MedKarute (メドカルテ) - research-helper

AI Orchestrator + Amanuensis for Research 研究を支えるAIオーケストレーターと書記

Languages: Tiếng Việt — more in docs/readme/ (human-only, not in agent load map)

MedKarute (formerly research-helper) is a chat-driven research assistant: an agent (orchestrator) runs the research workflow via chat, writes results to Markdown under research/{slug}/, and calls two MCP servers — MarkItDown (new PDFs) and endnote-mcp (curated EndNote library). Governance (AGENTS.md, CLAUDE.md, docs/) defines how the agent behaves; research data lives in separate per-project folders.

Getting started

1. Clone or open this repo.
2. Use an agent coding tool (Claude Code, Grok CLI, Cursor, …) or a plain CLI (claude, grok, …) — from the repo root, say "bắt đầu" (or "start").
3. The agent reads AGENTS.md / CLAUDE.md → runs onboarding (slug + purpose) → creates research/{slug}/ if you have no project yet.

Nothing fancy. A coding tool or IDE only makes files, diffs, and the tree easier to see — the agent still works from committed .md files. Plain CLI without an IDE works the same; no specific tool is required.

End-user guide (distilled, for the researcher — not the agent): docs/guides/huong-dan-su-dung.md.

Workflow (overview)

                         +------------------+
                         | EndNote via user |
                         +--------+---------+
                                  ^
                                  |
  +---------+              +------+--------+              +-------------+
  | New PDF |------------->|   paper note  |------------->|   insight   |
  +---------+              +---------------+              +------+------+
                                                                 |
  +--------------+         +---------------+                     |
  | chat session |-------->| session note  |---------------------+
  +--------------+         +---------------+                     |
                                                                 v
                                                           +-------------+
                                                           |   writing   |
                                                           +-------------+

Artifacts, INDEX routing, per-project git → docs/guides/research/00-overview.md.

Tools & roles

Tool	Role in MedKarute
MarkItDown MCP	Convert new PDFs → token-efficient Markdown for the agent (papers not yet in EndNote)
endnote-mcp	Read curated EndNote library — search, deep PDF read, citation/bibliography. Read-only (writes via EndNote desktop)
WhySchools / context-mapping (context-gen)	Same lineage — WhySchools Human is the brain agentic workflow: shared memory in .context/ (GLOBAL, MILESTONES, TENSIONS, modules). This repo adopts that governance layout → .context/GLOBAL.md. Early MCP brainstorm archived in docs/raws/research-helper.md. Not a runtime dependency for research sessions
Markpad	Local .md viewer for the user — not an MCP, viewer only

Quick links

File	Purpose
AGENTS.md	Invariants, startup order
CLAUDE.md	Orchestrator playbook
docs/guides/research/00-overview.md	research/ workflow detail
docs/decisions/endnote-workflow.md	EndNote workflow (canonical)
CONTRIBUTING.md	Đóng góp — test thật, báo lỗi, sửa governance