@research-copilot/plugin 1.1.17 → 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 → 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
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  143. package/dist/skills/llm-wiki/packages/graph-engine/src/model/storage.ts +4 -0
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  148. package/dist/skills/llm-wiki/packages/graph-engine/src/render/model.ts +593 -0
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  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
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@@ -0,0 +1,840 @@
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+ ---
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+ name: academic-paper-composer
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+ description: Systematic writing framework for philosophy and interdisciplinary academic papers from optimized outline to submission-ready manuscript. Use when users want to: (1) write a paper from a detailed outline, (2) ensure quality control during writing, (3) maintain consistency across chapters, (4) prepare a submission-ready manuscript, or (5) systematically execute a planned paper. Triggered by phrases like 'write the paper from this outline,' 'compose the full manuscript,' 'execute the outline,' or when users have completed strategic planning (academic-paper-strategist skill) and are ready to write. Takes optimized outline as input; outputs complete manuscript with iterative quality checks.
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+ ---
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+
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+ # Academic Paper Composer
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+
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+ ## Overview
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+
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+ This skill provides a systematic framework for writing academic papers from optimized outline to submission-ready manuscript. It implements iterative quality control at both chapter-level and paper-level, ensuring consistent high quality throughout the writing process.
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+
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+ **Input**: Detailed, optimized paper outline (from academic-paper-strategist or equivalent)
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+
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+ **Output**: Complete, submission-ready manuscript with quality validation reports
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+
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+ **Prerequisite**: Use **academic-paper-strategist** skill first to create optimized outline (or provide equivalent detailed outline)
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+
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+ ---
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+
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+ ## When to Use This Skill
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+
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+ Use **academic-paper-composer** when you need to:
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+
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+ **Writing Stage**:
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+ - Execute a detailed paper outline systematically
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+ - Write a complete academic paper chapter-by-chapter
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+ - Maintain quality control during writing process
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+ - Ensure consistency across all sections
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+
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+ **Quality Assurance Stage**:
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+ - Validate each chapter before proceeding
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+ - Check cross-chapter coherence
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+ - Perform final quality assessment
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+ - Verify submission readiness
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+
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+ **Submission Preparation Stage**:
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+ - Prepare manuscript for platform submission
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+ - Complete platform-specific checklists
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+ - Generate final submission package
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+
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+ **Triggers**:
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+ - "Write the paper from this outline"
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+ - "Compose the full manuscript"
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+ - "Execute the outline systematically"
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+ - "I have an outline, help me write the paper"
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+ - After completing academic-paper-strategist skill
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+
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+ ---
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+
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+ ## Workflow Overview
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+
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+ ```
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+ Phase 4: SYSTEMATIC WRITING (Chapter-by-Chapter + Quality Gates)
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+
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+ Phase 5: QUALITY CONTROL (Final Validation + Submission Prep)
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+
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+ Output: Submission-Ready Manuscript + Quality Reports
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+ ```
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+
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+ **Quality Gates**: After each chapter + final paper evaluation
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+
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+ ---
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+
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+ ## Required Input
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+
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+ Before using this skill, you must provide:
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+
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+ ### 1. Optimized Detailed Outline
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+ **Required structure**:
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+ ```markdown
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+ ## Abstract (250-300 words)
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+ - [Key points to cover]
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+
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+ ## 1. Introduction (1,500 words)
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+ ### 1.1 Opening Puzzle (400 words)
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+ - [Content guidance]
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+ ### 1.2 Literature Review (600 words)
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+ - [Theories to discuss]
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+ ### 1.3 This Paper's Contribution (500 words)
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+ - [Specific claims]
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+
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+ ## 2. [Main Chapter Title] (1,200 words)
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+ ### 2.1 [Section] (400 words)
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+ - [Argument structure]
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+ - [Key citations]
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+ ...
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+
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+ [Complete structure with word counts and content guidance]
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+ ```
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+
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+ **Quality check**: Outline should specify:
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+ - ✓ Chapter titles and word counts
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+ - ✓ Subsection structure (to 3rd level)
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+ - ✓ Content guidance for each section
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+ - ✓ Key citations to include
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+ - ✓ Argument structure notes
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+
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+ If outline lacks these, consider using **academic-paper-strategist** first.
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+
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+ ### 2. Platform Writing Standards Guide
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+ **From academic-paper-strategist Phase 1**, or equivalent document specifying:
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+ - Platform style patterns (voice, terminology, citation format)
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+ - Structural conventions
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+ - Example papers for reference
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+
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+ ### 3. Literature Base (Optional but Recommended)
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+ - List of core papers to cite
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+ - Research gap analysis
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+ - Key concepts to emphasize
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+
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+ ---
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+
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+ ## Phase 4: Systematic Writing
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+
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+ ### Goal
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+ Write complete manuscript chapter-by-chapter with iterative quality control.
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+
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+ ### Workflow
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+
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+ #### Step 4.1: Writing Environment Setup
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+
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+ Before writing, I will:
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+
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+ 1. **Verify outline completeness**:
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+ - All chapters specified with word counts
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+ - Content guidance provided
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+ - Argument structure clear
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+
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+ 2. **Load reference documents**:
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+ - Platform writing standards
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+ - Section writing guides (`references/section_guides.md`)
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+ - Quality standards (`references/writing_standards.md`)
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+
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+ 3. **Create writing tracker**:
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+ ```markdown
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+ # Writing Progress Tracker
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+ - [ ] Abstract (250 words)
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+ - [ ] Chapter 1: Introduction (1,500 words)
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+ - [ ] Chapter 2: [Title] (1,200 words)
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+ ...
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+ - [ ] Conclusion (1,000 words)
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+ - [ ] References
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+ ```
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+
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+ **Decision Point 1**: Confirm outline and standards loaded, ready to begin writing.
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+
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+ #### Step 4.2: Chapter-by-Chapter Writing
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+
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+ **For each chapter, I will follow this sequence**:
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+
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+ ##### A. Pre-Writing Review
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+ Before writing chapter N:
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+ 1. **Review outline specification** for this chapter:
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+ - Word count target
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+ - Subsection structure
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+ - Content guidance
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+ - Key arguments/citations
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+
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+ 2. **Review previous chapter** (if N>1):
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+ - Last paragraph of chapter N-1
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+ - Key concepts introduced
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+ - Promises to fulfill
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+
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+ 3. **Check section guide**:
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+ - Load appropriate template from `references/section_guides.md`
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+ - Review quality markers for this section type
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+
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+ ##### B. Writing Execution
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+
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+ I will write the chapter following:
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+
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+ **Content principles**:
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+ - **Follow outline exactly**: Respect structure and word counts
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+ - **Include specified citations**: Use literature from outline
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+ - **Maintain platform style**: Match voice and terminology
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+ - **Use section templates**: Follow appropriate guide from `section_guides.md`
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+
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+ **Quality targets (pre-emptive)**:
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+ - Argument quality: Clear thesis, justified premises
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+ - Citation quality: All claims supported, proper format
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+ - Clarity: Precise prose, terms defined, good transitions
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+ - Structure: Logical flow, proper proportions
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+ - Style conformity: Match platform conventions
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+
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+ **Output**: Complete chapter draft
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+
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+ ##### C. Post-Writing Evaluation
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+
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+ After completing chapter draft, I will:
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+
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+ 1. **Create evaluation document**:
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+ ```bash
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+ python scripts/chapter_quality_check.py
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+ # Option 1: Create template for this chapter
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+ ```
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+
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+ 2. **Perform 5-dimension assessment**:
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+ - **Argument Quality** (1-4): Thesis clear? Premises justified? Objections addressed?
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+ - **Citation Quality** (1-4): All claims cited? Format consistent? Key literature included?
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+ - **Clarity & Readability** (1-4): Prose clear? Terms defined? Transitions smooth?
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+ - **Structure & Flow** (1-4): Logical progression? Proper proportions? Follows outline?
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+ - **Platform Conformity** (1-4): Style match? Voice consistent? Format correct?
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+
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+ 3. **Generate quality report**:
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+ ```bash
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+ python scripts/chapter_quality_check.py
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+ # Option 2: Generate report from evaluation
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+ ```
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+
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+ This produces:
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+ - Total score (X/20)
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+ - Pass/fail (threshold: ≥16/20)
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+ - Weak dimensions identified
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+ - Specific revision recommendations
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+
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+ **Quality Gate 4A** (After Each Chapter):
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+ - ✓ Score ≥16/20 (80%)
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+ - ✓ All dimensions ≥3/4 (or revisions implemented)
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+ - ✓ Word count within ±10% of target
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+
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+ **If Failed**: Implement revisions before proceeding to next chapter
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+
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+ ##### D. Iteration (If Needed)
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+
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+ If chapter scores <16/20:
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+
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+ 1. **Identify weak dimension(s)**: Which scored <3/4?
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+
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+ 2. **Implement targeted revisions**:
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+ - Argument quality issue → Add justifications, address objections
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+ - Citation quality issue → Add supporting citations, fix format
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+ - Clarity issue → Simplify prose, add definitions, improve transitions
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+ - Structure issue → Reorganize paragraphs, adjust proportions
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+ - Style issue → Adjust voice, terminology, format
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+
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+ 3. **Re-evaluate**: Generate new quality report
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+
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+ 4. **Repeat until passing** (typically 1-2 iterations)
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+
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+ **Important**: Do not proceed to next chapter until current chapter passes quality gate.
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+
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+ ##### E. Chapter Completion
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+
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+ Once chapter passes quality gate:
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+
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+ 1. **Mark chapter complete** in writing tracker
247
+ 2. **Save chapter with quality report**
248
+ 3. **Note key concepts introduced** (for coherence check later)
249
+ 4. **Preview next chapter** requirements
250
+
251
+ **Decision Point 2** (After Major Chapters): After completing each main body chapter, I will:
252
+ - Present completed chapter summary
253
+ - Show quality score
254
+ - Ask: Proceed to next chapter or revise further?
255
+
256
+ #### Step 4.3: Writing Sequence
257
+
258
+ **Recommended order**:
259
+
260
+ 1. **Introduction** (write first)
261
+ - Establishes thesis and roadmap
262
+ - Use introduction guide from `section_guides.md`
263
+ - Quality check: Abstract promises, literature coverage, clear contribution
264
+
265
+ 2. **Main Body Chapters** (in outline order)
266
+ - Follow outline sequence
267
+ - Quality check after each
268
+ - Build on previous chapters
269
+
270
+ 3. **Conclusion** (write after main body)
271
+ - Synthesizes findings
272
+ - Addresses introduction promises
273
+ - Use conclusion guide from `section_guides.md`
274
+
275
+ 4. **Abstract** (write last)
276
+ - Summarizes complete paper
277
+ - Use abstract guide from `section_guides.md`
278
+ - Quality check: Standalone, accurate, compelling
279
+
280
+ 5. **References** (compile throughout)
281
+ - Format according to platform standards
282
+ - Verify all citations present
283
+
284
+ #### Step 4.4: Cross-Chapter Coherence Check
285
+
286
+ After all chapters written, before final evaluation:
287
+
288
+ 1. **Terminology consistency**:
289
+ - Extract key terms from each chapter
290
+ - Verify consistent usage throughout
291
+ - Check definitions consistent
292
+
293
+ 2. **Argument flow**:
294
+ - Verify chapter N+1 builds on chapter N
295
+ - Check roadmap (intro) matches execution
296
+ - Ensure conclusion addresses introduction promises
297
+
298
+ 3. **Citation patterns**:
299
+ - Check for uneven citation distribution
300
+ - Verify key works cited where relevant
301
+ - Ensure bibliography complete
302
+
303
+ **Output**: Cross-chapter coherence report identifying any inconsistencies
304
+
305
+ ---
306
+
307
+ ## Phase 5: Quality Control
308
+
309
+ ### Goal
310
+ Perform comprehensive final evaluation and prepare submission-ready manuscript.
311
+
312
+ ### Workflow
313
+
314
+ #### Step 5.1: Content Completeness Check
315
+
316
+ Using structured checklist, verify:
317
+
318
+ **Structural Completeness**:
319
+ - [ ] Abstract (250-300 words)
320
+ - [ ] Introduction with all required elements
321
+ - [ ] All outlined main chapters present
322
+ - [ ] Conclusion with all required elements
323
+ - [ ] References section formatted correctly
324
+
325
+ **Content Completeness**:
326
+ - [ ] All introduction promises fulfilled
327
+ - [ ] All claims supported by evidence or argument
328
+ - [ ] All technical terms defined
329
+ - [ ] All objections addressed
330
+ - [ ] All limitations acknowledged
331
+
332
+ **Citation Completeness**:
333
+ - [ ] Every citation in text has bibliography entry
334
+ - [ ] Every bibliography entry cited in text
335
+ - [ ] Citation format consistent throughout
336
+ - [ ] All citations include necessary information
337
+
338
+ **Format Completeness**:
339
+ - [ ] Title page (if required)
340
+ - [ ] Section numbering consistent
341
+ - [ ] Heading hierarchy logical
342
+ - [ ] Figure/table captions (if applicable)
343
+
344
+ **Output**: Completeness checklist report
345
+
346
+ #### Step 5.2: Final 7-Dimension Evaluation
347
+
348
+ I will perform comprehensive evaluation using:
349
+
350
+ ```bash
351
+ python scripts/final_evaluation.py
352
+ # Create evaluation template
353
+ ```
354
+
355
+ **7 Dimensions** (10 points each, 70 total):
356
+
357
+ 1. **Overall Argument Quality** (1-10)
358
+ - Thesis clarity throughout
359
+ - Chapter integration
360
+ - Logical completeness
361
+ - Objections addressed
362
+
363
+ 2. **Literature Integration** (1-10)
364
+ - Citation count (40-60 typical for philosophy)
365
+ - Key literature covered
366
+ - Citations well-integrated
367
+ - Critical engagement present
368
+
369
+ 3. **Clarity & Accessibility** (1-10)
370
+ - Prose clarity
371
+ - Complex ideas explained
372
+ - Appropriate for audience
373
+ - Technical terms defined
374
+
375
+ 4. **Originality & Contribution** (1-10)
376
+ - Clear original contribution
377
+ - Advance over literature
378
+ - Significance established
379
+ - Innovation present
380
+
381
+ 5. **Methodological Rigor** (1-10)
382
+ - Method explicit and justified
383
+ - Consistently applied
384
+ - Appropriate for question
385
+ - Limitations acknowledged
386
+
387
+ 6. **Structure & Organization** (1-10)
388
+ - Logical flow
389
+ - Optimal organization
390
+ - Proportions balanced
391
+ - Transitions seamless
392
+
393
+ 7. **Platform & Style Conformity** (1-10)
394
+ - Style matches platform
395
+ - Format correct
396
+ - Voice consistent
397
+ - Citation format perfect
398
+
399
+ **Scoring Process**:
400
+ 1. Evaluate each dimension (1-10)
401
+ 2. Provide detailed notes for each
402
+ 3. Complete completeness checklist
403
+ 4. List any specific issues
404
+
405
+ **Generate report**:
406
+ ```bash
407
+ python scripts/final_evaluation.py
408
+ # Generate final report
409
+ ```
410
+
411
+ This produces:
412
+ - Total score (X/70)
413
+ - Pass/fail (threshold: ≥56/70)
414
+ - Weak dimensions identified
415
+ - Completeness assessment
416
+ - Prioritized revision recommendations
417
+ - Submission readiness decision
418
+
419
+ **Quality Gate 5** (Final):
420
+ - ✓ Score ≥56/70 (80%)
421
+ - ✓ All completeness checklist items complete
422
+ - ✓ All high-priority issues addressed
423
+
424
+ **If Failed**: Implement revisions and re-evaluate
425
+
426
+ #### Step 5.3: Revision Implementation (If Needed)
427
+
428
+ If final score <56/70 or completeness incomplete:
429
+
430
+ 1. **Prioritize revisions**:
431
+ - HIGH priority: All issues affecting score or completeness
432
+ - MEDIUM priority: Issues improving quality
433
+ - LOW priority: Optional enhancements
434
+
435
+ 2. **Implement systematically**:
436
+ - Address high-priority first
437
+ - Document changes
438
+ - Maintain style consistency
439
+
440
+ 3. **Re-evaluate**:
441
+ - Generate new final report
442
+ - Verify score ≥56/70
443
+ - Check completeness 100%
444
+
445
+ 4. **Iterate until passing**
446
+
447
+ **Decision Point 3**: After final evaluation, I will:
448
+ - Present final score and assessment
449
+ - Show submission readiness status
450
+ - Recommend: Submit immediately / Implement optional improvements / Required revisions
451
+ - Ask: Proceed with submission or implement further improvements?
452
+
453
+ #### Step 5.4: Submission Package Preparation
454
+
455
+ Once final evaluation passes:
456
+
457
+ 1. **Platform-specific checklist**:
458
+ - **PhilArchive/PhilPapers**:
459
+ - [ ] PDF format
460
+ - [ ] Abstract <500 words
461
+ - [ ] Metadata (title, keywords, classification)
462
+ - [ ] Author information complete
463
+
464
+ - **arXiv**:
465
+ - [ ] LaTeX or PDF format
466
+ - [ ] Abstract <1920 characters
467
+ - [ ] Category selection correct
468
+ - [ ] No font embedding issues
469
+
470
+ - **PhilSci-Archive**:
471
+ - [ ] PDF format
472
+ - [ ] Subject classification
473
+ - [ ] Keywords (3-5)
474
+ - [ ] No copyright issues
475
+
476
+ 2. **Generate final outputs**:
477
+ - Formatted manuscript (PDF or LaTeX)
478
+ - Abstract (separate file if needed)
479
+ - Metadata file
480
+ - Cover letter (if applicable)
481
+
482
+ 3. **Pre-submission verification**:
483
+ - Re-read complete paper
484
+ - Check all formatting
485
+ - Verify all links/citations work
486
+ - Proofread for typos
487
+
488
+ **Output**: Complete submission package ready for platform upload
489
+
490
+ ---
491
+
492
+ ## Complete Output Package
493
+
494
+ Upon completion of both phases, you receive:
495
+
496
+ ### Quality Reports
497
+ 1. **Chapter Quality Reports** (one per chapter)
498
+ - 5-dimension scores
499
+ - Pass/fail status
500
+ - Revision recommendations implemented
501
+
502
+ 2. **Cross-Chapter Coherence Report**
503
+ - Terminology consistency check
504
+ - Argument flow verification
505
+ - Citation pattern analysis
506
+
507
+ 3. **Final Evaluation Report** ⭐ **Key Document**
508
+ - 7-dimension comprehensive assessment
509
+ - Completeness checklist (100%)
510
+ - Submission readiness decision
511
+ - Platform-specific checklist
512
+
513
+ ### Manuscript Files
514
+ 1. **Complete Manuscript** ⭐ **Main Deliverable**
515
+ - All chapters integrated
516
+ - Properly formatted
517
+ - Citations complete
518
+ - Submission-ready
519
+
520
+ 2. **Abstract** (separate file)
521
+ - Standalone 250-300 words
522
+ - Platform-formatted
523
+
524
+ 3. **Metadata Document**
525
+ - Title, keywords, classification
526
+ - Author information
527
+ - Platform-specific requirements
528
+
529
+ ### Supporting Documentation
530
+ 1. **Writing Progress Tracker**
531
+ - All chapters completed
532
+ - Quality scores logged
533
+ - Revision history
534
+
535
+ 2. **Citation List**
536
+ - All references used
537
+ - Formatted for platform
538
+ - Verified complete
539
+
540
+ ---
541
+
542
+ ## Quality Assurance System
543
+
544
+ ### Quality Standards Reference
545
+
546
+ For detailed evaluation criteria, all standards are defined in:
547
+ ```markdown
548
+ references/writing_standards.md
549
+ ```
550
+
551
+ This document provides:
552
+ - Chapter-level quality standards (5 dimensions)
553
+ - Final quality standards (7 dimensions)
554
+ - Section-specific quality criteria
555
+ - Scoring rubrics
556
+ - Issue identification and fixes
557
+
558
+ ### Section Writing Guides
559
+
560
+ For guidance on writing each section type:
561
+ ```markdown
562
+ references/section_guides.md
563
+ ```
564
+
565
+ This provides:
566
+ - Abstract writing template and checklist
567
+ - Introduction structure (6 subsections)
568
+ - Main body chapter templates (4 types)
569
+ - Conclusion structure
570
+ - Transition strategies
571
+ - Platform-specific style guidance
572
+ - Common mistakes and fixes
573
+
574
+ ### Evaluation Scripts
575
+
576
+ Two Python scripts support quality validation:
577
+
578
+ #### 1. Chapter Quality Check
579
+ ```bash
580
+ python scripts/chapter_quality_check.py
581
+ ```
582
+
583
+ **Function**: Evaluates individual chapters against 5-dimension standards
584
+ - Creates evaluation templates
585
+ - Calculates scores and pass/fail
586
+ - Identifies weak dimensions
587
+ - Generates revision recommendations
588
+ - Supports multi-chapter comparison
589
+
590
+ **When to Use**: After writing each chapter (Step 4.2.C)
591
+
592
+ #### 2. Final Paper Evaluation
593
+ ```bash
594
+ python scripts/final_evaluation.py
595
+ ```
596
+
597
+ **Function**: Evaluates complete paper against 7-dimension standards
598
+ - Comprehensive quality assessment
599
+ - Completeness checklist validation
600
+ - Submission readiness determination
601
+ - Platform-specific preparation
602
+ - Generates final report with recommendations
603
+
604
+ **When to Use**: After all chapters complete (Step 5.2)
605
+
606
+ ---
607
+
608
+ ## Decision Points (Interactive)
609
+
610
+ This skill has **3 key decision points** where I pause for your input:
611
+
612
+ ### Decision Point 1: Writing Commencement (Step 4.1)
613
+ **I provide**: Loaded outline, standards, and writing plan
614
+ **You confirm**: Ready to begin writing / Need adjustments
615
+
616
+ ### Decision Point 2: Chapter Completion (Step 4.2.E)
617
+ **I provide**: Completed chapter with quality score
618
+ **You decide**: Proceed to next / Revise further / Adjust approach
619
+
620
+ **Frequency**: After each main body chapter (3-5 times typically)
621
+
622
+ ### Decision Point 3: Final Submission (Step 5.3)
623
+ **I provide**: Final evaluation report with score and readiness assessment
624
+ **You decide**: Submit immediately / Implement optional improvements / Additional revisions
625
+
626
+ ---
627
+
628
+ ## Example Usage
629
+
630
+ ### User Request
631
+ "I have the optimized outline from the strategist skill. Please write the complete paper on self-continuity during sleep."
632
+
633
+ ### Skill Response
634
+
635
+ **Phase 4: Systematic Writing**
636
+
637
+ 1. **Setup**: Outline loaded (6 chapters, 9,600 words total). Platform: PhilArchive. Standards loaded. ✓
638
+
639
+ 2. **Chapter 1 - Introduction (1,500 words)**:
640
+ - Writing... [follows outline structure]
641
+ - Self-evaluation: Argument 4/4, Citation 3/4, Clarity 4/4, Structure 3/4, Style 4/4
642
+ - Score: 18/20 ✓ PASS
643
+ - **Decision Point 2**: Proceed to Chapter 2?
644
+
645
+ 3. **Chapter 2 - Narrative Compression Framework (1,200 words)**:
646
+ - Writing... [develops theoretical framework]
647
+ - Self-evaluation: All dimensions 3-4
648
+ - Score: 17/20 ✓ PASS
649
+ - **Decision Point 2**: Proceed to Chapter 3?
650
+
651
+ 4. **Chapter 3-5**: [Similar process for each chapter]
652
+
653
+ 5. **Chapter 6 - Conclusion (1,000 words)**:
654
+ - Writing... [synthesizes findings]
655
+ - Score: 18/20 ✓ PASS
656
+
657
+ 6. **Abstract (280 words)**:
658
+ - Writing... [summarizes complete paper]
659
+ - Score: 19/20 ✓ PASS
660
+
661
+ 7. **Cross-Chapter Coherence**: Terminology consistent ✓, Argument flow verified ✓, Citations complete ✓
662
+
663
+ **Phase 5: Quality Control**
664
+
665
+ 1. **Completeness Check**: All items complete ✓ (18/18)
666
+
667
+ 2. **Final Evaluation**:
668
+ - Overall Argument: 9/10
669
+ - Literature Integration: 8/10 (48 citations)
670
+ - Clarity: 9/10
671
+ - Originality: 8/10
672
+ - Methodology: 8/10
673
+ - Structure: 9/10
674
+ - Platform Fit: 9/10
675
+ - **Total: 60/70 (85.7%)** ✓ PASS
676
+
677
+ 3. **Decision Point 3**: Paper scored 60/70 (Good quality, ready for submission). Submit now or implement optional improvements?
678
+
679
+ 4. **Submission Package**: PDF generated, metadata prepared, PhilArchive checklist complete ✓
680
+
681
+ **Output**: Submission-ready manuscript + comprehensive quality reports
682
+
683
+ ---
684
+
685
+ ## Tips for Best Results
686
+
687
+ ### Provide Complete Outline
688
+ - The more detailed your outline, the better the writing quality
689
+ - Include content guidance for each section
690
+ - Specify key citations and argument structure
691
+ - Indicate expected word counts
692
+
693
+ ### Trust the Iterative Process
694
+ - Chapter-level quality gates ensure each section is solid
695
+ - Don't skip quality checks (they prevent cascading problems)
696
+ - Revisions at chapter-level are easier than whole-paper revisions
697
+
698
+ ### Engage at Decision Points
699
+ - Your input at decision points shapes the final manuscript
700
+ - Feel free to request additional revisions even if chapter passes
701
+ - Provide feedback on style or emphasis
702
+
703
+ ### Use Quality Reports
704
+ - Chapter reports show specific weaknesses
705
+ - Final report provides objective submission readiness assessment
706
+ - Use reports to track improvement across chapters
707
+
708
+ ### Leverage Section Guides
709
+ - I reference `section_guides.md` for each section type
710
+ - You can review these guides directly if you want to understand the approach
711
+ - Guides include templates, examples, and common mistakes
712
+
713
+ ---
714
+
715
+ ## Integration with Academic-Paper-Strategist
716
+
717
+ This skill is designed to work seamlessly with **academic-paper-strategist**:
718
+
719
+ **Ideal workflow**:
720
+ 1. Use **academic-paper-strategist** to:
721
+ - Identify optimal platform
722
+ - Conduct literature search
723
+ - Identify research gaps
724
+ - Assess originality
725
+ - Generate optimized detailed outline
726
+
727
+ 2. Use **academic-paper-composer** (this skill) to:
728
+ - Execute the outline systematically
729
+ - Maintain quality control during writing
730
+ - Produce submission-ready manuscript
731
+
732
+ **Can be used standalone**: If you already have a detailed outline from another source, you can use this skill directly (skip strategist).
733
+
734
+ ---
735
+
736
+ ## Limitations and Notes
737
+
738
+ - **Requires detailed outline**: Vague outlines produce lower-quality output; specificity is key
739
+ - **Iterative process takes time**: Quality writing with validation requires patience; typical timeline: 1-2 days for 10,000-word paper
740
+ - **Quality checks are systematic, not perfect**: Final human review recommended before submission
741
+ - **Platform-specific formatting**: I adapt to platform standards, but you should verify final format
742
+ - **Complementary to strategist skill**: Best results come from using both skills in sequence
743
+
744
+ ---
745
+
746
+ ## Common Issues and Solutions
747
+
748
+ ### Issue 1: Chapter Fails Quality Gate
749
+
750
+ **Symptom**: Score <16/20 after writing chapter
751
+
752
+ **Solution**:
753
+ 1. Review weak dimension(s) from report
754
+ 2. Implement specific recommendations
755
+ 3. Re-evaluate chapter
756
+ 4. Typical fix time: 30-60 minutes
757
+
758
+ **Prevention**: Follow section guides closely during initial writing
759
+
760
+ ### Issue 2: Inconsistent Style Across Chapters
761
+
762
+ **Symptom**: Some chapters feel different in tone or voice
763
+
764
+ **Solution**:
765
+ 1. Run cross-chapter coherence check (Step 4.4)
766
+ 2. Identify inconsistent terminology or voice
767
+ 3. Revise to match dominant style
768
+ 4. Re-run check to verify
769
+
770
+ **Prevention**: Reference platform standards before writing each chapter
771
+
772
+ ### Issue 3: Low Final Score (<56/70)
773
+
774
+ **Symptom**: Paper fails final quality gate
775
+
776
+ **Solution**:
777
+ 1. Identify weak dimensions from final report
778
+ 2. Focus on dimensions scoring <7/10
779
+ 3. Implement high-priority revisions systematically
780
+ 4. Re-evaluate after revisions
781
+
782
+ **Common causes**: Insufficient literature integration, unclear contribution, poor coherence
783
+
784
+ ### Issue 4: Completeness Checklist Incomplete
785
+
786
+ **Symptom**: Missing required elements
787
+
788
+ **Solution**:
789
+ 1. Review which category has incomplete items
790
+ 2. Add missing elements (e.g., missing objections section, incomplete references)
791
+ 3. Re-run completeness check
792
+
793
+ **Prevention**: Use writing tracker throughout; check outline completeness before starting
794
+
795
+ ---
796
+
797
+ ## Platform-Specific Notes
798
+
799
+ ### PhilArchive / PhilPapers
800
+ - **Style**: First-person acceptable ("I argue")
801
+ - **Length**: 5,000-12,000 words typical
802
+ - **Citations**: APA or Chicago author-year
803
+ - **Quality focus**: Philosophical rigor, argument clarity
804
+
805
+ ### arXiv (Philosophy-adjacent)
806
+ - **Style**: More formal, passive voice common
807
+ - **Length**: Varies widely (3,000-20,000)
808
+ - **Citations**: Varies by subcategory
809
+ - **Quality focus**: Interdisciplinary clarity, technical precision
810
+
811
+ ### PhilSci-Archive
812
+ - **Style**: Bridges philosophical and scientific
813
+ - **Length**: 6,000-15,000 words typical
814
+ - **Citations**: Author-year typical
815
+ - **Quality focus**: Integration of philosophy + science
816
+
817
+ ---
818
+
819
+ ## Summary
820
+
821
+ **academic-paper-composer** transforms an optimized outline into a submission-ready manuscript through:
822
+
823
+ 1. **Systematic Writing** (Phase 4): Chapter-by-chapter execution with 5-dimension quality checks after each (≥16/20 threshold)
824
+ 2. **Quality Control** (Phase 5): Final 7-dimension assessment (≥56/70 threshold) + completeness validation + submission preparation
825
+
826
+ **Quality Assurance**: Iterative evaluation at chapter and paper levels ensures consistent quality throughout.
827
+
828
+ **Output**: Submission-ready manuscript with comprehensive quality reports documenting systematic validation.
829
+
830
+ **Estimated Time**: 1-2 days for systematic writing and validation of 8,000-12,000 word paper (varies with outline detail and revision needs).
831
+
832
+ ---
833
+
834
+ ## Related Skills
835
+
836
+ **Prerequisite**: academic-paper-strategist
837
+ - Produces the optimized outline that this skill executes
838
+ - Highly recommended to use first for best results
839
+
840
+ **This skill can be used standalone**: If you have a detailed outline from another source, you can proceed directly with this skill.