dsh-aris-panel 0.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (442) hide show
  1. package/LICENSE +21 -0
  2. package/README.md +98 -0
  3. package/README_CN.md +87 -0
  4. package/dsh/checkout.patch.yml +38 -0
  5. package/dsh/client.js +634 -0
  6. package/dsh/cordis.patch.yml +44 -0
  7. package/dsh/index.mjs +76 -0
  8. package/dsh/run-status.mjs +182 -0
  9. package/dsh/scope-limits.mjs +50 -0
  10. package/dsh/workbench.mjs +291 -0
  11. package/mcp-servers/claude-review/README.md +93 -0
  12. package/mcp-servers/claude-review/run_with_claude_aws.sh +49 -0
  13. package/mcp-servers/claude-review/server.py +718 -0
  14. package/mcp-servers/codex-image2/README.md +65 -0
  15. package/mcp-servers/codex-image2/server.py +893 -0
  16. package/mcp-servers/feishu-bridge/requirements.txt +1 -0
  17. package/mcp-servers/feishu-bridge/server.py +240 -0
  18. package/mcp-servers/gemini-review/README.md +171 -0
  19. package/mcp-servers/gemini-review/server.py +1856 -0
  20. package/mcp-servers/llm-chat/requirements.txt +1 -0
  21. package/mcp-servers/llm-chat/server.py +664 -0
  22. package/mcp-servers/manual-review/README.md +133 -0
  23. package/mcp-servers/manual-review/server.py +910 -0
  24. package/mcp-servers/manual-review/ui.html +279 -0
  25. package/mcp-servers/minimax-chat/requirements.txt +1 -0
  26. package/mcp-servers/minimax-chat/server.py +381 -0
  27. package/package.json +51 -0
  28. package/skills/ablation-planner/SKILL.md +123 -0
  29. package/skills/alphaxiv/SKILL.md +196 -0
  30. package/skills/analyze-results/SKILL.md +46 -0
  31. package/skills/arxiv/SKILL.md +248 -0
  32. package/skills/auto-paper-improvement-loop/SKILL.md +651 -0
  33. package/skills/auto-review-loop/SKILL.md +1137 -0
  34. package/skills/auto-review-loop-llm/SKILL.md +259 -0
  35. package/skills/auto-review-loop-minimax/SKILL.md +302 -0
  36. package/skills/citation-audit/SKILL.md +502 -0
  37. package/skills/claims-drafting/SKILL.md +227 -0
  38. package/skills/comm-lit-review/SKILL.md +297 -0
  39. package/skills/deepxiv/SKILL.md +263 -0
  40. package/skills/dse-loop/SKILL.md +296 -0
  41. package/skills/embodiment-description/SKILL.md +129 -0
  42. package/skills/exa-search/SKILL.md +205 -0
  43. package/skills/experiment-audit/SKILL.md +311 -0
  44. package/skills/experiment-bridge/SKILL.md +376 -0
  45. package/skills/experiment-plan/SKILL.md +249 -0
  46. package/skills/experiment-queue/SKILL.md +431 -0
  47. package/skills/experiment-queue/scripts/build_manifest.py +142 -0
  48. package/skills/experiment-queue/scripts/queue_manager.py +433 -0
  49. package/skills/feishu-notify/SKILL.md +156 -0
  50. package/skills/figure-description/SKILL.md +138 -0
  51. package/skills/figure-spec/SKILL.md +262 -0
  52. package/skills/figure-spec/scripts/figure_renderer.py +799 -0
  53. package/skills/formula-derivation/SKILL.md +280 -0
  54. package/skills/gemini-search/SKILL.md +231 -0
  55. package/skills/grant-proposal/SKILL.md +698 -0
  56. package/skills/idea-creator/SKILL.md +542 -0
  57. package/skills/idea-discovery/SKILL.md +521 -0
  58. package/skills/idea-discovery-robot/SKILL.md +363 -0
  59. package/skills/integrity-forensics/SKILL.md +284 -0
  60. package/skills/interview-cheatsheet/SKILL.md +245 -0
  61. package/skills/invention-structuring/SKILL.md +188 -0
  62. package/skills/jurisdiction-format/SKILL.md +192 -0
  63. package/skills/kill-argument/SKILL.md +437 -0
  64. package/skills/mermaid-diagram/SKILL.md +419 -0
  65. package/skills/meta-apply/SKILL.md +141 -0
  66. package/skills/meta-optimize/SKILL.md +437 -0
  67. package/skills/monitor-experiment/SKILL.md +140 -0
  68. package/skills/novelty-check/SKILL.md +101 -0
  69. package/skills/openalex/SKILL.md +237 -0
  70. package/skills/overleaf-sync/SKILL.md +220 -0
  71. package/skills/paper-claim-audit/SKILL.md +348 -0
  72. package/skills/paper-compile/SKILL.md +266 -0
  73. package/skills/paper-figure/SKILL.md +312 -0
  74. package/skills/paper-illustration/SKILL.md +736 -0
  75. package/skills/paper-illustration-image2/SKILL.md +391 -0
  76. package/skills/paper-illustration-image2/scripts/paper_illustration_image2.py +255 -0
  77. package/skills/paper-plan/SKILL.md +386 -0
  78. package/skills/paper-poster/SKILL.md +19 -0
  79. package/skills/paper-poster-html/DESIGN_FINAL.md +176 -0
  80. package/skills/paper-poster-html/IMPLEMENTATION_CONVENTIONS.md +161 -0
  81. package/skills/paper-poster-html/LICENSES/posterly-MIT.txt +21 -0
  82. package/skills/paper-poster-html/NOTICE.md +57 -0
  83. package/skills/paper-poster-html/SKILL.md +323 -0
  84. package/skills/paper-poster-html/scripts/_posterly/__init__.py +0 -0
  85. package/skills/paper-poster-html/scripts/_posterly/canvas.py +200 -0
  86. package/skills/paper-poster-html/scripts/_posterly/measure.py +588 -0
  87. package/skills/paper-poster-html/scripts/_posterly/polish.py +498 -0
  88. package/skills/paper-poster-html/scripts/_posterly/preflight.py +489 -0
  89. package/skills/paper-poster-html/scripts/_posterly/render.py +215 -0
  90. package/skills/paper-poster-html/scripts/_posterly/textutil.py +16 -0
  91. package/skills/paper-poster-html/scripts/_posterly/verify_final.py +171 -0
  92. package/skills/paper-poster-html/scripts/asset_check.py +897 -0
  93. package/skills/paper-poster-html/scripts/extract_pdf_figures.py +666 -0
  94. package/skills/paper-poster-html/scripts/poster_check.py +251 -0
  95. package/skills/paper-poster-html/scripts/preprocess_figures.py +238 -0
  96. package/skills/paper-poster-html/scripts/render_preview.py +217 -0
  97. package/skills/paper-poster-html/scripts/run_gates.py +556 -0
  98. package/skills/paper-poster-html/scripts/style_check.py +1324 -0
  99. package/skills/paper-poster-html/templates/COMPONENTS.md +462 -0
  100. package/skills/paper-poster-html/templates/README.md +170 -0
  101. package/skills/paper-poster-html/templates/landscape_4col.html +1032 -0
  102. package/skills/paper-poster-html/templates/landscape_hero.html +1046 -0
  103. package/skills/paper-poster-html/templates/portrait_2col.html +947 -0
  104. package/skills/paper-poster-html/templates/tokens/acl.json +9 -0
  105. package/skills/paper-poster-html/templates/tokens/cvpr.json +9 -0
  106. package/skills/paper-poster-html/templates/tokens/generic.json +9 -0
  107. package/skills/paper-poster-html/templates/tokens/iclr.json +9 -0
  108. package/skills/paper-poster-html/templates/tokens/icml.json +9 -0
  109. package/skills/paper-poster-html/templates/tokens/neurips.json +9 -0
  110. package/skills/paper-slides/SKILL.md +635 -0
  111. package/skills/paper-talk/SKILL.md +381 -0
  112. package/skills/paper-write/SKILL.md +604 -0
  113. package/skills/paper-write/templates/IEEEtran.bst +2409 -0
  114. package/skills/paper-write/templates/IEEEtran.cls +6347 -0
  115. package/skills/paper-write/templates/iclr2026.tex +84 -0
  116. package/skills/paper-write/templates/icml2025.tex +87 -0
  117. package/skills/paper-write/templates/ieee_conference.tex +89 -0
  118. package/skills/paper-write/templates/ieee_journal.tex +93 -0
  119. package/skills/paper-write/templates/math_commands.tex +48 -0
  120. package/skills/paper-write/templates/neurips2025.tex +80 -0
  121. package/skills/paper-writing/SKILL.md +916 -0
  122. package/skills/patent-novelty-check/SKILL.md +153 -0
  123. package/skills/patent-pipeline/SKILL.md +344 -0
  124. package/skills/patent-review/SKILL.md +203 -0
  125. package/skills/pixel-art/SKILL.md +137 -0
  126. package/skills/prior-art-search/SKILL.md +146 -0
  127. package/skills/proof-checker/SKILL.md +866 -0
  128. package/skills/proof-orchestrator/NOTICE.md +24 -0
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  130. package/skills/proof-orchestrator/references/audit-output-contract.md +126 -0
  131. package/skills/proof-orchestrator/references/deepseek-routing.md +74 -0
  132. package/skills/proof-orchestrator/references/dispatch-prompts.md +227 -0
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  140. package/skills/render-html/scripts/render_html.py +1006 -0
  141. package/skills/render-html/scripts/templates/academic.html +703 -0
  142. package/skills/render-html/scripts/templates/dashboard.html +333 -0
  143. package/skills/research-lit/SKILL.md +756 -0
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  145. package/skills/research-refine/SKILL.md +770 -0
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  158. package/skills/shared-references/compute-env-contract.md +163 -0
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  160. package/skills/shared-references/evidence-precheck.md +65 -0
  161. package/skills/shared-references/experiment-integrity.md +49 -0
  162. package/skills/shared-references/external-cadence.md +326 -0
  163. package/skills/shared-references/fan-out-pattern.md +366 -0
  164. package/skills/shared-references/injection-hygiene.md +127 -0
  165. package/skills/shared-references/integration-contract.md +461 -0
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@@ -0,0 +1,419 @@
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+ ---
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+ name: mermaid-diagram
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+ description: "Generate Mermaid diagrams from user requirements. Supports flowcharts, sequence diagrams, class diagrams, ER diagrams, Gantt charts, and 18 more diagram types."
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+ argument-hint: "[diagram description or requirements]"
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+ allowed-tools: Bash(*), Read, Write, Edit, Glob, Grep
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+ ---
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+
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+ # Mermaid Diagram Generator
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+
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+ Generate high-quality Mermaid diagram code based on user requirements, with file output and verification.
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+
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+ ## Constants
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+
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+ - **OUTPUT_DIR = `figures/`** — Output directory for all generated files
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+ - **MAX_ITERATIONS = 3** — Maximum refinement rounds for syntax errors
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+
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+ ## Workflow: MUST EXECUTE ALL STEPS
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+
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+ ### Step 0: Pre-flight Check
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+
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+ ```bash
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+ # Create output directory
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+ mkdir -p figures
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+ ```
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+
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+ ### Step 1: Understand Requirements & Select Diagram Type
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+
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+ Parse the input: **$ARGUMENTS**
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+
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+ 1. Analyze user description to determine the most suitable diagram type
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+ 2. Read the corresponding syntax reference documentation (see Diagram Type Reference below)
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+ 3. **If the diagram involves mathematical notation** (formulas, equations, Greek letters, subscripts, superscripts, fractions, matrices, etc.), apply the math syntax rules from the **Math Formulas in Diagrams** section below
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+ 4. Identify all components, connections, and data flow
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+ 5. Plan the diagram structure
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+
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+ ### Step 2: Read Documentation
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+
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+ Select the appropriate diagram type based on the use case. Use your built-in knowledge of Mermaid syntax, or fetch up-to-date docs via the context7 MCP server if needed.
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+
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+ | Type | Use Cases |
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+ | ---- | --------- |
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+ | Flowchart | Processes, decisions, steps |
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+ | Sequence Diagram | Interactions, messaging, API calls |
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+ | Class Diagram | Class structure, inheritance, associations |
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+ | State Diagram | State machines, state transitions |
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+ | ER Diagram | Database design, entity relationships |
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+ | Gantt Chart | Project planning, timelines |
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+ | Pie Chart | Proportions, distributions |
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+ | Mindmap | Hierarchical structures, knowledge graphs |
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+ | Timeline | Historical events, milestones |
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+ | Git Graph | Branches, merges, versions |
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+ | Quadrant Chart | Four-quadrant analysis |
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+ | Requirement Diagram | Requirements traceability |
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+ | C4 Diagram | System architecture (C4 model) |
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+ | Sankey Diagram | Flow, conversions |
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+ | XY Chart | Line charts, bar charts |
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+ | Block Diagram | System components, modules |
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+ | Packet Diagram | Network protocols, data structures |
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+ | Kanban | Task management, workflows |
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+ | Architecture Diagram | System architecture |
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+ | Radar Chart | Multi-dimensional comparison |
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+ | Treemap | Hierarchical data visualization |
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+ | User Journey | User experience flows |
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+ | ZenUML | Sequence diagrams (code style) |
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+
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+ ### Configuration & Themes
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+
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+ - **Theming** - Custom colors and styles
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+ - **Directives** - Diagram-level configuration
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+ - **Layouts** - Layout direction and spacing
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+ - **Configuration** - Global settings
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+ - **Math** - LaTeX math support (see Math Formulas in Diagrams section below)
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+
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+ ### Step 3: Generate Mermaid Code & Save Files
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+
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+ Generate the Mermaid code following the reference specification, then save TWO files:
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+
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+ #### File 1: `figures/<diagram-name>.mmd` — Raw Mermaid source
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+
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+ The `.mmd` file contains ONLY the raw Mermaid code (no markdown fences). Example:
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+
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+ ```
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+ flowchart TD
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+ A[Start] --> B{Condition}
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+ B -->|Yes| C[Execute]
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+ B -->|No| D[End]
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+ C --> D
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+ ```
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+
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+ #### File 2: `figures/<diagram-name>.md` — Markdown with embedded Mermaid
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+
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+ The `.md` file wraps the same code in a mermaid code block for preview rendering, plus a title and description. Example:
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+
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+ ```markdown
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+ # Diagram Title
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+
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+ Brief description of what this diagram shows.
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+
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+ ​```mermaid
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+ flowchart TD
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+ A[Start] --> B{Condition}
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+ B -->|Yes| C[Execute]
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+ B -->|No| D[End]
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+ C --> D
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+ ​```
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+ ```
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+
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+ **Naming convention**: Use a descriptive kebab-case name derived from the user's request (e.g., `auth-flow`, `system-architecture`, `database-er`).
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+
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+ ### Step 4: Verify Mermaid Syntax (MANDATORY)
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+
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+ **Claude MUST verify the generated Mermaid code by running the Mermaid CLI (`mmdc`).**
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+
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+ ```bash
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+ # Check if mermaid-cli is available
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+ if command -v mmdc &> /dev/null; then
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+ # Render to PNG to verify syntax is correct
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+ mmdc -i figures/<diagram-name>.mmd -o figures/<diagram-name>.png -b transparent
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+ echo "✅ Syntax valid — PNG rendered to figures/<diagram-name>.png"
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+ else
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+ # Try npx as fallback
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+ npx -y @mermaid-js/mermaid-cli@latest -i figures/<diagram-name>.mmd -o figures/<diagram-name>.png -b transparent
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+ echo "✅ Syntax valid — PNG rendered to figures/<diagram-name>.png"
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+ fi
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+ ```
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+
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+ **If the verification fails:**
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+ 1. Read the error message carefully
129
+ 2. Fix the syntax issue in both `.mmd` and `.md` files
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+ 3. Re-run verification
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+ 4. Repeat up to MAX_ITERATIONS (3) times
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+
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+ ### Step 5: Claude STRICT Visual Review & Scoring (MANDATORY)
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+
135
+ After successful rendering, Claude MUST read the generated PNG and perform a STRICT review:
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+
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+ ```markdown
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+ ## Claude's STRICT Review of <diagram-name>
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+
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+ ### What I See
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+ [Describe the rendered diagram in DETAIL - every block, every arrow, every label]
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+
143
+ ### Files Generated
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+ - `figures/<diagram-name>.mmd` — Raw Mermaid source
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+ - `figures/<diagram-name>.md` — Markdown with embedded diagram
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+ - `figures/<diagram-name>.png` — Rendered PNG (if mmdc available)
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+
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+ ### ═══════════════════════════════════════════════════════════════
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+ ### STRICT VERIFICATION CHECKLIST (ALL must pass for score ≥ 9)
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+ ### ═══════════════════════════════════════════════════════════════
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+
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+ #### A. File Correctness
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+ - [ ] `.mmd` file contains valid Mermaid syntax (no markdown fences)
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+ - [ ] `.md` file has the mermaid code wrapped in ```mermaid``` fences
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+ - [ ] `.mmd` and `.md` contain IDENTICAL Mermaid code
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+ - [ ] Diagram renders without errors (via mmdc)
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+
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+ #### B. Arrow Correctness Verification (CRITICAL - any failure = score ≤ 6)
159
+ Check EACH arrow:
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+ - [ ] Arrow 1: [Source] → [Target] — Does it point to the CORRECT target?
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+ - [ ] Arrow 2: [Source] → [Target] — Does it point to the CORRECT target?
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+ - [ ] ... (check ALL arrows)
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+
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+ #### C. Block Content Verification (any failure = score ≤ 7)
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+ Check EACH block/node:
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+ - [ ] Block 1 "[Name]": Has correct label? Content correct?
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+ - [ ] Block 2 "[Name]": Has correct label? Content correct?
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+ - [ ] ... (check ALL blocks)
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+
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+ #### D. Completeness
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+ - [ ] All components from user requirements are present
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+ - [ ] All connections/arrows are correct
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+ - [ ] Node labels are meaningful and match requirements
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+
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+ #### E. Visual Quality
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+ - [ ] Layout is clean and readable
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+ - [ ] Color scheme is professional (not rainbow)
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+ - [ ] Text is readable at normal zoom
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+ - [ ] Proper spacing (not cramped, not sparse)
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+ - [ ] Data flow is traceable in 5 seconds
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+
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+ ### ═══════════════════════════════════════════════════════════════
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+
184
+ ### Issues Found (BE SPECIFIC)
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+ 1. [Issue 1]: [EXACTLY what is wrong] → [How to fix]
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+ 2. [Issue 2]: [EXACTLY what is wrong] → [How to fix]
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+
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+ ### Score: X/10
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+
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+ ### Score Breakdown Guide:
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+ - **10**: Perfect. No issues. Publication-ready.
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+ - **9**: Excellent. Minor issues that don't affect understanding.
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+ - **8**: Good but has noticeable issues (layout, styling).
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+ - **7**: Usable but has clear problems (wrong arrows, missing labels).
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+ - **6**: Has arrow direction errors or missing major components.
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+ - **1-5**: Major issues. Unacceptable.
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+
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+ ### Verdict
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+ [ ] ACCEPT (score ≥ 9 AND all critical checks pass)
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+ [ ] FIX (score < 9 OR any critical check fails — list EXACT fixes needed)
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+ ```
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+
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+ **If FIX: apply corrections to both `.mmd` and `.md` files, re-render, and re-verify. Loop until ACCEPT or MAX_ITERATIONS reached.**
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+
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+ ### Step 6: Final Output Summary
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+
207
+ When accepted, present to user:
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+
209
+ ```
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+ ✅ Mermaid diagram generated successfully!
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+
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+ Files:
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+ figures/<diagram-name>.mmd — Raw Mermaid source (use with mmdc, editors, CI)
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+ figures/<diagram-name>.md — Markdown preview (renders on GitHub, VS Code, etc.)
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+ figures/<diagram-name>.png — Rendered image (if mmdc was available)
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+
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+ To re-render manually:
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+ mmdc -i figures/<diagram-name>.mmd -o figures/<diagram-name>.png
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+ ```
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+
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+ ## Architecture Diagram Best Practices
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+
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+ When generating `architecture-beta` diagrams, apply these layout techniques for complex diagrams:
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+
225
+ ### Use Junctions for Layout Control
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+
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+ Think of the diagram as an invisible grid. Use `junction` nodes as virtual anchor points on that grid to precisely control where each component is placed. This is especially useful when a direct edge between two services produces unexpected positioning.
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+
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+ Instead of connecting services directly:
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+
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+ ```
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+ lb:R --> L:scim
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+ lb:R --> L:webapi
234
+ ```
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+
236
+ Route through junctions to control vertical/horizontal placement:
237
+
238
+ ```
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+ junction j_lb_r
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+ lb:R -- L:j_lb_r
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+ junction j_scim_l
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+ j_lb_r:T -- B:j_scim_l
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+ j_scim_l:R --> L:scim
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+ junction j_webapi_l
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+ j_lb_r:B -- T:j_webapi_l
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+ j_webapi_l:R --> L:webapi
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+ ```
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+
249
+ Place junctions on all four sides of components to anchor them logically on the grid.
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+
251
+ ### Use Edges out of Groups for Floating Components
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+
253
+ For services that have no logical connection to other nodes (e.g. a deployment tool, a monitoring agent), use a junction combined with the `{group}` modifier to position them without adding a semantically incorrect edge:
254
+
255
+ ```
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+ junction j_acd_t
257
+ j_algolia_proc_b{group}:B -- T:j_acd_t
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+ j_acd_t:B -- T:acd
259
+ ```
260
+
261
+ This anchors `acd` below its intended neighbor without implying a real relationship.
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+
263
+ ## CVPR/ICLR/NeurIPS Style Guide (for Academic Diagrams)
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+
265
+ When the diagram is intended for academic papers, apply these style standards:
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+
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+ ### Visual Standards
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+ - **Clean white background** — No decorative patterns or gradients (unless subtle)
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+ - **Sans-serif fonts** — Arial, Helvetica, or Computer Modern; minimum 14pt
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+ - **Subtle color palette** — Not rainbow colors; use 3-5 coordinated colors
271
+ - **Print-friendly** — Must be readable in grayscale (many reviewers print papers)
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+ - **Professional borders** — Thin (2-3px), solid colors, not flashy
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+
274
+ ### Layout Standards
275
+ - **Horizontal flow** — Left-to-right is the standard for pipelines
276
+ - **Clear grouping** — Use subtle background boxes to group related modules
277
+ - **Consistent sizing** — Similar components should have similar sizes
278
+ - **Balanced whitespace** — Not cramped, not sparse
279
+
280
+ ### Arrow Standards (MOST CRITICAL)
281
+ - **Thick strokes** — 4-6px minimum (thin arrows disappear when printed)
282
+ - **Clear arrowheads** — Large, filled triangular heads
283
+ - **Dark colors** — Black or dark gray (#333333); avoid colored arrows
284
+ - **Labeled** — Every arrow should indicate what data flows through it
285
+ - **No crossings** — Reorganize layout to avoid arrow crossings
286
+ - **CORRECT DIRECTION** — Arrows must point to the RIGHT target!
287
+
288
+ ### Color Palette (Academic Professional)
289
+ - **Inputs**: Green (#10B981 / #34D399)
290
+ - **Encoders**: Blue (#2563EB / #3B82F6)
291
+ - **Fusion**: Purple (#7C3AED / #8B5CF6)
292
+ - **Outputs**: Orange (#EA580C / #F97316)
293
+ - **Arrows**: Black or dark gray (#333333 / #1F2937)
294
+ - **Background**: Pure white (#FFFFFF)
295
+
296
+ ### What to AVOID
297
+ - Rainbow color schemes (too many colors)
298
+ - Thin, hairline arrows
299
+ - Heavy drop shadows or glowing effects
300
+ - 3D effects / perspective
301
+ - Excessive decorative icons
302
+ - Small text that's unreadable when printed
303
+
304
+ ## Math Formulas in Diagrams (KaTeX)
305
+
306
+ Mermaid supports rendering mathematical expressions via KaTeX (v10.9.0+). **When the diagram content involves math** (formulas, equations, Greek letters, subscripts/superscripts, fractions, matrices, operators, etc.), use KaTeX notation instead of plain-text approximations.
307
+
308
+ ### Supported Diagram Types for Math
309
+
310
+ Math rendering with `$$...$$` is supported in:
311
+ - **Flowcharts** (`flowchart` / `graph`) — in node labels and edge labels
312
+ - **Sequence Diagrams** — in participant aliases, messages, and notes
313
+
314
+ ### Syntax Rules
315
+
316
+ 1. **Wrap math expressions in `$$` delimiters** inside quoted strings:
317
+ ```
318
+ A["$$x^2$$"] -->|"$$\sqrt{x+3}$$"| B("$$\frac{1}{2}$$")
319
+ ```
320
+
321
+ 2. **Node labels with math MUST be quoted** — use `["$$...$$"]` or `("$$...$$")`:
322
+ ```
323
+ scaledDot["$$\text{softmax}\left(\frac{QK^T}{\sqrt{d_k}}\right)V$$"]
324
+ ```
325
+
326
+ 3. **Mix text and math** by placing `$$` only around the math portion:
327
+ ```
328
+ layer1["Linear Layer $$W_1 x + b_1$$"]
329
+ ```
330
+
331
+ 4. **Use `\text{}`** for non-math text inside a `$$` block:
332
+ ```
333
+ node["$$\text{Attention}(Q, K, V)$$"]
334
+ ```
335
+
336
+ ### Common Math Patterns for ML/Science Diagrams
337
+
338
+ | Concept | KaTeX Syntax | Renders As |
339
+ | ------- | ------------ | ---------- |
340
+ | Subscript | `$$W_Q$$` | W_Q |
341
+ | Superscript | `$$x^2$$` | x² |
342
+ | Fraction | `$$\frac{QK^T}{\sqrt{d_k}}$$` | QK^T / sqrt(d_k) |
343
+ | Greek letters | `$$\alpha, \beta, \gamma$$` | α, β, γ |
344
+ | Square root | `$$\sqrt{d_k}$$` | √d_k |
345
+ | Summation | `$$\sum_{i=1}^{n} x_i$$` | Σx_i |
346
+ | Matrix | `$$\begin{bmatrix} a & b \\ c & d \end{bmatrix}$$` | 2x2 matrix |
347
+ | Softmax | `$$\text{softmax}(z_i)$$` | softmax(z_i) |
348
+ | Norm | `$$\|\|x\|\|_2$$` | ‖x‖₂ |
349
+ | Hat/tilde | `$$\hat{y}, \tilde{x}$$` | ŷ, x̃ |
350
+
351
+ ### Example: Attention Mechanism with Math
352
+
353
+ ```
354
+ flowchart TD
355
+ Q["$$Q \in \mathbb{R}^{n \times d_k}$$"]
356
+ K["$$K \in \mathbb{R}^{n \times d_k}$$"]
357
+ V["$$V \in \mathbb{R}^{n \times d_v}$$"]
358
+ scores["$$\frac{QK^T}{\sqrt{d_k}}$$"]
359
+ softmax["$$\text{softmax}(\cdot)$$"]
360
+ output["$$\text{Attention}(Q,K,V)$$"]
361
+
362
+ Q --> scores
363
+ K --> scores
364
+ scores --> softmax
365
+ softmax --> weighted["$$\alpha V$$"]
366
+ V --> weighted
367
+ weighted --> output
368
+ ```
369
+
370
+ ### When to Use Math vs Plain Text
371
+
372
+ - **Use math** when the diagram is for academic/technical audiences and precision matters (papers, lectures, technical docs)
373
+ - **Use plain text** (`<br/>` for line breaks) when the diagram is for general audiences or when math would add visual clutter without improving clarity
374
+ - **Default behavior**: If the user's request contains mathematical notation, equations, or Greek symbols, automatically use KaTeX math rendering. Otherwise, use plain text labels.
375
+
376
+ ### Gotchas
377
+
378
+ - The `$$` delimiters must be **inside quoted strings** — unquoted `$$` will break parsing
379
+ - Backslashes in KaTeX (`\frac`, `\sqrt`, etc.) work normally in Mermaid strings
380
+ - Very long formulas may overflow node boxes — break them with `\\` (newline in KaTeX) or simplify
381
+ - **Always verify rendering** with `mmdc` — some KaTeX expressions may not render in all environments
382
+
383
+ ## Code Quality Rules
384
+
385
+ Generated Mermaid code MUST:
386
+
387
+ 1. Have correct syntax that renders directly
388
+ 2. Have clear structure with proper line breaks and indentation
389
+ 3. Use semantic node naming (not `A`, `B`, `C` — use `authServer`, `userDB`, etc.)
390
+ 4. Include styling when needed to improve visual appearance
391
+ 5. Use `<br/>` for line breaks inside node labels — never use `\n`, which renders as literal text
392
+ 6. Avoid special characters in labels that break Mermaid parsing (wrap in quotes if needed)
393
+
394
+ ## Output Structure
395
+
396
+ ```
397
+ figures/
398
+ ├── <diagram-name>.mmd # Raw Mermaid source (no markdown fences)
399
+ ├── <diagram-name>.md # Markdown with embedded mermaid block
400
+ └── <diagram-name>.png # Rendered PNG (if mmdc available)
401
+ ```
402
+
403
+ ## Key Rules (MUST FOLLOW)
404
+
405
+ 1. **ALWAYS save files to `figures/` directory** — Never just output code in chat
406
+ 2. **ALWAYS generate BOTH `.mmd` and `.md` files** — They must contain identical Mermaid code
407
+ 3. **ALWAYS read the reference documentation** before generating code for a diagram type
408
+ 4. **ALWAYS verify syntax** — Run mmdc or manually validate before accepting
409
+ 5. **ALWAYS review the rendered PNG** — Read the image and perform STRICT scoring
410
+ 6. **NEVER accept score < 9** — Keep refining until excellence
411
+ 7. **VERIFY EVERY ARROW DIRECTION** — Wrong direction = automatic fail (score ≤ 6)
412
+ 8. **VERIFY EVERY BLOCK CONTENT** — Wrong content = automatic fail (score ≤ 7)
413
+ 9. **BE SPECIFIC in feedback** — "Arrow from A to B points wrong" not "arrow is wrong"
414
+ 10. **FIX errors before accepting** — Do not deliver broken diagrams
415
+ 11. **Use descriptive file names** — kebab-case derived from the diagram content
416
+
417
+ ---
418
+
419
+ User requirements: $ARGUMENTS
@@ -0,0 +1,141 @@
1
+ ---
2
+ name: meta-apply
3
+ description: "Privileged applier that LANDS meta-optimize / corpus-audit patches the user approved — the ONLY skill permitted to mutate the skill corpus from a self-modification proposal, with cross-model jury and human approval at landing. Use when the user says \"meta apply\", \"/meta-apply\", \"land the staged patches\", \"应用优化\", after a /meta-optimize run."
4
+ argument-hint: "[patch-number-or-all]"
5
+ allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob, mcp__codex__codex, mcp__codex__codex-reply
6
+ ---
7
+
8
+ # Meta-Apply: the privileged landing gate for self-modification patches
9
+
10
+ This skill exists to enforce a **privilege boundary**. Producers like
11
+ [`/meta-optimize`](../meta-optimize/SKILL.md) (and, later, `corpus-audit`) are
12
+ **read-only** — no `Write`/`Edit`, no apply step; they can only *stage* candidate patches
13
+ under `.aris/meta/pending/`. **This skill is the only place a staged patch becomes a real
14
+ change to the corpus.** Splitting "propose" from "land" across two skills with different
15
+ tool grants is what makes "a loop cannot apply its own patch" structural rather than a
16
+ sentence the producer is asked to obey.
17
+
18
+ It is **human-invoked only.** It runs when the user explicitly types `/meta-apply` after
19
+ reading the producer's REPORT. That invocation IS the landing authorization (the locked
20
+ 2026-05-30 decision: the human stays at the landing gate).
21
+
22
+ ## The acquittal is generated HERE, not relayed
23
+
24
+ The earlier design trusted a `jury_verdict: pass` field in the producer's manifest. That
25
+ is **forgeable** — the producer writes that field, so a buggy/misaligned producer could
26
+ stage a killed patch labelled "pass." **So this skill does not trust any producer-written
27
+ verdict.** It runs the cross-model jury **itself, at landing time, on the actual staged
28
+ diff** (fresh thread, paths-only). The verdict is produced where it is consumed, by the
29
+ privileged human-invoked skill — nothing to forge.
30
+
31
+ ## The non-negotiable rules (jury-at-landing, reject-default)
32
+
33
+ For each staged patch the user asks to land, in order — any failure ⇒ skip & report,
34
+ never silently apply:
35
+
36
+ 1. **The human named THIS patch.** Apply only patches the user listed (`/meta-apply 1,3`
37
+ or `all`); default to applying nothing.
38
+ 2. **Fresh cross-model jury PASS, obtained now.** Run `mcp__codex__codex` (fresh thread,
39
+ NOT codex-reply; `model: gpt-5.6-sol`, `config: {"model_reasoning_effort": "ultra"}`, `sandbox: read-only`,
40
+ paths-only per [`reviewer-independence.md`](../shared-references/reviewer-independence.md))
41
+ on the staged `.diff` + its target. Ask: *does this change improve the harness without
42
+ regressions; PASS or KILL + one-line reason.* Include the scope-limits block from
43
+ [`review-scope-limits.md`](../shared-references/review-scope-limits.md) in that prompt:
44
+ this jury judges ARIS's own mechanism, so an over-defensive KILL permanently blocks a
45
+ good patch. Note the block bans *proposing new* hash binding — it is not a reason to
46
+ KILL a patch that touches the existing provenance stamp. **KILL ⇒ refuse.** The human
47
+ cannot override a KILL — they may only pick among jury-PASSED survivors. (A loop can
48
+ DRIVE; only the cross-model jury can ACQUIT.)
49
+ 3. **Author ≠ reviewer family.** The author is the producer's executor model; the reviewer
50
+ is the codex model that just judged it. Run `provenance.py assert_cross_family` — if it
51
+ raises (same family / unknown), refuse. (Here it always holds: producer=Claude,
52
+ jury=codex. The check is the structural backstop.)
53
+
54
+ ## Workflow
55
+
56
+ ### Step 0: Load staging + resolve the helper
57
+
58
+ ```bash
59
+ PENDING=".aris/meta/pending"
60
+ [ -d "$PENDING" ] || { echo "Nothing staged. Run /meta-optimize first."; exit 0; }
61
+ echo "Staged:"; cat "$PENDING/manifest.jsonl"
62
+ ```
63
+
64
+ Resolve `provenance.py` via the 4-layer chain in
65
+ [`integration-contract.md`](../shared-references/integration-contract.md) §2
66
+ (`.aris/tools/` → `tools/` → `$ARIS_REPO/tools/` → `$ARIS_REPO/tools/` via
67
+ `~/.aris/repo`).
68
+
69
+ ### Step 1: Jury-at-landing for each requested patch
70
+
71
+ For every patch the user asked to land, read its staged `.diff` and target, then run the
72
+ fresh codex jury (Rule 2) — paths-only, no producer reasoning, no prior-round context.
73
+ Record `{patch, jury_verdict, jury_thread_id, one_line_reason}`. Print a one-line result
74
+ per patch (`PASS → eligible` / `KILL → refused: <reason>`).
75
+
76
+ > The producer may have written an *advisory* pre-screen into the manifest to help the
77
+ > human read the REPORT — **ignore it for the landing decision.** Only this fresh verdict
78
+ > counts.
79
+
80
+ ### Step 2: Land the survivors (Write/Edit only — never Bash)
81
+
82
+ For each patch that PASSED Step 1 **and** was named by the user:
83
+
84
+ 1. **Back up** the target to `.aris/meta/backups/<date>/<target>` (use the **Write** tool
85
+ to copy contents; corpus paths are not Bash-writable when `corpus_write_guard` is
86
+ active — and the applier should use Write/Edit for corpus mutation anyway).
87
+ 2. **Apply** the diff by **Edit/Write** on the target corpus file.
88
+ 3. **Stamp provenance** on the changed file:
89
+ ```bash
90
+ python3 "$PROVENANCE" stamp "$TARGET" --author "$AUTHOR" \
91
+ --reviewer "$JURY_MODEL" --verdict-id "$JURY_THREAD_ID"
92
+ ```
93
+ `stamp()` re-asserts cross-family and refuses on same-family — the structural backstop
94
+ at the moment the authorization record is written. The stamp is a **process receipt**
95
+ (who authored, who acquitted-at-landing, content hash) — NOT a claim the change is
96
+ correct.
97
+ 4. **Log** to `.aris/meta/optimizations.jsonl`:
98
+ `{ts, patch, target, author_model, reviewer_model, jury_thread_id, applied: true}`.
99
+
100
+ ### Step 3: Report
101
+
102
+ Per patch: `LANDED <target>` (+ backup path + provenance sidecar) or
103
+ `REFUSED <patch>: <reason>`. Remove landed patches from `.aris/meta/pending/`. Remind the
104
+ user a landed patch is revertable from its backup, and to test the changed skill next run.
105
+
106
+ ## Provenance is a receipt, not an acquittal of correctness
107
+
108
+ A stamp records that a change passed *a process* (cross-model jury at landing + human
109
+ landing), not that it is *correct*. To prevent "approved-but-wrong with a stamp that
110
+ vouches for it" (false-authority laundering — worse than no stamp, because a later
111
+ auto-curator reads it as evidence):
112
+
113
+ - The stamp carries `verdict_id` (auditable review) + `content_hash` (a later hand-edit
114
+ invalidates it).
115
+ - **Recommended (not yet built):** a TTL forcing re-review of long-lived auto-authored
116
+ artifacts, and a behavioral auditor that REVOKES a stamp when a landed skill misbehaves.
117
+ Track as follow-up; never treat a stamp as permanent truth.
118
+
119
+ ## Key Rules
120
+
121
+ - **Human-invoked only.** Never run as a side-effect of another skill or a hook.
122
+ - **Jury-at-landing, reject-default, no override.** The binding verdict is produced HERE
123
+ on the staged diff; never trust a producer-written verdict; the human picks among
124
+ survivors, never resurrects a KILL.
125
+ - **Cross-family or refuse.** `assert_cross_family` must not raise. A
126
+ `deterministic:<verifier>` reviewer is valid per skill-governance.md.
127
+ - **Corpus mutation goes through Write/Edit** (reviewable, attributable), not Bash. The
128
+ `corpus_write_guard` hook (if installed) additionally denies Bash corpus writes — it
129
+ does NOT gate Write/Edit, so it does not by itself stop this skill from editing the
130
+ corpus; the jury-at-landing + stamp discipline above is what governs Write/Edit
131
+ mutations (that discipline is procedure, not a hook-enforced mechanism).
132
+ - **Back up before every mutation.** Reversible by construction.
133
+ - **Only land staged patches.** Applies what producers staged in `.aris/meta/pending/`;
134
+ invents nothing of its own.
135
+
136
+ ## Review Tracing
137
+
138
+ Save each landing-jury codex call's trace per
139
+ [`review-tracing.md`](../shared-references/review-tracing.md) to
140
+ `.aris/traces/meta-apply/<date>_run<NN>/` — the acquittal that landed a corpus change must
141
+ be forensically recoverable.