git:20260513.3288106 to git:20260930.913abeb

34 added, 58 removed. Audit A to A.

---

name: setup-medsci

description: Diagnostic checklist for the MedSci Skills runtime. Verifies Python, R, Node, Claude Code, Git, Zotero, and configured MCP servers, and prints a pass/fail table with links to the right setup doc for any missing component. Read-only — does not install anything.

triggers: setup, install, environment, diagnostic, check setup, why doesn't this work, missing python, missing R, MCP not connected, 환경 설정, 설치 점검

tools: Bash, Read

model: inherit

---

# Setup-MedSci Skill

- You are helping a medical researcher verify that their environment is correctly configured to run MedSci Skills. You **do not install anything** — you only diagnose what's present, what's missing, and where to find the setup doc for any missing component. This skill is intentionally read-only so that a doctor can run it safely without worrying about breaking their system.

- ## Communication Rules

+ Diagnose only. **Never install, upgrade or configure anything** — no `brew install`,

+ `winget install`, `pip install`, `Rscript -e 'install.packages(...)'`, and no edits to

+ `~/.claude.json` or any MCP configuration (read `claude mcp list` only) — because auto-installers

+ for system Python and R are a support nightmare for non-developer users. If a tool is missing,

+ the user follows the setup doc themselves. Skill versions and content are out of scope

+ (`validate_skills.sh`, `/manage-project status`).

- - Communicate with the user in their preferred language (Korean or English).

- - The diagnostic table itself is in English so it can be pasted into GitHub issues for support.

- - All recommended remediation links point to `docs/setup/` markdown guides in the medsci-skills repo.

+ The diagnostic table is in English so it can be pasted into a GitHub issue. Remediation links

+ point to the `docs/setup/` guides in the medsci-skills repository, and only these five exist:

+ `docs/setup/README.md`, `docs/setup/mac.md`, `docs/setup/windows.md`, `docs/setup/mcp-setup.md`,

+ `docs/setup/common-issues.md`.

## Workflow

### Phase 1: Detect OS

- Run:

```bash

uname -s

```

- - `Darwin` → macOS path → recommend `docs/setup/mac.md`

- - `Linux` → Linux path (uses similar tooling to Mac) → recommend `docs/setup/mac.md`

- - `MINGW*`, `MSYS*`, `CYGWIN*`, or detection failure on Windows → recommend `docs/setup/windows.md`

+ - `Darwin` → macOS → `docs/setup/mac.md`

+ - `Linux` → Linux (similar tooling to Mac) → `docs/setup/mac.md`

+ - `MINGW*`, `MSYS*`, `CYGWIN*`, or detection failure on Windows → `docs/setup/windows.md`

### Phase 2: Run Diagnostic Commands

- For each tool, run the command and capture both the version output and the exit code:

- | Tool | Command | Required version |

- |---|---|---|

- | Python | `python3 --version` (Mac/Linux) or `python --version` (Windows) | 3.11 or higher |

- | R | `Rscript --version` (writes to stderr) | 4.0 or higher |

- | Node.js | `node --version` | v20 or higher |

- | Git | `git --version` | 2.30 or higher |

- | Claude Code CLI | `claude --version` | any |

- | MCP servers | `claude mcp list` | at least one of: zotero, gdrive, pubmed, filesystem |

- Use `command -v <tool>` first to detect presence without running it (avoids triggering long initialization).

+ Read `references/setup-checklist.md` and run every check in it — R1-R5 required, O1-O5 optional —

+ with its detect command, version command, minimum version and status rule. Use `command -v <tool>`

+ first to detect presence without running it (avoids triggering long initialization). Capture the

+ version output and the exit code, and report the version exactly as printed: if a command fails,

+ report the failure verbatim rather than a version that is "probably" installed. If `command -v`

+ finds the tool but the version command or its parse fails, mark the row ❌ and report the failing

+ command — the install is broken, not just outdated. An MCP server is ✅ only when

+ `claude mcp list` shows it connected; configured-but-disconnected is ⚠️.

### Phase 3: Emit Checklist Table

- Print a single Markdown table to stdout in this exact format:

+ Print a single Markdown table to stdout in this exact format, one row per check, with the doc

+ link from the reference for the detected OS:

```

## MedSci Skills Setup Diagnostic

OS detected: <macOS | Linux | Windows>

Date: <YYYY-MM-DD>

|---|:---:|---|---|---|

| Python 3.11+ | ✅ / ❌ | 3.11.9 | 3.11+ | OK / See docs/setup/mac.md Step 2 |

- | R 4.x | ✅ / ❌ | 4.3.1 | 4.0+ | OK / See docs/setup/mac.md Step 3 |

- | Node.js 20+ | ✅ / ❌ | v20.11.1 | v20+ | OK / See docs/setup/mac.md Step 4 |

- | Git | ✅ / ❌ | 2.42.0 | 2.30+ | OK / See docs/setup/<os>.md Step 5 |

- | Claude Code CLI | ✅ / ❌ | 1.5.x | any | OK / See docs/setup/<os>.md Step 6 |

Summary: <X required components passed, Y missing>

Next step: <one-sentence action>

```

Status legend:

- ✅ Present and meets minimum version

- ❌ Missing or below minimum version

- ⚠️ Present but optional and not connected

### Phase 4: Suggest Remediation

- If everything ✅: "Your environment is ready. Try Demo 1 with `cd ~/medsci-skills/demo/01_wisconsin_bc && claude '/orchestrate --e2e'`."

- If anything ❌ in **required** rows: print the corresponding doc link. Do **not** offer to install — direct the user to follow the doc step. The doc tells them exactly what to copy-paste.

- If only **optional MCP** rows are ❌: explain that MedSci Skills work without MCP servers but `lit-sync`, `verify-refs`, and `write-paper` are smoother with Zotero MCP. Offer the `docs/setup/mcp-setup.md` link.

- ## Reference Files

- - `references/setup-checklist.md` — verbatim list of every check this skill runs and the corresponding documentation link

- ## Output Contract

- | Artifact | Filename | Format |

- |----------|----------|--------|

- | Diagnostic report | stdout (Markdown table) | Markdown |

- | Optional log | `~/.medsci-skills/diagnostic-YYYY-MM-DD.md` | Markdown |

- If the user asks for a copyable report (e.g., for a GitHub issue), write the diagnostic to the optional log path and tell them where it is.

- ## What This Skill Does NOT Do

+ Use the reference's Summary Rules for the closing sentence.

- - **Does not install anything.** No `brew install`, `winget install`, `pip install`, `Rscript -e 'install.packages(...)'`, or any other state-changing command. Read-only diagnostics only.

- - **Does not modify `~/.claude.json` or any MCP configuration.** It only reads `claude mcp list` output.

- - **Does not check skill versions or skill content.** That is the job of `validate_skills.sh` and `manage-project status`.

- - **Does not auto-fix anything.** If a tool is missing, the user must go to the setup doc and follow the steps themselves. This is intentional — auto-installers for system Python and R are a support nightmare for non-developer users.

+ - Everything required ✅ → point to Demo 1:

+ `cd ~/medsci-skills/demo/01_wisconsin_bc && claude '/orchestrate --e2e'`.

+ - Any **required** row ❌ → print its doc link and tell them to follow that step. Do **not** offer

+ to install; the doc tells them exactly what to copy-paste.

+ - Only **optional MCP** rows ❌ → explain that MedSci Skills work without MCP servers, but

+ `lit-sync`, `verify-refs` and `write-paper` are smoother with Zotero MCP; link

+ `docs/setup/mcp-setup.md`.

- ## Anti-Hallucination

+ ## Output

- - **Never fabricate version numbers.** Always run the actual command and report the exact stdout. If the command fails, report the failure verbatim — do not guess what version is "probably" installed.

- - **Never invent doc paths.** The five setup docs are: `docs/setup/README.md`, `docs/setup/mac.md`, `docs/setup/windows.md`, `docs/setup/mcp-setup.md`, `docs/setup/common-issues.md`. Do not link to a doc that does not exist in the repo.

- - **Never claim an MCP server works without verifying via `claude mcp list`.** A configured-but-disconnected server is ⚠️, not ✅.

- - **If `command -v` reports a tool present but the version flag fails**, mark the row ❌ and report the failure command — the install is broken, not just outdated.

+ The diagnostic report goes to stdout. If the user asks for a copyable report (e.g. for a GitHub

+ issue), also write it to `~/.medsci-skills/diagnostic-YYYY-MM-DD.md` and tell them where it is.