What is scholaraio AGENTS.md?

Project instructions for ScholarAIO, an all-in-one academic research tool used through a coding agent. They explain the project, preferred workflows, and where its code and guidance live.

Use them when developing ScholarAIO, using its command-line interface, choosing project skills, or handling literature, evidence, and research outputs.

They help agents work through the project’s normal tools and preserve research context instead of making isolated changes.

How ZimoLiao/scholaraio configures Codex and OpenCode

Reuse

Borrowing it

Nothing to install: this file belongs to ZimoLiao/scholaraio. 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/ZimoLiao/scholaraio/main/AGENTS.md

Clone the repo

git clone --depth 1 https://github.com/ZimoLiao/scholaraio

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.

README.md

[![agentmods](https://agentmods.dev/badge/instructions/zimoliao/scholaraio/agents-md/github.svg)](https://agentmods.dev/instructions/zimoliao/scholaraio/agents-md)

Your own site

<a href="https://agentmods.dev/instructions/zimoliao/scholaraio/agents-md"><img src="https://agentmods.dev/badge/instructions/zimoliao/scholaraio/agents-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/zimoliao/scholaraio/agents-md"><img src="https://agentmods.dev/badge/instructions/zimoliao/scholaraio/agents-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 1,988 This file is loaded in full into every session.

When invoked 1,988 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	$0.01988	$0.01988
Opus 5.5	$0.00795	$0.00795
Sonnet 5.5	$0.00398	$0.00398
Haiku 4.5	$0.00199	$0.00199

Measured 1mo ago against content hash 458e3bb495d4, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

scholaraio 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 1mo 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 · 137 lines

How it starts

The opening of the file, as written. The whole thing — 137 lines — stays where its author put it; the contents beside it link to each section on GitHub.

ScholarAIO - Agent Entry

This is the repository entry document for coding agents. It is intentionally short:

keep durable project facts and hard constraints here
move multi-step procedures into skills
move deep reference material into the indexed docs/ knowledge base

What ScholarAIO Is

ScholarAIO is an All-in-One academic harness for agents. Researchers work through a coding agent to search literature, inspect evidence, organize persistent project context, produce reviewable research outputs, and use bounded scientific-tool adapters without ScholarAIO replacing the agent's native reasoning or orchestration.

The Python package is scholaraio. Real work should usually happen through the ScholarAIO CLI and project skills, not by bypassing runtime helpers with ad hoc file edits.

How To Work In This Repo

Prefer a matching project skill in .claude/skills/ when the user request clearly maps to one.
Use the scholaraio CLI to do real work instead of only describing what should be done.
Load information progressively. Prefer metadata or abstracts first, then conclusions or full text only when needed.
Treat paper conclusions as claims, not facts. Compare evidence, point out limitations, and distinguish supported results from author interpretation.
Keep user-facing drafts, reports, exports, and research outputs under workspace/, not the repository root or scholaraio/.
Do not casually rewrite or delete runtime data. When touching runtime layout, use Config, migration helpers, and tested accessors.
When changing runtime layout, compatibility behavior, agent entry docs, or skill discovery, update tests and aligned docs in the same change.
After code or doc changes, run the relevant checks and at least one real smoke path when feasible.

Start Here

Read these in roughly this order:

README.md for the product overview and top-level structure.
STRATEGY.md before changing product scope or adding an external integration.
docs/DESIGN.md for the repository knowledge map.
docs/getting-started/agent-setup.md for repo-open vs plugin or cross-project setup.
docs/guide/cli-reference.md for the current user-facing CLI surface.
docs/guide/agent-reference.md for deeper agent, runtime, and skill organization details.
docs/internal/PLANS.md and docs/internal/exec-plans/completed/scholaraio-upgrade-plan.md before changing runtime layout, migration, or compatibility behavior.

Read the full file on GitHub · 137 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.

1mo ago Changed · -4 lines · -58 tokens per session 458e3bb495d4
2mo ago First seen · 141 lines · 2,046 tokens per session scan A 9eb5501516f7

Subscribe to this mod's changes

scholaraio AGENTS.md is an instructions file published in the GitHub repository ZimoLiao/scholaraio (584 stars, last pushed 10d ago), licensed MIT. It adds 1,988 tokens to every session, about $0.0080 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.

Research agentic-science agentic-search ai-agent computational-research research-workflow scientific-computing

scholaraio AGENTS.md next to 6 instructions from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
scholaraio AGENTS.mdZimoLiao/scholaraio	Instructions file	584	10d ago	MIT	A	1,988	Codex, OpenCode
vscode buildNext.instructions.mdmicrosoft/vscode	Instructions file	195k	yesterday	MIT	A	9,719	GitHub Copilot
next.js AGENTS.mdvercel/next.js	Instructions file	143k	today	MIT	A	7,461	Codex, OpenCode
langchain AGENTS.mdlangchain-ai/langchain	Instructions file	149k	yesterday	MIT	A	4,680	Codex, OpenCode
vscode oss-third-party-notices.instructions.mdmicrosoft/vscode	Instructions file	195k	yesterday	MIT	A	5,516	GitHub Copilot
vscode copilot-instructions.mdmicrosoft/vscode	Instructions file	195k	yesterday	MIT	A	3,093	GitHub Copilot
deepseek-harness AGENTS.mddeepseek-ai/deepseek-harness	Instructions file	274k	2d ago	MIT	A	4,313	Codex, OpenCode

scholaraio: Instructions file for Codex