MedPaper Assistant - VS Code Extension

Compact-first MCP research workspace for manuscript and library-wiki workflows, with Phase 0 source-material intake, managed tools, prompts, Foam graph views, and bundled guides.

Features

• 🧭 Dual Workflow Workspace - Manuscript Path + Library Wiki Path with the same @mdpaper entrypoint
• Auto Paper - 全自動 13 main gate checkpoints + Phase 2.1 sub-gate 論文撰寫 + 3 層 Audit Hooks
• Source Material Intake - Phase 0 掃描用戶提供的 DOCX/XLSX/PDF/CSV，並提示哪些檔案要先走 asset-aware
• 🔍 PubMed Literature Search - Search and save references
• ✍️ Draft Writing - Write paper sections with citation-aware editing
• 💡 Concept Development - Develop and validate research novelty
• 📊 Data Analysis - Statistical tests, Table 1, visualizations
• 📄 Word Export - Export to journal-ready Word documents
• 📚 LLM Wiki / Library Wiki Path - inbox/concepts/projects note triage, dashboards, and managed Foam graph views
• 🔔 Dual-Hook Architecture - 79 個品質檢查（56 Code-Enforced / 23 Agent-Driven）

What This VSIX Actually Ships

This extension is the packaged end-user surface, not the entire monorepo authoring workspace.

Installation

From VSIX

code --install-extension medpaper-assistant-<version>.vsix

Or in VS Code: Ctrl+Shift+P → Extensions: Install from VSIX...

Requirements

• VS Code 1.100.0 or higher
• GitHub Copilot (for Agent Mode)
• Python 3.12+ with uv (recommended for full MedPaper repo parity; CGU itself supports 3.11+)

MCP Installation Behavior

• MCP Python tools are installed persistently per machine with uv tool install, not once per folder.
• On later MedPaper extension updates, existing managed tools are checked with uv tool upgrade so older installs can move forward without manual reinstall.
• If another installed VS Code extension already provides PubMed Search or Zotero Keeper MCP servers, MedPaper skips both persistent tool installation and MCP registration for those servers to avoid duplicated tools.
• A workspace-level .vscode/mcp.json still has highest priority. If the workspace already manages mdpaper itself, MedPaper skips auto-registration.
• CGU is registered only when bundled CGU code or a workspace integrations/cgu submodule is present. If CGU is absent, MedPaper continues without it.
• Draw.io fallback uses npx -y @drawio/mcp, so Node.js/npm must be installed if you rely on the npm path.

Quick Start

🚀 全自動寫論文 (Auto Paper)

1. 安裝擴充功能
2. 在 Agent Mode 輸入：「全自動寫論文」
3. 系統自動執行 13 main gate checkpoints，並在 Phase 2 後插入 Phase 2.1 fulltext/source-material sub-gate：

Usage

Chat Commands (@mdpaper)

Command Palette (Ctrl+Shift+P)

Agent Mode 自然語言

直接在 Agent Mode 輸入：

• 「全自動寫論文」「一鍵寫論文」→ Auto Paper Pipeline
• 「找論文」「搜尋 PubMed」→ 文獻搜尋
• 「寫 Introduction」→ 草稿撰寫
• 「驗證 novelty」→ 概念驗證

Workflow Modes

• Library Wiki Path：建立 workflow_mode="library-wiki" 專案後，先做文獻保存、筆記 triage、dashboard 與 Foam graph 巡覽。
• Manuscript Path：建立 workflow_mode="manuscript" 專案後，走 concept → draft → review → export。
• 建議順序：先用 Library Wiki Path 累積與整理知識，再切去 Manuscript Path 正式寫稿。

If you want the broader repository workflow surface, use the main repository checkout. The VSIX is intentionally the narrower packaged path.

Foam + Copilot Knowledge Base

MedPaper uses Foam as the reading and graph layer, while Copilot handles ingest, identity resolution, knowledge-map and synthesis generation, evidence-anchor materialization, and the managed Foam graph views.

The current Foam/Copilot layer now includes orphan / placeholder cleanup loops, template-driven capture into inbox/, review/, and daily/, richer foam-query dashboards, publish-safe wikilink reference packs under notes/publish/, and project-specific graph_views_json slices.

Docs shipped with MedPaper: Setup Workspace:

• docs/how-to/llm-wiki.md
• docs/reference/foam.md

You can also open the main guide directly with MedPaper: Open LLM Wiki Guide.

The bundled LLM Wiki guide now includes a ready-to-paste graph_views_json example for an ICU sedation / delirium review workflow.

Architecture

Capability → Skill → Hook → MCP Tool

🔔 Hook Architecture（79 checks — 56 Code-Enforced / 23 Agent-Driven）

Bundled Assets

The marketplace package bundles 14 skills, 13 prompt workflows, 9 reviewer/analysis agents, 4 templates (1 journal profile + 3 CSL styles), 7 support/reference files, 10 chat commands, and 11 palette commands. The full repository still contains a broader authoring and maintenance surface.

These counts are release-gated against bundle-manifest.json and tool-surface-authority.json, so the marketplace docs stay aligned with the packaged surface.

Bundled prompt workflows: mdpaper.write-paper, mdpaper.literature-survey, mdpaper.manuscript-revision, mdpaper.search, mdpaper.concept, mdpaper.draft, mdpaper.project, mdpaper.format, mdpaper.strategy, mdpaper.analysis, mdpaper.clarify, mdpaper.help, mdpaper.audit.

Bundled reviewer/analysis agents: concept-challenger, domain-reviewer, literature-searcher, meta-learner, methodology-reviewer, paper-reviewer, reference-analyzer, review-orchestrator, statistics-reviewer.

Bundled support/reference files: .github/prompts/_capability-index.md, .github/copilot-instructions.md, .copilot-mode.json, docs/reference/foam.md, docs/reference/llm-wiki.md, docs/how-to/llm-wiki.md, docs/assets/medpaper_llm_wiki_workflow_clean.png.

That means a VSIX-only user can now run MedPaper: Setup Workspace and receive the Foam dependency reference, the LLM wiki reference/how-to docs, and the workflow figure directly under docs/ in their workspace.

MCP Tools (117 full / 22 compact default)

The 117/22 tool counts plus the 3 MCP prompts and 3 MCP resources are runtime-validated through tool-surface-authority.json during validate/release gates.

自動註冊 MCP Server：

• MedPaper Assistant - 預設 compact 22 工具（可切換 full 117），另含 3 個 MCP prompts 與 3 個 MCP resources
• CGU Creativity - 創意發想工具
• PubMed Search - 文獻搜尋工具，若未被其他已安裝 VS Code 擴充功能提供才會由 MedPaper 註冊
• Zotero Keeper - Zotero 文獻工具，若未被其他已安裝 VS Code 擴充功能提供才會由 MedPaper 註冊
• Draw.io Diagrams - 圖表繪製

預設 compact 走 facade-first surface，保留 project_action、library_action、draft_action、validation_action、run_quality_checks、pipeline_action、export_document、inspect_export 等高階入口。若你要在 VSIX 版直接跑 full-surface 的 agent wiki workflow，請把 mdpaper.toolSurface 切成 full；這會額外暴露 import_local_papers、ingest_web_source、ingest_markdown_source、resolve_reference_identity、build_knowledge_map、build_synthesis_page、materialize_agent_wiki 等 granular orchestration 工具。

MCP prompts: project_bootstrap, draft_section_plan, word_export_checklist.

MCP resources: medpaper://workspace/state, medpaper://workspace/projects, medpaper://templates/catalog.

Configuration

Development

# Clone
git clone https://github.com/u9401066/med-paper-assistant
cd med-paper-assistant/vscode-extension

# Install & Build
npm install
./scripts/build.sh    # Copies skills, prompts, Python source, compiles, packages

# Manual steps
npm run compile       # TypeScript only
npm run validate      # Cross-platform bundle sync / package consistency checks
npm run package       # Generate .vsix

npm run validate automatically selects the PowerShell validator on Windows and the shell validator on Unix-like systems, so the same command can be used locally and in CI.

License

Apache-2.0