med-paper-assistant: Skill for Claude Code

.claude/skills/auto-paper/SKILL.md

auto-paper is a skill for Claude Code from u9401066/med-paper-assistant. It costs 89 tokens per session (34,632 once invoked), scanned A, original, Apache-2.0.

An automated academic-paper writing workflow takes a research project from planning through drafting and review. It records searches, source-selection decisions, methods, quality checks, and the steps taken so the work can be audited or resumed.

In plain words
What is it for?
Use it to draft a complete research paper, check references and methodology, validate novelty, and review compliance. It stores audit records and checkpoints so an interrupted project can continue from a later phase.
Why use it?
It reduces the need to coordinate many separate research and writing checks by hand. It also exposes problems with citations, reproducibility, writing quality, and adherence to the required process.

Skill for Claude Code

Written for Claude Code: installed under .claude/. Also seen: reads .claude/ paths; mentions subagents; mentions AGENTS.md.

This is u9401066/med-paper-assistant's own configuration. It tells Claude Code how to work on med-paper-assistant 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 med-paper-assistant configures →

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/skills/auto-paper/SKILL.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.

agentmods badge for auto-paper

README.md
[![agentmods](https://agentmods.dev/badge/skills/u9401066/med-paper-assistant/auto-paper/github.svg)](https://agentmods.dev/skills/u9401066/med-paper-assistant/auto-paper)
Your own site
<a href="https://agentmods.dev/skills/u9401066/med-paper-assistant/auto-paper"><img src="https://agentmods.dev/badge/skills/u9401066/med-paper-assistant/auto-paper/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.

agentmods 80×15 button for auto-paper

Your own site · 80×15
<a href="https://agentmods.dev/skills/u9401066/med-paper-assistant/auto-paper"><img src="https://agentmods.dev/badge/skills/u9401066/med-paper-assistant/auto-paper.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 89 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 34,632 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector warn 7 Sept 2026
SkillSpector: 6 findings, up to medium

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

  • medium Prompt Injection · line 60
    Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.
    Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
  • medium Tool Misuse · line 364
    Tool defaults are unsafe or overly permissive (e.g. disabled TLS verification, no authentication, world-writable permissions). Unsafe defaults widen the attack surface.
    Fix: Override unsafe defaults with secure settings (verify=True, auth required, restrictive permissions). Review and harden all tool configurations.
  • medium Agent Snooping · line 1985
    Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.
    Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
  • medium Agent Snooping · line 1989
    Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.
    Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
  • medium Prompt Injection · line 2122
    Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.
    Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
  • medium Prompt Injection · line 2133
    Large whitespace padding was detected (a block of blank lines or a long run of spaces). This can push injected instructions below or to the right of the visible area so a human reviewer never sees them while the agent still reads them. Manual review of the hidden content is recommended.
    Fix: Remove the large whitespace padding (blank-line blocks or long space runs) and review any content hidden below or to the right of it. Keep skill files compact and reviewable so no instructions can be
How audits are shown
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 $0.00089 $0.34632
Opus 5 $0.00044 $0.17316
Sonnet 5 $0.00018 $0.06926
Haiku 4.5 $0.00009 $0.03463

Measured 7d ago against content hash 3c5bb370b790, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

auto-paper 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 7d 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/skills/auto-paper/SKILL.md · 2,219 lines

How it starts

The opening of the file, as written. The whole thing — 2,219 lines — stays where its author put it; the contents beside it link to each section on GitHub.

全自動論文撰寫 + 閉環自我改進

閉環架構

Instructions (AGENTS.md) → Skill (auto-paper) → Writing (drafts/) → Hooks (audit) → 回頭更新 Skill/Instructions

核心理念(CONSTITUTION §22):可審計、可拆解、可重組。詳見 AGENTS.md。

四個審計維度:

維度 檢查 更新對象
Paper 引用、字數、Anti-AI draft_action(action="patch") 修正論文
Methodology 方法學可再現性 補充方法學細節
Compliance Agent 是否遵循流程 .memory/ 記錄偏差
Meta Skill/Hook/Instruction 更新 SKILL/Hook/AGENTS

執行審計軌跡(Audit Trail)

每次執行在 projects/{slug}/.audit/ 產出:

檔案 內容
pipeline-run-{ts}.md Phase 摘要 + Hook 統計 + Decision Log
search-strategy.md 搜尋策略和結果
reference-selection.md 文獻篩選決策
concept-validation.md Novelty 驗證過程
hook-effectiveness.md Hook 觸發率/通過率/誤報率
quality-scorecard.md 方法學 + 文字品質(0-10 分)
checkpoint.json 斷點恢復:last_completed_phase, phase_outputs

恢復邏輯:偵測 checkpoint.json → 詢問從 Phase N+1 繼續或重來。


雙重 Hook 系統

Copilot Hooks(A-D,寫作時即時修正)定義於本檔。 Pre-Commit Hooks(P1-P8 + G1-G7)定義於 git-precommit/SKILL.md。 兩者互補:Copilot 處理細節,Pre-Commit 處理全局。


🚧 Hard Gate Enforcement(Code-Level,不可跳過)

SKILL.md 是 soft constraint(Agent 可能忽略)。以下 MCP Tools 是 code-enforced hard limits

必要 MCP Tool 呼叫

時機 MCP Tool 說明
每個 Phase 完成後 pipeline_action(action="validate_phase", phase=...) 返回 PASS/FAIL + 缺少的 artifact,FAIL 則禁止進入下一 Phase
Phase 7 每輪開始 pipeline_action(action="start_review") 啟動 AutonomousAuditLoop 狀態機,返回 round context
Phase 7 每輪結束 pipeline_action(action="submit_review", scores=...) 提交分數,返回 verdict (CONTINUE/QUALITY_MET/MAX_ROUNDS/REWRITE_NEEDED)
Phase 7 需要大幅重寫 pipeline_action(action="rewrite_section", sections=..., reason=...) 回退到 Phase 5 重寫指定 section,最多 2 次回退
Phase 5 每 section 完成後 pipeline_action(action="approve_section", section=..., decision=...) Autopilot: Agent 自我審閱後自動 approve。手動: 用戶審閱 → approve 或 revise。Phase 5 gate 要求全部 approved
用戶要求暫停時 pipeline_action(action="pause", reason=...) 暫停 pipeline,記錄 draft hash 以偵測用戶編輯
暫停後恢復 pipeline_action(action="resume") 恢復 pipeline,偵測用戶修改並建議重新驗證
Pipeline 中途任意時刻 pipeline_action(action="heartbeat") 返回全 Phase 狀態 + 剩餘工作項,Agent 無法自稱 "done"
Agent 需要一次總檢查時 pipeline_action(action="doctor") 返回 11-phase readiness、外部 MCP 宣告/command 可用性、最近 gate cache
Phase 5 每次 Hook 評估後 record_hook_event(hook_id, event_type) 記錄 A/B/C/E Hook 的 trigger/pass/fix/false_positive,Phase 6 gate 會驗證有實際記錄
Phase 6 之前(審計階段) run_quality_checks(action="quality_audit", scores=...) 設定 ≥4 維度品質分數 + 產生 scorecard/hook-effectiveness 報告,Phase 6 gate 驗證分數數據
Phase 10 之前(自我改進) run_quality_checks(action="meta_learning") 執行 D1-D9 分析 + 寫入 meta-learning-audit.yaml / meta-learning-feedback.yaml,Phase 10 gate 驗證 analysis_steps

Read the full file on GitHub · 2,219 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. 7d ago Changed · -4 lines 3c5bb370b790
  2. 11d ago First seen · 2,223 lines · 89 tokens per session scan A 9f968081602b

Subscribe to this mod's changes

auto-paper is a skill published in the GitHub repository u9401066/med-paper-assistant (12 stars, last pushed 9d ago), licensed Apache-2.0. It adds 89 tokens to every session and 34,632 once invoked, about $0.0004 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.

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