OpenELIS-Global-2: Instructions file for Codex

AGENTS.md

OpenELIS-Global-2 AGENTS.md is an instructions file for Codex, OpenCode from DIGI-UW/OpenELIS-Global-2. It costs 21,663 tokens per session, scanned A, original, MPL-2.0.

General instructions for AI coding agents working on OpenELIS Global 2, an open-source laboratory information management system for public-health laboratories. They define who owns file-based data transfer and provide project prerequisites such as the required Java version.

In plain words
What is it for?
Use them when working on OpenELIS laboratory workflows, file ingestion, bridge integration, result processing, or setup and compatibility checks.
Why use it?
They prevent agents from putting functionality in the wrong part of the system or violating the stated ownership model. They also provide essential project context before code changes begin.

Instructions file for CodexOpenCode

Written for Codex and OpenCode: the file is AGENTS.md. Also seen: reads .claude/ paths; mentions CLAUDE.md; mentions Claude Code.

This is DIGI-UW/OpenELIS-Global-2's own configuration. It tells Codex and OpenCode how to work on OpenELIS-Global-2 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 OpenELIS-Global-2 configures →

Needs its repository: it reads a path above its own folder, which exists only inside the repository. The line is import messages from "../../../languages/en.json";.

Reuse

Borrowing it

Nothing to install: this file belongs to DIGI-UW/OpenELIS-Global-2. 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/DIGI-UW/OpenELIS-Global-2/develop/AGENTS.md
Clone the repo
git clone --depth 1 https://github.com/DIGI-UW/OpenELIS-Global-2

Made for: Codex, OpenCode.

Wrote this? Show the measurements

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Per session 21,663 This file is loaded in full into every session.
When invoked 21,663 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 $0.21663 $0.21663
Opus 5.5 $0.08665 $0.08665
Sonnet 5.5 $0.04333 $0.04333
Haiku 4.5 $0.02166 $0.02166

Measured 8d ago against content hash f006ad98180e, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

OpenELIS-Global-2 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 · 2,507 lines

How it starts

The opening of the file, as written. The whole thing — 2,507 lines — stays where its author put it; the contents beside it link to each section on GitHub.

AGENTS.md - README for AI Coding Agents

Start here — do these three things before any other work

These are not optional and not "if needed". Skipping them is the single most common way an agent wastes a session in this repository.

1. Install the agent command assets

python3 scripts/install-agent-skills.py -y claude

This installs /fix-ci, /download-ci-logs, /address-pr-comments, /careful-rebase and ~22 others, plus the packaged skills.

.claude/ is gitignored. It is created by this script, not by git clone and not by git pull. A second clone or worktree of this repository therefore has no commands at all until you run the installer there — and nothing warns you, the commands are simply absent. Run it once per checkout, including every worktree.

2. Never judge CI from a run's conclusion

Use gh pr checks <PR>. It matches the GitHub UI and exits non-zero unless everything passes.

gh pr checks 1234                      # the whole picture
gh pr checks 1234 | grep -E "fail"     # just the failures

The three build checkpoints are 01 Checkpoint - Backend, 02 Checkpoint - Frontend, and 03 Checkpoint - E2E. The trusted Validation / Submodule pins check is also required after its rollout below. Early in a run only some checks exist, so confirm all required checks are present and none are pending before calling a PR green.

Do not use gh run watch --exit-status: 03 Checkpoint - E2E is posted by a workflow_run follow-up stage, so the underlying run's own conclusion does not tell you whether the checkpoint passed, and gh run watch exits 0 on failure for this pipeline. Do not write ad hoc jq over statusCheckRollup either: it mixes CheckRun nodes (.conclusion) with StatusContext nodes (.state), an in-flight check reports an empty conclusion rather than null, and a re-run leaves the earlier run of a check in the list. Naive jq reports passing checks as queued and single checks as "all green"; scripts/download-ci-logs.sh handles all three.

Read the full file on GitHub · 2,507 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 Changed · +3 lines · +53 tokens per session f006ad98180e
  2. 9d ago Changed · +2 lines · +30 tokens per session 4a6833d3d0bb
  3. 11d ago Changed · -59 lines · -691 tokens per session d94a04ee9139
  4. 15d ago Changed · +26 lines · +379 tokens per session 9223faf5e8c0
  5. 17d ago Changed · -36 lines · -4 tokens per session 236dac224b8c
  6. 19d ago Changed · +17 lines · +257 tokens per session 8faad2150674
  7. 20d ago Changed 07f8d19c46be
  8. 21d ago Changed · -1 tokens per session 2396c2ff07c5
  9. 22d ago Changed · +42 tokens per session 876da49f3098
  10. 25d ago First seen · 2,554 lines · 21,598 tokens per session scan A 6278e983f3c8

Subscribe to this mod's changes

OpenELIS-Global-2 AGENTS.md is an instructions file published in the GitHub repository DIGI-UW/OpenELIS-Global-2 (272 stars, last pushed today), licensed MPL-2.0. It adds 21,663 tokens to every session, about $0.0867 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 2026-08-30.

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