rootcause-mcp: Instructions file for GitHub Copilot

.github/copilot-instructions.md

rootcause-mcp copilot-instructions.md is an instructions file for GitHub Copilot from u9401066/rootcause-mcp. It costs 2,974 tokens per session, scanned A, original, Apache-2.0.

A set of project instructions for coding agents working on RootCause MCP, a medical root-cause analysis project that organizes de-identified medical records and evidence. It defines how agents should handle clinical reasoning, sources, privacy, and human review.

In plain words
What is it for?
Use it when developing or reviewing RootCause MCP, especially for clinical timelines, differential diagnoses, evidence links, bias reviews, causal audits, and handover documents.
Why use it?
It gives agents the project context and safety rules needed to produce traceable, cautious work instead of treating the system as an automatic diagnosis or treatment tool.

Instructions file for GitHub Copilot

Written for GitHub Copilot: a Copilot instructions file. Also seen: reads .claude/ paths; mentions Claude Code; reads ~/.codex paths.

This is u9401066/rootcause-mcp's own configuration. It tells GitHub Copilot how to work on rootcause-mcp itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything rootcause-mcp configures →

Reuse

Borrowing it

Nothing to install: this file belongs to u9401066/rootcause-mcp. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/u9401066/rootcause-mcp/master/.github/copilot-instructions.md
Clone the repo
git clone --depth 1 https://github.com/u9401066/rootcause-mcp

Made for: GitHub Copilot.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for rootcause-mcp copilot-instructions.md

README.md
[![agentmods](https://agentmods.dev/badge/instructions/u9401066/rootcause-mcp/copilot-instructions/github.svg)](https://agentmods.dev/instructions/u9401066/rootcause-mcp/copilot-instructions)
Your own site
<a href="https://agentmods.dev/instructions/u9401066/rootcause-mcp/copilot-instructions"><img src="https://agentmods.dev/badge/instructions/u9401066/rootcause-mcp/copilot-instructions/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

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Your own site · 80×15
<a href="https://agentmods.dev/instructions/u9401066/rootcause-mcp/copilot-instructions"><img src="https://agentmods.dev/badge/instructions/u9401066/rootcause-mcp/copilot-instructions.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 2,974 This file is loaded in full into every session.
When invoked 2,974 The same file — it is already loaded in full.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.02974 $0.02974
Opus 5.5 $0.01190 $0.01190
Sonnet 5.5 $0.00595 $0.00595
Haiku 4.5 $0.00297 $0.00297

Measured 1mo ago against content hash b9ee079be6d5, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

rootcause-mcp copilot-instructions.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.github/copilot-instructions.md · 238 lines

How it starts

The opening of the file, as written. The whole thing — 238 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Copilot 自定義指令

此文件為 VS Code GitHub Copilot 及 Claude Code 提供專案上下文與操作規範。


專案概述

這是 RootCause MCP 2.x 臨床推理與醫療根因分析專案。它以 MCP SDK 2 提供 46 個 discrete tools 或 8 個 condensed facade tools,讓不同 host agent 將多來源、去識別化病歷整理成具來源血緣的時間線、鑑別診斷、evidence links、認知偏誤審查、Fishbone/Why/HFACS 保守因果稽核與標準化交接產物。

RootCause 是回溯性決策支援與稽核 harness,不是自主診斷或治療系統。所有 case workflow 必須遵守 exact provenance、PHI 最小化、保守因果判定及 qualified-human review。

MCP 本身不會思考或下診斷;host Agent 負責臨床推論,RootCause MCP 只保存、驗證與約束可稽核產物。對醫師的敘述使用繁體中文,diagnosis、test、drug、procedure 等標準名稱保留 English;首次出現的既定縮寫可附繁中對照,來源中的原文與單位不得翻譯改寫。

建立 DDx 時,先以 phenotype、time course 與不同 mechanism category 展開最大合理廣度,再選 syndrome-appropriate framework 逐一審查所有 required cells。Final PRIMARY breadth audit 不得留下 NOT_ASSESSED;REVIEWED_INSUFFICIENT_DATA 必須保留 unknowns 與 typed planned discriminators,不能視為排除。三個不重複候選是 deterministic finalization floor,不是推理目標或上限;同時避免同義重複與無限 laundry list。每個 active candidate 都要說明 why considered、source-linked support/refute/neutral evidence、unknown、discriminating test 與 qualitative certainty,並用具理由的 mutation 明確選擇 leading diagnosis。unknown 不是 negative finding;不得捏造 probability 或 LR,LR=1.0 只能表示 neutral/quantitatively unknown。非中性 LR 必須另外連到 verified LITERATURE calibration evidence,不能只寫一個看似合法的 citation 字串。

時間必須保留來源精度:只有來源自帶 offset 的 instant 可排序或支持 temporality;date、range、relative、unknown 都是合法 final 狀態,但不可被補成假時間。Pinned manifest 的 identity/digest 不可改;抽取後以 allowlisted reviewer 的 rc_adjudicate_source append review/independence event。每個 Fishbone cause 也必須由 allowlisted reviewer persist HFACS CONFIRMED 或 NOT_APPLICABLE disposition,不能把 suggestion 或 rc_add_cause 的任意 code 當人工確認。


開發哲學 💡

「想要寫文件的時候,就更新 Memory Bank 吧!」

「想要零散測試的時候,就寫測試檔案進 tests/ 資料夾吧!」

  • 不要另開檔案寫筆記,直接寫進 Memory Bank
  • 今天的零散測試,就是明天的回歸測試

法規層級

CONSTITUTION.md          ← 最高原則(不可違反)
  │
  ├── .github/bylaws/    ← 子法(細則規範)
  │     ├── ddd-architecture.md
  │     ├── git-workflow.md
  │     ├── python-environment.md
  │     └── memory-bank.md
  │
  └── .codex/skills/rootcause-clinical-reasoning-harness/  ← RootCause case workflow canonical skill

Read the full file on GitHub · 238 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 1mo ago First seen · 238 lines · 2,974 tokens per session scan A b9ee079be6d5

Subscribe to this mod's changes

rootcause-mcp copilot-instructions.md is an instructions file published in the GitHub repository u9401066/rootcause-mcp (0 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 2,974 tokens to every session, about $0.0119 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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