What is med-paper-assistant CLAUDE.md?

Repository instructions for an academic-writing code project. They set rules for safe changes, project structure, source verification, and formal writing tasks.

Following repository governance, checking required files, preserving verified content, using the stated Python workflow, and guiding manuscript, proposal, preprint, or report work.

They give a coding agent the project’s rules before it acts, reducing unsafe edits, unsupported academic claims, and confusion about which instructions take priority.

How u9401066/med-paper-assistant configures Claude Code

Reuse

Borrowing it

Nothing to install: this file belongs to u9401066/med-paper-assistant. 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/med-paper-assistant/master/CLAUDE.md

Clone the repo

git clone --depth 1 https://github.com/u9401066/med-paper-assistant

Made for: Claude Code.

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.

README.md

[![agentmods](https://agentmods.dev/badge/instructions/u9401066/med-paper-assistant/claude-md/github.svg)](https://agentmods.dev/instructions/u9401066/med-paper-assistant/claude-md)

Your own site

<a href="https://agentmods.dev/instructions/u9401066/med-paper-assistant/claude-md"><img src="https://agentmods.dev/badge/instructions/u9401066/med-paper-assistant/claude-md/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.

Your own site · 80×15

<a href="https://agentmods.dev/instructions/u9401066/med-paper-assistant/claude-md"><img src="https://agentmods.dev/badge/instructions/u9401066/med-paper-assistant/claude-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 395 This file is loaded in full into every session.

When invoked 395 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.

Model	Per session	Once invoked
Fable 5.1	$0.00395	$0.00395
Opus 5	$0.00198	$0.00198
Sonnet 5	$0.00079	$0.00079
Haiku 4.5	$0.00040	$0.00040

Measured 9d ago against content hash 3b1c603bd345, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

med-paper-assistant CLAUDE.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 9d 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.

CLAUDE.md · 45 lines

What it actually says

Claude Code Repository Guide

This repository is a production-oriented academic-writing harness. The full governance source is AGENTS.md; this file keeps Claude Code's always-loaded context concise.

Before any operation

Read .copilot-mode.json. Only modify protected code paths in development mode.
Follow the authority order: CONSTITUTION.md > .github/bylaws/*.md > skill instructions.
Preserve user changes in a dirty worktree and use uv for Python tasks.

Architecture and safety

Keep dependencies directed as Presentation -> Application -> Domain <- Infrastructure.
Prefer PubMed-originated verified metadata over agent-transcribed metadata.
Never edit verified source content, user notes, or constitutional safeguards through an autonomous evolution step.
Treat exemplar papers as structure/style evidence only. Never copy wording, claims, data, citations, or conclusions from them without independent verification and attribution.

Academic-writing work

Use .claude/skills/academic-writing-harness/SKILL.md for manuscripts, proposals, closeout reports, student papers, preprints, and other formal academic outputs.
Resume state from .mdpaper-state.json and project .memory/ before restarting a pipeline.
Respect phase gates, audit artifacts, section approval, and citation provenance. Do not claim completion until the final gate passes.

Verification

Python: uv run ruff check src tests scripts, uv run mypy src, uv run pytest.
Security/dead code: uv run bandit -q -r src and uv run vulture src scripts --min-confidence 80.
Extension: run the relevant npm checks under vscode-extension/.
Update tests, documentation, Memory Bank, and release notes when behavior or public contracts change.

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.

9d ago First seen · 45 lines · 395 tokens per session scan A 3b1c603bd345

Subscribe to this mod's changes

med-paper-assistant CLAUDE.md is an instructions file published in the GitHub repository u9401066/med-paper-assistant (12 stars, last pushed 8d ago), licensed Apache-2.0. It adds 395 tokens to every session, about $0.0020 per session on Opus 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 2026-08-30.

Writing and docs academic-writing ai-assistant ai-tools citation-manager clinical-research copilot

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med-paper-assistant: Instructions file for Claude Code