template AGENTS.md

A project instruction document for a reproducible research template. It explains the system, its documentation, publications, and guidance for assistants and automation.

In plain words
What is it for?
Use it to understand the template’s structure, find the right documentation, and follow the project’s research and publication procedures.
Why use it?
It gives coding agents a shared map of the project instead of making them infer how the research files and processes fit together.

Instructions file for CodexOpenCode

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

agentmods
npx agentmods add instructions/docxology/template/agents-md
Clone the repo
git clone --depth 1 https://github.com/docxology/template

Made for: Codex, OpenCode.

Per session 17,938 This file is loaded in full into every session.
When invoked 17,938 The same file β€” it is already loaded in full.
Security scan D 4 findings. Scan, not verified.
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 $0.17938 $0.17938
Opus 5 $0.08969 $0.08969
Sonnet 5 $0.03588 $0.03588
Haiku 4.5 $0.01794 $0.01794

Measured 2d ago against content hash c747c2e415e0, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade D, and why

template AGENTS.md scanned grade D with 4 findings against 26 rules in 11 categories β€” prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency β€” measured 2d 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.

Asks for rootmediumPrivilege escalation

A mod that escalates privileges can change anything on the machine, not only the project.

sudo tlmgr update --self

Recursive force deletehighDestructive command

rm -rf with a variable or a broad path is one typo away from removing the wrong tree.

remove the stale env entirely: `rm -rf projects/{name}/.venv` (it is regenerated on demand;

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

with patch('requests.post') as mock_post:

Runs shell commandslowCapability

Expected in a hook, worth knowing in a rule or an instructions file.

result = subprocess.run(
AGENTS.md Β· 1,564 lines

How it starts

The opening of the file, as written. The whole thing β€” 1,564 lines β€” stays where its author put it; the contents beside it link to each section on GitHub.

πŸ€– AGENTS.md - System Documentation

🎯 System Overview

This document provides documentation for the Research Project Template system, ensuring understanding of all functionality, configuration options, and operational procedures.

πŸ“„ Publication

Title: A template/ approach to Reproducible Generative Research: Architecture and Ergonomics from Configuration through Publication DOI: 10.5281/zenodo.19139090 Β· Record: zenodo.org/records/19139090

template/ applies Infrastructure as Code to the research lifecycle: version-controlled manuscripts, tests, provenance, and a declared pipeline DAG. Layer 1 (infrastructure/) is separated from Layer 2 (self-contained projects under projects/). Current measured counts and stage facts live in docs/_generated/COUNTS.md; re-derive them instead of copying literals into prose. Each directory carries README.md + AGENTS.md; infrastructure packages usually add SKILL.md for agent routing. Full paper, metrics, and claims: Zenodo record above and root README.md.

Documentation map

Entry Role
README.md Onboarding, documentation hub links, exemplar table
.cursorrules Cursor agents: layer rules, CI scope, editing discipline
CLAUDE.md Command cheat sheet, patterns; keep in sync with this file for pipeline wording
This file (AGENTS.md) Full reference: stages, validation, modules, troubleshooting
docs/documentation-index.md Flat index of long-lived docs
docs/_generated/active_projects.md Authoritative public CI/documentation project names β€” never hard-code rotating private paths in docs
docs/_generated/COUNTS.md Measured coverage and counts; refresh after changing gates or discovery
.github/README.md GitHub: CI overview, templates, Dependabot
.github/AGENTS.md Actions job names, coverage gates, local reproduction commands
TO-DO.md Current backlog, scoped by acceptance line
CHANGELOG.md Release history

Read the full file on GitHub Β· 1,564 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. 2d ago First seen Β· 1,564 lines Β· 17,938 tokens per session scan D c747c2e415e0

Subscribe to this mod's changes

template AGENTS.md is an instructions file published in the GitHub repository docxology/template (19 stars, last pushed 2d ago), licensed Apache-2.0. It adds 17,938 tokens to every session, about $0.0897 per session on Opus 5. A static security scan graded it D with 4 findings (asks for root, recursive force delete, makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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