PaperEcho: Instructions file for Codex

AGENTS.md

PaperEcho AGENTS.md is an instructions file for Codex, OpenCode from Chip-G0202/PaperEcho. It costs 13,794 tokens per session, scanned A, original, MIT.

Repository instructions for an AI agent working on a medical-literature project, including its workflow, operating limits, delegated capabilities, and version-control rules.

In plain words
What is it for?
Useful for maintaining the project, handling literature-related work, making changes in Git, and following its permission and execution rules.
Why use it?
They define how the agent should carry out research and coding tasks safely, including which files, services, and external systems it may use.

Instructions file for CodexOpenCode

Written for Codex and OpenCode: the file is AGENTS.md. Also seen: mentions Codex.

This is Chip-G0202/PaperEcho's own configuration. It tells Codex and OpenCode how to work on PaperEcho 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 PaperEcho configures →

Reuse

Borrowing it

Nothing to install: this file belongs to Chip-G0202/PaperEcho. 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/Chip-G0202/PaperEcho/main/AGENTS.md
Clone the repo
git clone --depth 1 https://github.com/Chip-G0202/PaperEcho

Made for: Codex, OpenCode.

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 PaperEcho AGENTS.md

README.md
[![agentmods](https://agentmods.dev/badge/instructions/chip-g0202/paperecho/agents-md.svg)](https://agentmods.dev/instructions/chip-g0202/paperecho/agents-md)
Your own site
<a href="https://agentmods.dev/instructions/chip-g0202/paperecho/agents-md"><img src="https://agentmods.dev/badge/instructions/chip-g0202/paperecho/agents-md.svg" alt="Measured on agentmods" height="20"></a>
Per session 13,794 This file is loaded in full into every session.
When invoked 13,794 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 $0.13794 $0.13794
Opus 5 $0.06897 $0.06897
Sonnet 5 $0.02759 $0.02759
Haiku 4.5 $0.01379 $0.01379

Measured 8d ago against content hash 2213f85a3dca, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-08, from the pricing page.

Security

Grade A, and why

PaperEcho AGENTS.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 8d 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.

AGENTS.md · 707 lines

How it starts

The opening of the file, as written. The whole thing — 707 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Medical Literature Workflow Agent Reference

General Execution Environment And Permission Boundaries

  • Default to completing tasks within the current repository/workspace.
  • Recommended sandbox permission is Workspace write.
  • Use Read only mode for auditing and planning work.
  • Full access is a temporary exception only. Before requesting it, report exact paths, reason, scope of impact, risk, and rollback method, then wait for user approval.
  • Keep project files, generated artifacts, temporary files, and test outputs inside the workspace.
  • Prefer workspace runtime, project-local configuration, or standard user-level cache directories for Node, dependencies, and caches.
  • Do not access, copy, index, or expose unrelated sensitive paths, including SSH private keys, browser data, Desktop, Downloads, personal Documents, or system configuration directories.
  • Before network access, dependency installation, Zotero access, external API calls, global configuration changes, or reading/writing files outside workspace, report exact commands, necessity, impact scope, rollback availability, and whether a workspace-local alternative exists, then wait for approval.
  • Before each major modification round, run git status --short; if the working tree is not clean, report existing changes first.
  • Suggest creating a branch before large or high-risk modifications.
  • Never reset, checkout, clean, delete, or overwrite existing user changes without explicit permission.
  • If node/npm/python or other runtimes are not executable or lack permission, classify as an environment failure, not a business test failure.
  • Prioritize diagnosing PATH and runtime paths, and prioritize workspace-provided or project-approved runtimes. Do not request Full access only because one path is not executable.

Goal

Operate a weekly medical literature pipeline with parallel entry channels:

  • RSS ingestion
  • PubMed/PMC retrieval via direct NCBI requests in the scripts

Then run unified dedup, triage, Zotero writeback, translation backfill, and workbook export in the existing Research OS structure.

Read the full file on GitHub · 707 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. 8d ago First seen · 707 lines · 13,794 tokens per session scan A 2213f85a3dca

Subscribe to this mod's changes

PaperEcho AGENTS.md is an instructions file published in the GitHub repository Chip-G0202/PaperEcho (56 stars, last pushed 8d ago), licensed MIT. It adds 13,794 tokens to every session, about $0.0690 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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