/templates/aaai2026.sty +315 -0
  671. package/dist/skills/paper-write/templates/aaai2026.tex +952 -0
  672. package/dist/skills/paper-write/templates/acl.sty +312 -0
  673. package/dist/skills/paper-write/templates/acl2026.tex +377 -0
  674. package/dist/skills/paper-write/templates/acl_natbib.bst +1940 -0
  675. package/dist/skills/paper-write/templates/acm.bst +3081 -0
  676. package/dist/skills/paper-write/templates/acm_mm2026.tex +204 -0
  677. package/dist/skills/paper-write/templates/acmart.cls +3520 -0
  678. package/dist/skills/paper-write/templates/cvpr.bst +1448 -0
  679. package/dist/skills/paper-write/templates/cvpr.sty +508 -0
  680. package/dist/skills/paper-write/templates/cvpr2026.tex +63 -0
  681. package/dist/skills/paper-write/templates/iclr2026.tex +84 -0
  682. package/dist/skills/paper-write/templates/iclr2026_conference.bst +1440 -0
  683. package/dist/skills/paper-write/templates/iclr2026_conference.sty +246 -0
  684. package/dist/skills/paper-write/templates/icml2025.tex +87 -0
  685. package/dist/skills/paper-write/templates/icml2026.sty +767 -0
  686. package/dist/skills/paper-write/templates/icml2026.tex +662 -0
  687. package/dist/skills/paper-write/templates/ieee_conference.tex +89 -0
  688. package/dist/skills/paper-write/templates/ieee_journal.tex +93 -0
  689. package/dist/skills/paper-write/templates/math_commands.tex +48 -0
  690. package/dist/skills/paper-write/templates/neurips2025.tex +80 -0
  691. package/dist/skills/paper-write/templates/neurips2026.tex +493 -0
  692. package/dist/skills/paper-write/templates/neurips_2026.sty +437 -0
  693. package/dist/skills/paper-writing/SKILL.md +632 -0
  694. package/dist/skills/patent-novelty-check/SKILL.md +153 -0
  695. package/dist/skills/patent-pipeline/SKILL.md +344 -0
  696. package/dist/skills/patent-review/SKILL.md +202 -0
  697. package/dist/skills/pixel-art/SKILL.md +139 -0
  698. package/dist/skills/pre-submission-reviewer/SKILL.md +247 -0
  699. package/dist/skills/pre-submission-reviewer/references/forbidden-patterns.md +163 -0
  700. package/dist/skills/pre-submission-reviewer/references/grammar-rules.md +135 -0
  701. package/dist/skills/pre-submission-reviewer/references/latex-rules.md +158 -0
  702. package/dist/skills/pre-submission-reviewer/references/logic-and-structure.md +125 -0
  703. package/dist/skills/pre-submission-reviewer/references/section-guides.md +169 -0
  704. package/dist/skills/prior-art-search/SKILL.md +146 -0
  705. package/dist/skills/proof-checker/SKILL.md +499 -0
  706. package/dist/skills/proof-writer/SKILL.md +222 -0
  707. package/dist/skills/qzcli/SKILL.md +316 -0
  708. package/dist/skills/rebuttal/SKILL.md +304 -0
  709. package/dist/skills/render-html/SKILL.md +299 -0
  710. package/dist/skills/render-html/scripts/render_html.py +905 -0
  711. package/dist/skills/render-html/scripts/templates/academic.html +342 -0
  712. package/dist/skills/render-html/scripts/templates/dashboard.html +333 -0
  713. package/dist/skills/research-lit/SKILL.md +353 -0
  714. package/dist/skills/research-paper-writing/SKILL.md +99 -0
  715. package/dist/skills/research-paper-writing/agents/openai.yaml +4 -0
  716. package/dist/skills/research-paper-writing/references/abstract.md +102 -0
  717. package/dist/skills/research-paper-writing/references/conclusion.md +35 -0
  718. package/dist/skills/research-paper-writing/references/does-my-writing-flow-source.md +45 -0
  719. package/dist/skills/research-paper-writing/references/examples/abstract/template-a.md +21 -0
  720. package/dist/skills/research-paper-writing/references/examples/abstract/template-b.md +34 -0
  721. package/dist/skills/research-paper-writing/references/examples/abstract/template-c.md +28 -0
  722. package/dist/skills/research-paper-writing/references/examples/abstract-examples.md +13 -0
  723. package/dist/skills/research-paper-writing/references/examples/index.md +21 -0
  724. package/dist/skills/research-paper-writing/references/examples/introduction/novel-task-challenge-decomposition.md +18 -0
  725. package/dist/skills/research-paper-writing/references/examples/introduction/pipeline-not-recommended-abstract-only.md +30 -0
  726. package/dist/skills/research-paper-writing/references/examples/introduction/pipeline-version-1-one-contribution-multi-advantages.md +30 -0
  727. package/dist/skills/research-paper-writing/references/examples/introduction/pipeline-version-2-two-contributions.md +34 -0
  728. package/dist/skills/research-paper-writing/references/examples/introduction/pipeline-version-3-new-module-on-existing-pipeline.md +18 -0
  729. package/dist/skills/research-paper-writing/references/examples/introduction/pipeline-version-4-observation-driven.md +16 -0
  730. package/dist/skills/research-paper-writing/references/examples/introduction/technical-challenge-version-1-existing-task.md +32 -0
  731. package/dist/skills/research-paper-writing/references/examples/introduction/technical-challenge-version-2-existing-task-insight-backed-by-traditional.md +33 -0
  732. package/dist/skills/research-paper-writing/references/examples/introduction/technical-challenge-version-3-novel-task.md +21 -0
  733. package/dist/skills/research-paper-writing/references/examples/introduction/version-1-task-then-application.md +14 -0
  734. package/dist/skills/research-paper-writing/references/examples/introduction/version-2-application-first.md +10 -0
  735. package/dist/skills/research-paper-writing/references/examples/introduction/version-3-general-to-specific-setting.md +14 -0
  736. package/dist/skills/research-paper-writing/references/examples/introduction/version-4-open-with-challenge.md +20 -0
  737. package/dist/skills/research-paper-writing/references/examples/introduction-examples.md +25 -0
  738. package/dist/skills/research-paper-writing/references/examples/method/example-of-the-three-elements.md +67 -0
  739. package/dist/skills/research-paper-writing/references/examples/method/method-writing-common-issues-note.md +10 -0
  740. package/dist/skills/research-paper-writing/references/examples/method/module-design-instant-ngp.md +55 -0
  741. package/dist/skills/research-paper-writing/references/examples/method/module-motivation-patterns.md +15 -0
  742. package/dist/skills/research-paper-writing/references/examples/method/module-triad-neural-body.md +19 -0
  743. package/dist/skills/research-paper-writing/references/examples/method/neural-body-annotated-figure-text.md +66 -0
  744. package/dist/skills/research-paper-writing/references/examples/method/overview-template.md +30 -0
  745. package/dist/skills/research-paper-writing/references/examples/method/pre-writing-questions.md +17 -0
  746. package/dist/skills/research-paper-writing/references/examples/method/section-skeleton.md +9 -0
  747. package/dist/skills/research-paper-writing/references/examples/method-examples.md +24 -0
  748. package/dist/skills/research-paper-writing/references/experiments.md +102 -0
  749. package/dist/skills/research-paper-writing/references/introduction.md +408 -0
  750. package/dist/skills/research-paper-writing/references/method.md +196 -0
  751. package/dist/skills/research-paper-writing/references/paper-review.md +86 -0
  752. package/dist/skills/research-paper-writing/references/related-work.md +41 -0
  753. package/dist/skills/research-pipeline/SKILL.md +257 -0
  754. package/dist/skills/research-proposal/SKILL.md +573 -0
  755. package/dist/skills/research-proposal/assets/proposal_scaffold_en.md +323 -0
  756. package/dist/skills/research-proposal/assets/proposal_scaffold_zh.md +346 -0
  757. package/dist/skills/research-proposal/references/DOMAIN_TEMPLATES.md +518 -0
  758. package/dist/skills/research-proposal/references/LITERATURE_WORKFLOW.md +529 -0
  759. package/dist/skills/research-proposal/references/QUALITY_CHECKLIST.md +325 -0
  760. package/dist/skills/research-proposal/references/STRUCTURE_GUIDE.md +398 -0
  761. package/dist/skills/research-proposal/references/WRITING_STYLE_GUIDE.md +661 -0
  762. package/dist/skills/research-refine/SKILL.md +716 -0
  763. package/dist/skills/research-refine-pipeline/SKILL.md +186 -0
  764. package/dist/skills/research-review/SKILL.md +119 -0
  765. package/dist/skills/research-wiki/SKILL.md +373 -0
  766. package/dist/skills/resubmit-pipeline/SKILL.md +427 -0
  767. package/dist/skills/result-to-claim/SKILL.md +190 -0
  768. package/dist/skills/run-experiment/SKILL.md +227 -0
  769. package/dist/skills/scientific-figure-making/SKILL.md +38 -0
  770. package/dist/skills/scientific-figure-making/references/api.md +152 -0
  771. package/dist/skills/scientific-figure-making/references/common-patterns.md +74 -0
  772. package/dist/skills/scientific-figure-making/references/demos.md +30 -0
  773. package/dist/skills/scientific-figure-making/references/design-theory.md +138 -0
  774. package/dist/skills/scientific-figure-making/references/tutorials.md +135 -0
  775. package/dist/skills/semantic-scholar/SKILL.md +219 -0
  776. package/dist/skills/serverless-modal/SKILL.md +324 -0
  777. package/dist/skills/slides-polish/SKILL.md +563 -0
  778. package/dist/skills/specification-writing/SKILL.md +211 -0
  779. package/dist/skills/strategist/SKILL.md +670 -0
  780. package/dist/skills/strategist/references/quality_standards.md +336 -0
  781. package/dist/skills/strategist/references/search_strategy.md +459 -0
  782. package/dist/skills/strategist/scripts/evaluate_samples.py +300 -0
  783. package/dist/skills/strategist/scripts/gap_analysis.py +399 -0
  784. package/dist/skills/system-profile/SKILL.md +103 -0
  785. package/dist/skills/tech-paper-template/SKILL.md +192 -0
  786. package/dist/skills/tech-paper-template/references/consistency-checks.md +166 -0
  787. package/dist/skills/tech-paper-template/references/paper-types.md +127 -0
  788. package/dist/skills/tech-paper-template/references/thinking-template.md +194 -0
  789. package/dist/skills/tech-paper-template/references/worked-examples.md +124 -0
  790. package/dist/skills/training-check/SKILL.md +83 -0
  791. package/dist/skills/vast-gpu/SKILL.md +380 -0
  792. package/dist/skills/vibe-research-workflow/SKILL.md +189 -0
  793. package/dist/skills/vibe-research-workflow/references/behavior-guidelines.md +149 -0
  794. package/dist/skills/vibe-research-workflow/references/tool-selection.md +144 -0
  795. package/dist/skills/vibe-research-workflow/references/vibe-coding.md +154 -0
  796. package/dist/skills/vibe-research-workflow/references/vibe-figure.md +131 -0
  797. package/dist/skills/vibe-research-workflow/references/vibe-writing.md +181 -0
  798. package/dist/skills/wiki-enrich/SKILL.md +254 -0
  799. package/dist/skills/writing-systems-papers/SKILL.md +184 -0
  800. package/package.json +1 -1
@@ -0,0 +1,220 @@
1
+ ---
2
+ name: overleaf-sync
3
+ description: "Two-way sync between a local paper directory and an Overleaf project, so ARIS audit/edit workflows stay on the local copy while collaborators edit in the Overleaf web UI. Use when user says \"ๅŒๆญฅ overleaf\", \"overleaf sync\", \"ๆŽจ้€ๅˆฐ overleaf\", \"connect overleaf\", \"Overleaf ๆกฅๆŽฅ\", \"pull overleaf\", \"push overleaf\", or wants to bridge their ARIS paper directory with an Overleaf project."
4
+ argument-hint: [setup <project-id> | pull | push | status]
5
+ allowed-tools: Bash(*), Read, Grep, Glob, Edit, Write
6
+ ---
7
+
8
+ # Overleaf Sync
9
+
10
+ Bridge a local paper directory with an Overleaf project so that:
11
+
12
+ - **You** can keep editing in the Overleaf web UI (or share editing access with collaborators)
13
+ - **ARIS** can read your changes, run audits (`/paper-claim-audit`, `/citation-audit`, `/auto-paper-improvement-loop`), and push fixes back
14
+
15
+ This uses the official **Overleaf Git bridge** (Premium feature). The agent **never sees your authentication token** โ€” you do the one-time auth manually so the token lives in macOS Keychain, not in chat history or `.git/config`.
16
+
17
+ ## When to Use This Skill
18
+
19
+ - You want to use Overleaf as the editing surface (better collaboration, shared with team) but still run ARIS pipelines locally
20
+ - You want to take an existing local ARIS paper and push it to Overleaf for a co-author to edit
21
+ - A collaborator made changes in Overleaf and you want to pull + diff them before continuing local work
22
+
23
+ ## Constants
24
+
25
+ - **CLONE_DIR_DEFAULT** = `paper-overleaf` (sibling of existing `paper/`, NOT inside `paper/`)
26
+ - **CREDENTIAL_HELPER** = `osxkeychain` (macOS) / `manager` (Windows) / `cache` (Linux fallback)
27
+ - **TOKEN_HANDLING** = **NEVER write token to disk, env var, or chat**. User pastes it once into the terminal credential prompt; the OS keychain stores it from then on.
28
+
29
+ ## Architecture
30
+
31
+ ```
32
+ โ”Œโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ” git pull/push โ”Œโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”
33
+ โ”‚ Local paper/ โ”‚ โ—„โ”€โ”€โ”€ rsync โ”€โ”€โ”€โ”€ โ–บ โ”‚ paper-overleaf/ โ”‚ โ—„โ”€โ”€โ–บ Overleaf web
34
+ โ”‚ (ARIS audits) โ”‚ โ”‚ (git bridge) โ”‚ (collaborators)
35
+ โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”˜ โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”˜
36
+ ```
37
+
38
+ The `paper-overleaf/` directory is a **git clone of the Overleaf project**. The `paper/` directory is the working copy where ARIS skills run. They are kept in sync via `rsync`.
39
+
40
+ **Single-source-of-truth rule**: at any given time, treat *one* of them as authoritative for active editing. Switch directions explicitly with `pull` or `push`, and run a `status` check before either to surface unexpected divergence.
41
+
42
+ ## Sub-commands
43
+
44
+ ### `setup <project-id>` โ€” one-time
45
+
46
+ Sets up the bridge for a new Overleaf project. **The user runs this in their own terminal, never through the agent.** The skill ships with a hardened setup script that:
47
+
48
+ 1. Refuses to run unless stdin/stdout are a TTY (won't run inside an agent harness)
49
+ 2. Reads the token from a hidden prompt (no chat history, no shell history)
50
+ 3. Strips the token from the remote URL immediately after cloning
51
+ 4. Primes the OS keychain so subsequent agent operations are auth-free
52
+ 5. **Auto-installs a `pre-commit` hook in `paper-overleaf/.git/hooks/` that refuses to commit any blob containing the token pattern `olp_[A-Za-z0-9]{20,}`** โ€” a hard technical block, not a behavioral rule
53
+
54
+ The agent's only role here is to print the user instruction:
55
+
56
+ ```
57
+ Run this in your own terminal (NOT through me):
58
+
59
+ bash <ARIS_REPO>/tools/overleaf_setup.sh <project-id-or-url>
60
+
61
+ When it finishes, tell me "setup done" and I'll verify.
62
+ ```
63
+
64
+ After the user reports "setup done", the agent verifies (token-free):
65
+
66
+ ```bash
67
+ cd paper-overleaf
68
+ git remote -v # must show URL WITHOUT token
69
+ git config --get credential.helper
70
+ git fetch && git log --oneline -3 # must succeed without prompting
71
+ ls .git/hooks/pre-commit # must exist
72
+ bash <ARIS_REPO>/tools/overleaf_audit.sh . # must report "Audit clean"
73
+ ```
74
+
75
+ If `paper-overleaf/` exists but is empty (new Overleaf project), the agent then mirrors local `paper/` into it (see `push` workflow).
76
+
77
+ ### `pull` โ€” before each editing session
78
+
79
+ ```bash
80
+ cd paper-overleaf && git pull --ff-only
81
+
82
+ # Show what changed since last pull
83
+ LAST=$(git rev-parse HEAD@{1})
84
+ git diff --stat $LAST..HEAD
85
+ git diff $LAST..HEAD -- 'sec/*.tex' # detailed view for prose changes
86
+ ```
87
+
88
+ **Diff protocol โ€” DO NOT blindly merge into local `paper/`.** Overleaf edits frequently include:
89
+
90
+ - **Half-finished sentences** (collaborator clicked save mid-thought)
91
+ - **Typos** that aren't in canonical references (`Lrage` for `Large`)
92
+ - **Commented-out blocks** that may be intentional or may be a stash
93
+ - **Number changes** that should re-trigger `/paper-claim-audit`
94
+ - **Cite key changes** that should re-trigger `/citation-audit`
95
+
96
+ For each diff hunk, decide one of:
97
+
98
+ | Hunk character | Action |
99
+ |----------------|--------|
100
+ | Clean editorial improvement | Sync into `paper/`, no audit needed |
101
+ | Numerical / claim change | Sync, then re-run `/paper-claim-audit` |
102
+ | New `\cite{...}` | Sync, then re-run `/citation-audit` |
103
+ | Half-sentence / obvious typo | Flag to user, do NOT auto-sync |
104
+ | New section / restructure | Stop, ask user before syncing |
105
+
106
+ After deciding per-hunk:
107
+
108
+ ```bash
109
+ # Sync only the files the user approved into local paper/
110
+ rsync -av paper-overleaf/sec/0.abstract.tex paper/sec/0.abstract.tex
111
+ # (or use Edit tool for surgical changes that skip half-sentences)
112
+ ```
113
+
114
+ ### `push` โ€” after local editing
115
+
116
+ Use after ARIS skills have edited `paper/` and you want collaborators on Overleaf to see the changes.
117
+
118
+ ```bash
119
+ # 1. Always pull first to surface remote drift
120
+ cd paper-overleaf && git pull --ff-only
121
+
122
+ # 2. If pull was a no-op, sync local paper โ†’ paper-overleaf
123
+ rsync -av --delete \
124
+ --exclude='.git' --exclude='.DS_Store' \
125
+ --exclude='*.aux' --exclude='*.log' --exclude='*.bbl' --exclude='*.blg' \
126
+ --exclude='*.fls' --exclude='*.fdb_latexmk' --exclude='*.out' \
127
+ --exclude='*.synctex.gz' --exclude='*.toc' \
128
+ paper/ paper-overleaf/
129
+
130
+ # 3. Show what would be pushed
131
+ git status --short
132
+ git diff --stat
133
+
134
+ # 4. Commit + push
135
+ git add -A
136
+ git commit -m "<descriptive message โ€” what ARIS changed and why>"
137
+ git push
138
+ ```
139
+
140
+ **Commit message protocol**: include the ARIS skill that produced the change so collaborators on Overleaf understand provenance. Examples:
141
+
142
+ - `paper-write: regenerated sec/3.assurance after audit cascade refactor`
143
+ - `citation-audit: fix 14 metadata entries (madaan2023, lee2024, ...)`
144
+ - `paper-claim-audit: correct sec/5 numbers vs results/run_2026_04_19.json`
145
+
146
+ **Confirmation gate**: `push` writes to a shared resource. ALWAYS show the user `git diff --stat` (and a representative hunk for prose changes) before running `git push`. Wait for explicit confirmation unless the user said `auto: true` upfront.
147
+
148
+ ### `status` โ€” diagnostic
149
+
150
+ ```bash
151
+ cd paper-overleaf
152
+ git fetch
153
+ echo "=== Remote-vs-local divergence ==="
154
+ git log --oneline HEAD..origin/master # remote ahead
155
+ git log --oneline origin/master..HEAD # local ahead
156
+ echo "=== paper/ vs paper-overleaf/ divergence ==="
157
+ diff -rq --brief paper/ paper-overleaf/ 2>/dev/null \
158
+ | grep -v "Only in paper/.*\.\(aux\|log\|out\|fls\|fdb_latexmk\|bbl\|blg\|synctex\|toc\)" \
159
+ | grep -v "Only in paper-overleaf/.git" \
160
+ | grep -v "DS_Store"
161
+ ```
162
+
163
+ Three-way state assessment:
164
+
165
+ | Remote ahead? | paper/ vs paper-overleaf/ differ? | Meaning | Recommended action |
166
+ |:-------------:|:---------------------------------:|---------|--------------------|
167
+ | No | No | Clean | Nothing to do |
168
+ | Yes | No | Overleaf has new edits | Run `pull`, then re-run status |
169
+ | No | Yes | Local ARIS edits unsynced | Run `push` |
170
+ | Yes | Yes | Diverged โ€” needs merge | Stop, surface to user, do NOT auto-resolve |
171
+
172
+ ## Conflict Resolution
173
+
174
+ If `git pull --ff-only` fails because of true divergence:
175
+
176
+ 1. **Do not** run `git pull` (which would auto-merge).
177
+ 2. **Do not** run `git reset --hard` or `git push --force` (destructive).
178
+ 3. Show the user `git log origin/master ^HEAD` (their Overleaf commits) and `git log HEAD ^origin/master` (local ARIS commits).
179
+ 4. Ask the user which side to take per file, or to manually merge in Overleaf and then re-pull.
180
+
181
+ ## Token Security โ€” Defense in Depth
182
+
183
+ Behavioral rules alone are not enough โ€” the next agent reading this skill might forget them. The skill therefore relies on **technical guards** that hold even if the agent misbehaves:
184
+
185
+ | Layer | Guard | Where enforced |
186
+ |-------|-------|---------------|
187
+ | 1. Setup | `overleaf_setup.sh` refuses to run without an interactive TTY (agents don't have one) | `tools/overleaf_setup.sh` |
188
+ | 2. Input | Token is read by `read -s` (hidden prompt, no shell history, never enters chat) | `tools/overleaf_setup.sh` |
189
+ | 3. Storage | Token goes straight into OS keychain via `git credential approve`; remote URL is stripped to a token-free form | `tools/overleaf_setup.sh` |
190
+ | 4. Commits | `paper-overleaf/.git/hooks/pre-commit` greps staged content for `olp_[A-Za-z0-9]{20,}` and aborts | auto-installed by setup script |
191
+ | 5. Audit | `overleaf_audit.sh` scans working tree, remote URLs, git history, credential files | `tools/overleaf_audit.sh` |
192
+
193
+ Behavioral rules (still apply, but secondary):
194
+
195
+ - **Never** ask the user to paste a token into chat. If they do anyway: (a) acknowledge it, (b) tell them to revoke it at https://www.overleaf.com/user/settings, (c) recover via keychain if already primed.
196
+ - **Never** write a token to a file (`.env`, `.netrc`, `tools/*.sh`, etc.) committed to any repo.
197
+ - **Never** include a token in a `git remote -v` URL โ€” strip it after clone.
198
+ - On `401 Unauthorized` from push/pull, tell the user the keychain entry expired and to re-run `overleaf_setup.sh`. Do **not** ask for a fresh token.
199
+
200
+ ## Mutual-Exclusion Rule
201
+
202
+ The single biggest source of pain in two-way sync is **simultaneous editing on both sides**.
203
+
204
+ - If the user is in an active Overleaf editing session, ARIS skills should **read-only** access `paper/` until the user runs `/overleaf-sync pull`.
205
+ - If ARIS is in the middle of `/auto-paper-improvement-loop` or `/paper-write`, the user should pause Overleaf editing until the loop finishes and `/overleaf-sync push` is run.
206
+
207
+ When in doubt, run `status` first.
208
+
209
+ ## Output Contract
210
+
211
+ - `paper-overleaf/` directory at repo root, git clone of Overleaf project (origin URL has NO token)
212
+ - `paper/` directory unchanged in role โ€” still the ARIS working copy
213
+ - Each `pull`/`push` operation: a one-line summary back to the user (commits pulled / pushed, file count, link to Overleaf project URL)
214
+
215
+ ## See Also
216
+
217
+ - `/paper-claim-audit` โ€” re-run after pulling Overleaf changes that touch numbers
218
+ - `/citation-audit` โ€” re-run after pulling Overleaf changes that add/edit `\cite{...}`
219
+ - `/paper-compile` โ€” local LaTeX build; Overleaf compiles independently in the cloud
220
+ - Overleaf Git bridge docs: https://www.overleaf.com/learn/how-to/Using_Git_and_GitHub
@@ -0,0 +1,340 @@
1
+ ---
2
+ name: paper-claim-audit
3
+ 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 \"ๅฎกๆŸฅ่ฎบๆ–‡ๆ•ฐๆฎ\", \"check paper claims\", \"verify numbers\", \"่ฎบๆ–‡ๆ•ฐๅญ—ๆ ธๅฏน\", or before submission to ensure paper-to-evidence fidelity."
4
+ argument-hint: [paper-directory]
5
+ allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob
6
+ ---
7
+
8
+ # Paper Claim Audit: Zero-Context Evidence Verification
9
+
10
+ Verify that every claim in the paper matches raw evidence for: **$ARGUMENTS**
11
+
12
+ ## Why This Exists
13
+
14
+ The executor writes experiments AND writes the paper. It "knows" what the results should be. This creates confirmation bias:
15
+ - Rounding 84.7% up to 85.3%
16
+ - Reporting best seed instead of average
17
+ - Citing metrics from a different experiment config
18
+ - Claiming "improves by 15%" when the delta is actually 12.8%
19
+
20
+ A **fresh reviewer with zero prior context** catches these because it has no expectations โ€” it just compares paper text vs raw files.
21
+
22
+ ## How This Differs From Other Audit Skills
23
+
24
+ | Skill | Question it answers |
25
+ |-------|-------------------|
26
+ | `/experiment-audit` | Is the experiment code honest? (fake GT, normalization fraud) |
27
+ | `/result-to-claim` | Does the data scientifically support this claim? |
28
+ | **`/paper-claim-audit`** | **Does the paper report the data truthfully and precisely?** |
29
+
30
+ ## Core Principle
31
+
32
+ **Zero-context, fresh reviewer.** The auditor receives ONLY:
33
+ - Paper .tex files (the claims)
34
+ - Raw result files (the evidence)
35
+
36
+ It does NOT receive:
37
+ - โŒ EXPERIMENT_LOG.md
38
+ - โŒ EXPERIMENT_TRACKER.md
39
+ - โŒ AUTO_REVIEW.md
40
+ - โŒ NARRATIVE_REPORT.md
41
+ - โŒ Any executor summary or interpretation
42
+ - โŒ Any prior audit results
43
+ - โŒ Any conversation history
44
+
45
+ This is **stricter than reviewer-independence** โ€” it's zero-context evidence audit.
46
+
47
+ ## Workflow
48
+
49
+ ### Step 1: Collect Files (Executor โ€” Claude)
50
+
51
+ Locate paper and result files WITHOUT reading or interpreting them.
52
+
53
+ **Paper files** (claims) โ€” paths shown relative to the shell's working
54
+ directory so you can find them with `ls`; when writing them into
55
+ `audited_input_hashes`, use paths relative to the paper dir (no `paper/`
56
+ prefix) per the "Submission Artifact Emission" section below:
57
+ ```
58
+ paper/main.tex # โ†’ hash key: main.tex
59
+ paper/sections/*.tex # โ†’ hash key: sections/*.tex
60
+ paper/tables/*.tex (if separate) # โ†’ hash key: tables/*.tex
61
+ ```
62
+
63
+ **Result files** (evidence):
64
+ ```
65
+ results/*.json, results/*.jsonl, results/*.csv, results/*.tsv
66
+ outputs/*.json, outputs/*.csv
67
+ wandb-summary.json (if exists)
68
+ **/metrics.json, **/eval_results.json
69
+ **/config.yaml, **/args.json (experiment configs)
70
+ ```
71
+
72
+ **Exclude** (no summaries, no interpretations):
73
+ ```
74
+ EXPERIMENT_LOG.md, EXPERIMENT_TRACKER.md, AUTO_REVIEW*.md
75
+ NARRATIVE_REPORT.md, PAPER_PLAN.md, findings.md
76
+ Any .md file that is an executor-written summary
77
+ ```
78
+
79
+ ### Step 2: Fresh Reviewer Audit (GPT-5.5 โ€” NEW thread, no reply)
80
+
81
+ **CRITICAL: Use a fresh reviewer agent every run.** Never reuse an old reviewer context for this audit.
82
+
83
+ ```text
84
+ spawn_agent:
85
+ model: gpt-5.5
86
+ reasoning_effort: xhigh
87
+ message: |
88
+ You are a paper-to-evidence auditor. You have ZERO prior context about
89
+ this research. You will receive only paper source files and raw result
90
+ files. Your job is to verify that every number in the paper exactly
91
+ matches the raw evidence.
92
+
93
+ Paper files to read:
94
+ [list .tex file paths]
95
+
96
+ Result files to read:
97
+ [list .json/.csv/.yaml file paths]
98
+
99
+ ## Audit Protocol
100
+
101
+ ### A. Extract Every Quantitative Claim
102
+ For each number, percentage, comparison, or scope statement in the paper:
103
+ - Location (section, table, caption, or inline text)
104
+ - Exact claim text
105
+ - The number or comparison being made
106
+
107
+ ### B. Trace Each Claim to Evidence
108
+ For each extracted claim, find the supporting raw data:
109
+ - Which result file contains this number?
110
+ - What is the EXACT value in that file?
111
+ - Match status: exact_match / rounding_ok / mismatch
112
+
113
+ ### C. Check These Specific Failure Modes
114
+
115
+ 1. **Number inflation**: Paper says 85.3%, raw file says 84.7%
116
+ Rule: only standard rounding to displayed precision is allowed
117
+
118
+ 2. **Best-seed cherry-pick**: Paper says "achieves 90.2%" but
119
+ that's the best of 5 seeds; mean is 87.1%
120
+ Rule: check if paper specifies "average" / "best" / "median"
121
+
122
+ 3. **Config mismatch**: Paper compares Method A vs Baseline B,
123
+ but they used different hyperparameters / datasets / splits
124
+ Rule: verify config files show same settings for compared methods
125
+
126
+ 4. **Aggregation mismatch**: Paper says "average over 5 seeds"
127
+ but result files show only 3 runs
128
+ Rule: count actual runs vs claimed count
129
+
130
+ 5. **Delta error**: Paper says "improves by 15%" but
131
+ actual delta is (85.3 - 73.1) / 73.1 = 16.7%
132
+ Rule: verify arithmetic of all relative improvements
133
+
134
+ 6. **Caption-table mismatch**: Figure caption describes
135
+ something different from what the figure/table actually shows
136
+ Rule: cross-check every caption against its content
137
+
138
+ 7. **Scope overclaim**: Paper says "consistently outperforms"
139
+ but only tested on 2 datasets
140
+ Rule: check if language matches actual evaluation scope
141
+
142
+ ## Output Format (per claim)
143
+ For each claim, report:
144
+ - claim_id: sequential number
145
+ - location: section/table/figure
146
+ - paper_text: exact quote from paper
147
+ - paper_value: the number claimed
148
+ - evidence_file: which raw file
149
+ - evidence_value: the actual number
150
+ - status: exact_match | rounding_ok | ambiguous_mapping |
151
+ missing_evidence | config_mismatch | aggregation_mismatch |
152
+ number_mismatch | scope_overclaim | unsupported_claim
153
+ - details: explanation if not exact_match
154
+
155
+ Overall verdict: PASS | WARN | FAIL
156
+ ```
157
+
158
+ ### Step 3: Write Report (Executor โ€” Claude)
159
+
160
+ Parse the reviewer's response and write `PAPER_CLAIM_AUDIT.md`:
161
+
162
+ ```markdown
163
+ # Paper Claim Audit Report
164
+
165
+ **Date**: [today]
166
+ **Auditor**: GPT-5.5 xhigh (fresh zero-context thread)
167
+ **Paper**: [paper title from tex]
168
+
169
+ ## Overall Verdict: [PASS | WARN | FAIL]
170
+
171
+ ## Claims Verified: [N total]
172
+ - exact_match: [count]
173
+ - rounding_ok: [count]
174
+ - ambiguous_mapping: [count]
175
+ - missing_evidence: [count]
176
+ - mismatch: [count]
177
+
178
+ ## Issues Found
179
+
180
+ ### [FAIL/WARN] Claim #N: [description]
181
+ - **Location**: Section X / Table Y / Figure Z
182
+ - **Paper says**: "..."
183
+ - **Evidence shows**: ...
184
+ - **Status**: [status]
185
+ - **Fix**: [specific correction needed]
186
+
187
+ ## All Claims (detailed)
188
+
189
+ | # | Location | Paper Value | Evidence Value | Status |
190
+ |---|----------|-------------|---------------|--------|
191
+ | 1 | Table 2 | 85.3% | 85.28% | rounding_ok |
192
+ | 2 | Abstract | "15% improvement" | 12.8% | number_mismatch |
193
+ | ... |
194
+ ```
195
+
196
+ Also write `PAPER_CLAIM_AUDIT.json` for machine consumption.
197
+
198
+ ### Step 4: Print Summary
199
+
200
+ ```
201
+ ๐Ÿ“‹ Paper Claim Audit Complete
202
+
203
+ Claims verified: 24
204
+ exact_match: 18
205
+ rounding_ok: 3
206
+ ambiguous: 1
207
+ โš ๏ธ mismatch: 2
208
+
209
+ Overall: โš ๏ธ WARN
210
+
211
+ See PAPER_CLAIM_AUDIT.md for details.
212
+ ```
213
+
214
+ ## When to Run
215
+
216
+ 1. **After `/paper-write`** โ€” first check before improvement loop
217
+ 2. **After `/auto-paper-improvement-loop`** โ€” recheck if improvement loop changed numbers
218
+ 3. **Before submission** โ€” final verification
219
+
220
+ ## Integration with Other Skills
221
+
222
+ ### Read by `/auto-paper-improvement-loop` (if exists)
223
+
224
+ ```
225
+ if PAPER_CLAIM_AUDIT.json exists:
226
+ read mismatched claims
227
+ fix them as priority items in the improvement round
228
+ ```
229
+
230
+ ### Advisory, Never Blocking
231
+
232
+ Same pattern as `/experiment-audit`:
233
+ - `PASS` โ†’ continue normally
234
+ - `WARN` โ†’ print warning, continue, flag draft as "check numbers before submission"
235
+ - `FAIL` โ†’ print alert, continue, but do NOT mark as submission-ready
236
+
237
+ ## Render HTML view (auto, when `RENDER_HTML = true`, default)
238
+
239
+ After writing `paper/PAPER_CLAIM_AUDIT.md` and `paper/PAPER_CLAIM_AUDIT.json`, invoke `/render-html` on the audit report:
240
+
241
+ ```
242
+ /render-html "paper/PAPER_CLAIM_AUDIT.md" --json "paper/PAPER_CLAIM_AUDIT.json"
243
+ ```
244
+
245
+ Uses **full review gate** (audit-class artifact โ€” render-fidelity check matches the skill's zero-context cross-model audit invariant). Output: `paper/PAPER_CLAIM_AUDIT.html` with embedded source SHA256 + `.review.json` sidecar.
246
+
247
+ **Non-blocking**: if `/render-html` fails (helper missing, secondary Codex agent unavailable, file write error), log the failure and treat the audit as complete โ€” the JSON + MD verdict files are canonical; the HTML view is a human-reader convenience.
248
+
249
+ Skip if `RENDER_HTML = false` is set in `AGENTS.md` / `CLAUDE.md` or passed as `โ€” render html: false`.
250
+
251
+ ## Key Rules
252
+
253
+ - **Fresh thread EVERY run.** Never use a continuation reply. Never carry context.
254
+ - **Zero executor interpretation.** Only file paths. No summaries.
255
+ - **Only raw results.** No EXPERIMENT_LOG, no AUTO_REVIEW, no human summaries.
256
+ - **Rounding rule.** Only standard rounding to displayed precision. 84.7% โ†’ 84.7% or 85% is OK. 84.7% โ†’ 85.3% is NOT OK.
257
+ - **Cross-model.** Reviewer must be a different model family from executor.
258
+
259
+ ## Review Tracing
260
+
261
+ After each reviewer agent call, save the trace following `shared-references/review-tracing.md` (Policy C โ€” forensic; never silently skip). Use `save_trace.sh` (resolved per the chain in `shared-references/integration-contract.md` ยง2) or write files directly to `.aris/traces/<skill>/<date>_run<NN>/`. Respect the `--- trace:` parameter (default: `full`).
262
+
263
+ ## Submission Artifact Emission
264
+
265
+ This skill **always** writes `paper/PAPER_CLAIM_AUDIT.json`, regardless of
266
+ caller or detector outcome. A detector-negative run (paper has no numeric
267
+ claims) emits verdict `NOT_APPLICABLE`; a paper-with-numeric-claims-but-no-
268
+ raw-results run emits `BLOCKED`. Silent skip is forbidden โ€” `paper-writing`
269
+ Phase 6 and `verify_paper_audits.sh` both rely on this artifact
270
+ existing at a predictable path.
271
+
272
+ The artifact conforms to the schema in `shared-references/assurance-contract.md`:
273
+
274
+ ```json
275
+ {
276
+ "audit_skill": "paper-claim-audit",
277
+ "verdict": "PASS | WARN | FAIL | NOT_APPLICABLE | BLOCKED | ERROR",
278
+ "reason_code": "all_numbers_match | rounding_drift | missing_raw_results | ...",
279
+ "summary": "One-line human-readable verdict summary.",
280
+ "audited_input_hashes": {
281
+ "main.tex": "sha256:...",
282
+ "sections/5.evidence.tex": "sha256:...",
283
+ "/abs/path/to/results/run_2026_04_19.json": "sha256:..."
284
+ },
285
+ "trace_path": ".aris/traces/paper-claim-audit/<date>_run<NN>/",
286
+ "thread_id": "<codex mcp thread id>",
287
+ "reviewer_model": "gpt-5.5",
288
+ "reviewer_reasoning": "xhigh",
289
+ "generated_at": "<UTC ISO-8601>",
290
+ "details": {
291
+ "total_claims": <int>,
292
+ "mismatches": [ ... per-claim issue records ... ],
293
+ "result_files": [ ... raw files consulted ... ]
294
+ }
295
+ }
296
+ ```
297
+
298
+ ### `audited_input_hashes` scope
299
+
300
+ Hash the **declared input set** passed into this audit invocation โ€” i.e. the
301
+ exact `.tex` files and raw result / config files this run read โ€” not a
302
+ repo-wide union and not the reviewer's self-reported subset. If a caller
303
+ passed only `main.tex` + a single result file, hash those two files and no
304
+ others. The external verifier rehashes these entries; any mismatch flags
305
+ `STALE`.
306
+
307
+ **Path convention** (must match what `verify_paper_audits.sh`
308
+ expects): keys are **paths relative to the paper directory** (the arg
309
+ passed to the verifier) for in-paper files โ€” so `main.tex`, not
310
+ `paper/main.tex` โ€” and **absolute paths** for out-of-paper files such as
311
+ external `results/` dirs. The verifier resolves relative entries via
312
+ `os.path.join(paper_dir, key)`; prefixing with `paper/` produces
313
+ `paper/paper/main.tex` and false-fails as STALE.
314
+
315
+ ### Verdict decision table
316
+
317
+ | Input state | Verdict | `reason_code` example |
318
+ |-------------------------------------------------------|------------------|-----------------------|
319
+ | No numeric claims detected in paper | `NOT_APPLICABLE` | `no_numeric_claims` |
320
+ | Numeric claims detected, no raw result files found | `BLOCKED` | `no_raw_evidence` |
321
+ | All claims reconcile to raw data | `PASS` | `all_numbers_match` |
322
+ | Minor rounding drift only, no material mismatch | `WARN` | `rounding_drift` |
323
+ | Any material mismatch (wrong number, config mismatch) | `FAIL` | `claim_mismatch` |
324
+ | Reviewer invocation failed (network / malformed) | `ERROR` | `reviewer_error` |
325
+
326
+ ### Thread independence
327
+
328
+ Every invocation uses a fresh reviewer agent. Never continue a prior audit via
329
+ `send_input`. Do not accept prior audit outputs (PROOF_AUDIT, CITATION_AUDIT,
330
+ EXPERIMENT_LOG, AUTO_REVIEW summaries) as input to this audit โ€” the fresh
331
+ thread preserves reviewer independence per
332
+ `shared-references/reviewer-independence.md`.
333
+
334
+ ### Human-readable sibling
335
+
336
+ `paper/PAPER_CLAIM_AUDIT.md` is written alongside the JSON for readers.
337
+ The JSON is authoritative for `verify_paper_audits.sh`; the Markdown
338
+ is for humans. The parent skill (`paper-writing` Phase 6) plus the verifier
339
+ decide whether the verdict blocks finalization โ€” this skill itself never
340
+ blocks; it only emits.