Medical Paper Assistant

🔬 An MCP-Orchestrated Research Workspace for Medical Paper Writing and LLM Wiki Workflows

3 MCP Servers · 188+ Tools · 38 Skills · 15 Prompt Workflows — a cross-agent authoring surface plus the packaged VSIX experience

📖 繁體中文版 🤖 Auto-Paper: Fully Autonomous Paper Writing Guide — 13 main gate checkpoints + Phase 2.1 sub-gate, 79 Quality Hooks, Structured Review Loop 🧭 GitHub Pages Wiki — 32 topic pages with Mermaid workflows, SVG architecture maps, full-text search, and dark mode

MedPaper Assistant overview

📦 What's in the Box

This repository is the full authoring and integration workspace behind MedPaper Assistant. It combines the core MCP runtime, the packaged VSIX extension, bundled guides, and pinned integration submodules in one place.

Component	Type	Tools	Description
mdpaper	Core MCP Server	118 (full) / 22 (compact default)	Dual workflow server for manuscript and library-wiki paths, plus 3 MCP prompts and 3 MCP resources
pubmed-search	MCP Server (submodule)	46	PubMed/Europe PMC/CORE search, PICO, citation metrics, session mgmt
CGU	MCP Server (submodule)	24	Creative generation: brainstorm, deep think, spark collision
VS Code Extension	Extension	11 cmds + 10 chat	MCP auto-registration, compact-first packaged surface, workspace setup, LLM wiki guide, Foam graph views, `@mdpaper` chat participant
Dashboard	Next.js Web App	—	Project management UI, diagram editor
Foam	VS Code Extension	—	`[[wikilink]]` citation linking, hover preview, graph view
Skills	Agent Workflows	38	Guided multi-tool workflows plus a shared Claude Code / Codex / OpenClaw academic-writing contract
Prompts	Prompt Files	15	`/mdpaper.search`, `/mdpaper.draft`, etc.

External MCP Servers (optional, installed via uvx):

asset-aware — Ingest user-provided DOCX/XLSX/PDF/PPTX source materials and reference full text before drafting
drawio — CONSORT/PRISMA flowchart generation
zotero-keeper — Import references from Zotero library

Counts in these tables are release-gated via tool-surface-authority.json and vscode-extension/bundle-manifest.json.

Choose Your Install Surface

Surface	Best for	What you get
Full repository	Maintainers, power users, and workflow authors	Core `mdpaper` runtime, pinned MCP integrations/submodules, 38 skills, 15 prompt workflows, cross-agent harness, repo scripts, tests, and authoring docs
VSIX extension	End users who want the packaged experience	`@mdpaper`, 11 palette commands, compact-first `mdpaper` runtime (22 tools by default / 118 optional), 14 bundled skills, 13 bundled prompt workflows, 9 bundled agents, and bundled LLM wiki docs

The repository is the broader engineering surface. The VSIX is the curated end-user surface.

VSX note: The MedPaper VS Code extension installs Python MCP tools persistently per machine via uv tool install, attempts uv tool upgrade on later activations, and skips duplicate PubMed Search / Zotero Keeper registration when another installed VS Code extension already provides those MCP servers. CI smoke now covers ubuntu-latest, windows-latest, and macos-14, including official MCP client checks plus VSX validation smoke.

How the Pieces Fit Together

MedPaper Assistant architecture

Claude Code, Codex, and OpenClaw

The same evidence and quality gates are available across agent runtimes:

Runtime	Project instructions	Academic-writing skill
Claude Code	`CLAUDE.md` and `AGENTS.md`	`.claude/skills/academic-writing-harness/`
Codex	`AGENTS.md`	`.agents/skills/academic-writing-harness/`
OpenClaw	`AGENTS.md` plus workspace policy	`.agents/skills/academic-writing-harness/`

The platform-neutral academic-writing workflow covers manuscripts, proposals, project closeout reports, student papers, preprints, audit gates, and safe exemplar use.

🎯 Why This Tool?

Traditional paper writing tools require you to know exactly what you want before you start. But research is rarely that linear.

Medical Paper Assistant is not just a writing assistant. It is a research workspace orchestrator:

🔍 Explore First, Decide Later — Browse literature freely, save interesting papers, then decide your research direction
📥 Source Material Intake First — Phase 0 scans user-provided DOCX/XLSX/PDF/CSV inputs and flags files that must go through asset-aware ingestion before drafting
💬 Conversational Workflow — Chat naturally with AI to refine your ideas, not fight with forms
🧭 Guided Process — Step-by-step prompts guide you from concept to publication-ready manuscript
🔗 All-in-One — Search, write, cite, analyze, export — all integrated inside VS Code

Traditional Tools	Medical Paper Assistant
Fixed templates, rigid workflow	Flexible, exploratory approach
Separate apps for search/write/cite	One orchestrated workspace: 188+ tools and packaged workflows in VS Code
Manual reference management	Auto-save with verified PubMed data
Export then format	Direct Word export with journal styles
Learn complex UI	Natural language conversation

🚀 Quick Start

Prerequisites

Requirement	Version	Check
Python	3.12+	`python3 --version`
Git	Any recent	`git --version`
VS Code	Latest	Help → About
GitHub Copilot	Extension	Extensions panel

Install

# Clone with submodules
git clone --recursive https://github.com/u9401066/med-paper-assistant.git
cd med-paper-assistant

# Run setup script
./scripts/setup.sh          # Linux/macOS
.\scripts\setup.ps1         # Windows PowerShell

The script will:

✅ Create Python virtual environment (.venv/)
✅ Initialize pinned Git submodules from this repository
✅ Install all dependencies (via uv)
✅ Create .vscode/mcp.json configuration for mdpaper, pubmed-search, cgu, zotero-keeper, asset-aware, and drawio
✅ Verify MedPaper and CGU startup paths

Important installation notes:

The setup script uses pinned submodule commits for reproducible installs. It does not auto-track the latest upstream submodule HEAD.
If you intentionally want newer submodule code, run git submodule update --remote --merge yourself and test before committing.
drawio uses npx -y @drawio/mcp, so Node.js/npm must be available on the machine.
zotero-keeper and pubmed-search are launched via uvx in the repo workflow. In the VSX workflow they may be provided either by MedPaper itself or by separate installed VS Code extensions.

Verify: In Copilot Chat, type /mcp — you should see mdpaper listed 🎉

Optional Integrations

# Foam for reference linking (highly recommended)
code --install-extension foam.foam-vscode

# Draw.io for diagram generation
./scripts/setup-integrations.sh && ./scripts/start-drawio.sh

Windows PowerShell:

.\scripts\setup-integrations.ps1
.\scripts\start-drawio.ps1

💬 MCP Prompts — Just Type and Go

In Copilot Chat, type these prompts to trigger guided workflows:

Prompt	Description
`/mdpaper.search`	🔍 Start here! Explore literature, save papers
`/mdpaper.concept`	📝 Develop research concept with novelty validation
`/mdpaper.draft`	✍️ Write manuscript with auto-citations
`/mdpaper.analysis`	📊 Analyze CSV data, generate figures & Table 1
`/mdpaper.format`	📄 Export to Word with journal formatting
`/mdpaper.clarify`	🔄 Refine specific sections through conversation
`/mdpaper.project`	📁 Create or switch research projects
`/mdpaper.strategy`	⚙️ Configure search strategy (dates, filters)
`/mdpaper.help`	❓ Show all available commands

Two Workflow Paths

Library Wiki Path

Create a project with workflow_mode="library-wiki"
Move through search/save_reference_mcp → write_library_note / move_library_note → show_reading_queues / build_library_dashboard
Use materialize_agent_wiki, Foam graph views, and docs/how-to/llm-wiki.md for cross-note synthesis and traversal

Manuscript Path

Create a project with workflow_mode="manuscript"
Move through /mdpaper.search → /mdpaper.concept → /mdpaper.draft → /mdpaper.format
Only this path enforces concept validation, review loops, and export gates

💡 Recommended usage: converge your literature and concepts in Library Wiki Path first, then switch to Manuscript Path for formal drafting.

Foam + Copilot Knowledge Base

MedPaper already uses Foam as the browse-and-graph layer while Copilot drives ingestion, identity resolution, knowledge-map generation, synthesis pages, block-anchor embeds, and managed graph slices.

The current Foam/Copilot layer now includes orphan / placeholder repair 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 and tutorials:

🧠 Skill System + Project Memory

Our core differentiator: We don't just provide tools — we provide guided workflows that know how to combine tools effectively, AND project memory that remembers your research journey across sessions.

What is a Skill?

Tool  = Single capability (search, save, analyze...)
Skill = Complete knowledge (how to combine tools to accomplish tasks)

Representative skill families across the 38 skills:

Category	Skills	Triggers
🔬 Research	`literature-review`, `concept-development`, `concept-validation`, `parallel-search`	"找論文", "search", "concept", "validate"
✍️ Writing	`draft-writing`, `reference-management`, `word-export`	"寫草稿", "draft", "citation", "export"
📁 Management	`project-management`, `memory-updater`, `memory-checkpoint`	"新專案", "切換", "存檔"
🛠️ Development	`git-precommit`, `code-refactor`, `test-generator`, `code-reviewer`	"commit", "refactor", "test"

Project Memory

Each project maintains its own .memory/ folder so the AI can continue previous research coherently. The directory layout now splits by workflow mode:

Manuscript Path

projects/{slug}/
├── .memory/
│   ├── activeContext.md   ← Agent's working memory
│   └── progress.md        ← Research milestones
├── concept.md             ← Research concept (with 🔒 protected sections)
├── references/            ← Foam-compatible literature library
├── drafts/                ← Markdown drafts with [[citations]]
├── data/                  ← CSV data files
└── results/               ← Figures, .docx exports

Library Wiki Path

projects/{slug}/
├── .memory/
│   ├── activeContext.md   ← Current library/wiki focus and triage state
│   └── progress.md        ← ingest / organize / synthesize milestones
├── concept.md             ← library workspace seed
├── references/            ← materialized reference notes
├── inbox/                 ← raw notes and capture queue
├── concepts/              ← atomic concept pages and backlinks
├── review/                ← graph repair worklists and review notes
├── daily/                 ← templated daily capture pages
└── projects/              ← synthesis pages / workstreams

✨ Key Features

Literature & References

PubMed + Europe PMC + CORE search (46 search tools)
PICO parsing for clinical questions
MCP-to-MCP verified data — PMID sent directly, no agent hallucination
Layered trust: 🔒 VERIFIED (PubMed) · 🤖 AGENT (AI notes) · ✏️ USER (your notes)
Foam wikilinks: [[author2024_12345678]] with hover preview & backlinks
Library Wiki Path — inbox/, concepts/, and projects/ note flow with reading queues and cross-note dashboards
LLM wiki materialization — auto-generated notes/index.md, notes/library/overview.md, context hubs, and draft / figure / table graph notes

Writing & Editing

AI draft generation per section (Introduction, Methods, Results, Discussion)
Citation-Aware Editing — patch_draft validates all [[wikilinks]] before saving
Auto-fix citation format — [[12345678]] → [[author2024_12345678]]
Novelty validation — 3-round independent scoring (threshold: 75/100)
Anti-AI writing rules — Evidence funnel structure, no clichés

Data Analysis

CSV dataset analysis with descriptive statistics
Statistical tests (t-test, ANOVA, chi², correlation, Mann-Whitney, Fisher's)
Table 1 generator — Baseline characteristics with automatic variable detection
Publication-ready figures (matplotlib/seaborn)

Export & Submission

Word export with journal template support
Cover letter + highlights generation
Manuscript consistency checker
Reviewer response generator (point-by-point format)
Submission checklist (word count, figure format, etc.)

Infrastructure

DDD Architecture (Domain-Driven Design) with clean layer separation
16 pre-commit hooks (ruff, mypy, bandit, pytest, prettier, doc-update...)
Workspace State recovery for cross-session continuity
uv for all Python package management
MCP SDK features in active use — tools, elicitation, and progress notifications for long-running audit/review operations
Managed Foam graph views — named Default, Evidence, Writing, Assets, and Review graph slices

🏗️ Architecture

┌──────────────────────────────────────────────────────────────────────────┐
│                          👤 User Layer                                    │
│  ┌─────────────────┐    ┌──────────────────────────────┐  ┌──────────┐  │
│  │   VS Code        │    │  Foam Extension               │  │Dashboard │  │
│  │   Editor         │    │  [[wikilinks]] autocomplete    │  │(Next.js) │  │
│  │                  │    │  hover preview · backlinks     │  │          │  │
│  └─────────────────┘    └──────────────────────────────┘  └──────────┘  │
└──────────────────────────────────────────────────────────────────────────┘
                                    │
                                    ▼
┌──────────────────────────────────────────────────────────────────────────┐
│               🤖 Copilot Agent (Orchestrator)                             │
│      38 Skills + 15 Prompt Workflows + Cross-Agent Customization         │
│   /mdpaper.search → /mdpaper.concept → /mdpaper.draft → export          │
└───────┬──────────────────┬──────────────────┬──────────────────┬─────────┘
        │                  │                  │                  │
        ▼                  ▼                  ▼                  ▼
┌───────────────┐  ┌───────────────┐  ┌───────────────┐  ┌───────────────┐
│ 📝 mdpaper    │  │🔍 pubmed-     │  │💡 cgu         │  │🔌 External    │
│ 118/22 tools  │  │  search       │  │  24 tools     │  │   MCPs (uvx)  │
│               │  │  46 tools     │  │               │  │               │
│ • projects    │  │ • PubMed      │  │ • brainstorm  │  │ 🎨 drawio     │
│ • references  │  │ • Europe PMC  │  │ • deep_think  │  │ • diagrams    │
│ • drafts      │  │ • CORE        │  │ • spark       │  │               │
│ • validation  │  │ • PICO        │  │ • methods     │  │ 📖 zotero     │
│ • analysis    │  │ • Gene/Chem   │  │               │  │ • import refs │
│ • export      │  │ • Session     │  │               │  │ 📥 asset-aware│
│               │  │               │  │               │  │ • docx/xlsx   │
│               │  │               │  │               │  │ • fulltext    │
└───────┬───────┘  └───────────────┘  └───────────────┘  └───────────────┘
        │
        ▼
┌──────────────────────────────────────────────────────────────────────────┐
│                          💾 Local Storage                                 │
│  projects/{slug}/                                                        │
│  ├── .audit/source-materials.yaml ← Phase 0 scan of user-provided inputs │
│  ├── .audit/exemplar-usage.yaml  ← non-evidentiary exemplar audit        │
│  ├── concept.md          ← Research concept with 🔒 protected sections   │
│  ├── references/{pmid}/  ← Foam-compatible .md + metadata.json           │
│  ├── drafts/             ← Markdown drafts with [[citations]]            │
│  ├── data/               ← CSV data files                                │
│  └── results/            ← Figures, .docx exports                        │
└──────────────────────────────────────────────────────────────────────────┘

MCP-to-MCP Direct Communication

When saving references, data flows directly between MCP servers — the Agent only passes a PMID, never full metadata:

Agent: "save PMID:24891204"
     │
     ▼
mdpaper.save_reference_mcp(pmid="24891204")
     │  Direct HTTP call (not through Agent)
     ▼
pubmed-search: GET /api/cached_article/24891204
     │  Returns verified PubMed data
     ▼
Saved with layered trust:
  🔒 VERIFIED: PubMed data (immutable)
  🤖 AGENT:    AI notes (marked source)
  ✏️ USER:     Your notes (editable)

🛠️ mdpaper MCP Tools

The mdpaper MCP server exposes 118 (full) / 22 (compact default) tools, plus 3 MCP prompts and 3 MCP resources for official MCP clients.

These counts are runtime-validated via tool-surface-authority.json and scripts/check_tool_surface_authority.py, and the validate/release gates fail if the docs drift from that authority.

Compact mode keeps the main facade entrypoints (project/workspace/review/pipeline/export) and hides most granular public verbs; set MEDPAPER_TOOL_SURFACE=full to expose the complete surface.

📁 Project Management

Projects, exploration mode, workspace state recovery, diagram management.

Key Tools	Description
`create_project` / `switch_project` / `delete_project`	Project lifecycle
`start_exploration` / `convert_exploration_to_project`	Explore-first workflow
`get_workspace_state` / `sync_workspace_state`	Cross-session recovery
`save_diagram` / `list_diagrams`	Draw.io integration
`setup_project_interactive`	Interactive paper type configuration
`update_authors`	Manage structured author metadata

📚 Reference Management

Save, search, format, and manage references with Foam integration.

Key Tools	Description
`save_reference_mcp`	Recommended — Save by PMID via MCP-to-MCP (verified data)
`list_saved_references` / `search_local_references`	Browse & search library
`format_references` / `set_citation_style`	Vancouver / APA / Nature
`sync_references`	Sync `[[wikilinks]]` to numbered references

✍️ Draft & Editing

Write, edit, cite — with built-in validation.

Key Tools	Description
`draft_section` / `write_draft`	Create and write sections
`list_drafts` / `read_draft` / `delete_draft`	Draft lifecycle
`get_available_citations`	List all valid `[[citation_key]]` before editing
`patch_draft`	Citation-aware partial edit with wikilink validation
`insert_citation` / `suggest_citations`	Smart citation insertion
`scan_draft_citations` / `sync_references`	Citation management
`count_words`	Section and manuscript word-count checks

✅ Validation

Tool	Description
`validate_concept`	Full novelty scoring against the active concept
`validate_wikilinks`	Auto-fix `[[12345678]]` → `[[author2024_12345678]]`
`compare_with_literature`	Compare the current idea against saved references

📊 Data Analysis

Tool	Description
`analyze_dataset`	Descriptive statistics for CSV
`run_statistical_test`	t-test, ANOVA, chi², correlation, etc.
`generate_table_one`	Baseline characteristics with auto variable detection
`create_plot`	Publication-ready figures
`insert_figure`	Insert figure into draft with archive validation
`insert_table`	Insert table into draft with archive validation
`list_assets`	List figures and tables in project results

🔍 Review & Audit

Category	Key Tools
Pipeline Gates	`validate_phase_gate`, `pipeline_heartbeat`, `validate_project_structure`
Review Loop	`start_review_round`, `submit_review_round`, `request_section_rewrite`
Pipeline Control	`pause_pipeline`, `resume_pipeline`, `approve_section`
Audit & Hooks	`run_quality_audit`, `run_writing_hooks`, `record_hook_event`
Self-Evolution	`run_meta_learning`, `verify_evolution`, `apply_pending_evolutions`
Domain Constraints	`check_domain_constraints`, `evolve_constraint`
Data & Health	`validate_data_artifacts`, `diagnose_tool_health`, `check_formatting`

📄 Export & Submission

Category	Key Tools
Inspection	`inspect_export(action="list_templates")`, `inspect_export(action="read_template")`, `inspect_export(action="verify_document")`
Session	`export_document(action="session_start")`, `export_document(action="session_insert")`, `export_document(action="session_save")`
Pandoc	`export_document(action="docx")`, `export_document(action="pdf")`, `inspect_export(action="docx_smoke")`
Submission	`generate_cover_letter`, `generate_highlights`

🧩 MCP Prompts & Resources

Capability	Names / URIs	Purpose
Prompts	`project_bootstrap`, `draft_section_plan`, `word_export_checklist`	Materialize guided prompt workflows through the official MCP prompt API
Resources	`medpaper://workspace/state`, `medpaper://workspace/projects`, `medpaper://templates/catalog`	Surface live workspace state, project lists, and template metadata via MCP resources

🔍 pubmed-search MCP Tools (46 tools)

Category	Key Tools
Search	`unified_search`, `generate_search_queries`, `parse_pico`
Databases	PubMed, Europe PMC (fulltext + text mining), CORE (200M+ open access)
Gene/Chem	`search_gene`, `get_gene_details`, `search_compound`, `search_clinvar`
Exploration	`find_related_articles`, `find_citing_articles`, `get_article_references`
Export	`prepare_export` (RIS/BibTeX/CSV), `get_citation_metrics` (iCite RCR)
Session	`read_session(action="pmids")`, `get_session_log` (survives AI memory limits)

💡 CGU Creative Tools (24 tools)

Category	Key Tools
Ideation	`generate_ideas`, `spark_collision`, `spark_collision_deep`
Analysis	`deep_think`, `multi_agent_brainstorm`
Methods	`list_methods`, `select_method`, `apply_method`

CGU runtime notes:

In the repository workflow, CGU is started from the pinned submodule with uv run --directory integrations/cgu python -m cgu.server.
In the VSX workflow, MedPaper registers CGU when bundled code or the workspace submodule is available; otherwise CGU is simply skipped.
CGU itself supports Python >=3.11, but this repository currently requires Python >=3.12, so cross-platform repo setup should be treated as Python 3.12 baseline on macOS, Linux, and Windows.
The default repo MCP example uses CGU_THINKING_ENGINE=simple, which is the low-friction mode. Advanced LLM-backed modes still depend on CGU-side model/provider configuration.

🔗 Foam Integration

Feature	How to Use	Benefit
Wikilinks	`[[greer2017_27345583]]`	Link drafts, concept pages, and synthesis notes
Hover Preview	Mouse over any `[[link]]`	See abstract without opening file
Backlinks Panel	Open reference file	See which drafts or wiki notes cite this paper
Graph View	`Ctrl+Shift+P` → `MedPaper: Show Foam Graph: ...`	Jump directly to Default / Evidence / Writing / Assets / Review
Materialized Views	`notes/index.md`, `notes/library/overview.md`	Review live counts, context hubs, and asset/draft graph nodes
Project Isolation	Auto-switches on `switch_project`	Only see current project's references

LLM Wiki Enhancements

notes/index.md emits live Foam query counts
registered figures and tables materialize as first-class graph notes
draft sections plus journal/author/topic/context hubs carry graph-friendly frontmatter
the library dashboard now exposes overview, queues, concepts, links, and synthesis cross-note views

Citation Autocomplete

Type [[ in any draft to trigger the autocomplete menu:

According to previous studies [[    ← Type [[ here
                              ┌─────────────────────────────┐
                              │ 🔍 greer2017_27345583       │
                              │    smith2020_12345678       │
                              │    chen2019_87654321        │
                              └─────────────────────────────┘

Search by author ([[greer), year ([[2017), PMID ([[27345583), or keyword ([[sedation).

📚 Reference File Structure

References are stored with Foam-optimized, layered-trust structure:

references/{pmid}/
├── {citation_key}.md   ← YAML frontmatter + abstract (human-readable)
└── metadata.json       ← Full metadata (programmatic access)

---
# 🔒 VERIFIED (from PubMed, immutable)
title: "Complications of airway management"
author:
  - { family: Pacheco-Lopez, given: Paulette C }
year: 2014
journal: Respiratory Care
pmid: "24891204"
_source:
  mcp: pubmed-search
  verified: true

# 🤖 AGENT (AI-generated, marked)
_agent:
  notes: "Key review on airway complications"
  relevance: high

# Foam
aliases: [pachecolopez2014, "PMID:24891204"]
tags: [reference, airway, review]
---

📂 Project Structure

med-paper-assistant/
├── src/med_paper_assistant/       # Core MCP server (DDD architecture)
│   ├── domain/                    #   Business logic, entities, value objects
│   ├── application/               #   Use cases, services
│   ├── infrastructure/            #   DAL, external services
│   └── interfaces/mcp/            #   MCP server, 118 full / 22 compact tools + 3 prompts + 3 resources
│
├── integrations/                  # Bundled MCP servers
│   ├── pubmed-search-mcp/         #   PubMed/PMC/CORE search (46 tools)
│   └── cgu/                       #   Creative generation (24 tools)
│
├── vscode-extension/              # Packaged VSIX surface
│   ├── src/                       #   Extension source
│   ├── bundled/tool/              #   Mirrored Python runtime for marketplace installs
│   ├── skills/                    #   Bundled skill definitions
│   ├── docs/                      #   Bundled Foam / LLM wiki docs
│   └── prompts/                   #   Quick-action prompts
│
├── dashboard/                     # Next.js project management UI
│   └── src/
│
├── projects/                      # Research projects (isolated workspaces)
│   └── {slug}/
│       ├── .memory/               #   Cross-session AI memory
│       ├── concept.md             #   Research concept or library workspace seed
│       ├── references/            #   Local reference library
│       ├── drafts/                #   Markdown drafts (manuscript path)
│       ├── inbox/                 #   Raw notes (library-wiki path)
│       ├── concepts/              #   Atomic concept pages (library-wiki path)
│       ├── projects/              #   Synthesis pages / workstreams (library-wiki path)
│       └── results/               #   Figures, exports
│
├── .agents/skills/                # Codex + OpenClaw repository skills
├── .claude/skills/                # 38 Claude Code / workflow skill definitions
├── .github/prompts/               # 15 Prompt workflow files
├── templates/                     # Journal Word templates
├── memory-bank/                   # Global project memory
└── tests/                         # pytest test suite

🗺️ Roadmap

Status	Feature	Description
✅	3 MCP Servers	mdpaper (118 full / 22 compact) + pubmed-search (46) + CGU (24)
✅	Foam Integration	Wikilinks, hover preview, backlinks, named graph views, project isolation
✅	Project Memory	`.memory/` for cross-session AI context
✅	Table 1 Generator	Auto-generate baseline characteristics
✅	Novelty Validation	3-round scoring with 75/100 threshold
✅	Citation-Aware Editing	`patch_draft` with wikilink validation
✅	MCP-to-MCP Trust	Verified PubMed data via direct HTTP
✅	Pre-commit Hooks	16 hooks (ruff, mypy, bandit, pytest, prettier...)
🔜	Richer VSX UX	TreeView, CodeLens, Diagnostics, and deeper in-editor surfaces (Direction C)
🔜	Pandoc Export	Word + LaTeX dual export with CSL citations
📋	Systematic Review	PRISMA flow, Risk of Bias, meta-analysis
📋	AI Writing Intelligence	Citation intelligence, coherence engine
📋	REST API Mode	Expose tools as REST API

Architecture Direction: Direction C — Full VSX + Foam + Pandoc

Legend: ✅

Med Paper Assistant

README