research-skills: Instructions file for Codex

AGENTS.md

research-skills AGENTS.md is an instructions file for Codex, OpenCode from neuromechanist/research-skills. It costs 3,565 tokens per session, scanned A, original, BSD-3-Clause.

Repository-specific instructions for a research-skills marketplace, which distributes add-ons for academic research and development workflows.

In plain words
What is it for?
Use it when maintaining marketplace plugins, research workflow skills, manifests, or explicit project-management commands.
Why use it?
It explains the marketplace layout and the skills-first model, where natural-language requests select skills automatically instead of relying mainly on command wrappers.

Instructions file for CodexOpenCode

Written for Codex and OpenCode: the file is AGENTS.md. Also seen: mentions .claude-plugin; mentions CLAUDE.md; mentions subagents.

This is neuromechanist/research-skills's own configuration. It tells Codex and OpenCode how to work on research-skills 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 research-skills configures →

Reuse

Borrowing it

Nothing to install: this file belongs to neuromechanist/research-skills. 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/neuromechanist/research-skills/main/AGENTS.md
Clone the repo
git clone --depth 1 https://github.com/neuromechanist/research-skills

Made for: Codex, OpenCode.

Wrote this? Show the measurements

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README.md
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Per session 3,565 This file is loaded in full into every session.
When invoked 3,565 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 $0.03565 $0.03565
Opus 5.5 $0.01426 $0.01426
Sonnet 5.5 $0.00713 $0.00713
Haiku 4.5 $0.00357 $0.00357

Measured 2d ago against content hash b509a5e472eb, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

research-skills 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 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.

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 · 120 lines

How it starts

The opening of the file, as written. The whole thing — 120 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Research Skills Marketplace

Purpose

Cross-agent marketplace providing plugins and skills for academic research workflows and development tooling: literature search and review, grant writing and review, manuscript preparation, figures, presentations, project lifecycle management, neuroinformatics, and cloud GPU provisioning for model training.

Skills-first model

This marketplace follows a skills-first surface. Skills auto-trigger from natural-language intent (description matching). Commands are kept only for workflows that need explicit /command args orchestration: project init, epic/sprint management, version bumps. Thin command wrappers around skills have been removed; do not reintroduce them.

Marketplace Structure

research-skills/
├── .claude-plugin/marketplace.json  # Claude Code marketplace manifest; legacy-compatible for Codex/Copilot
├── .agents/plugins/marketplace.json # Native Codex repo marketplace manifest
├── .github/plugin/marketplace.json  # Native Copilot CLI marketplace manifest
├── plugins/
│   ├── project/                      # Project lifecycle toolkit
│   │   ├── .claude-plugin/plugin.json
│   │   ├── .codex-plugin/plugin.json
│   │   ├── .github/plugin/plugin.json
│   │   ├── commands/{init-project,update-rules,epic-dev,epic-status,release-prep}.md
│   │   ├── skills/{init-project,project-preflight,update-rules,install-user-instructions,workflow-reference,epic-dev,pr-review-toolkit,codebase-onboarding,implementation-planning,engineering-loop,debugging,agent-fanout,ci-scaffolding,docker-packaging,security-audit,document-processing}/
│   │   ├── agents/{dependency-auditor,release-prep,pr-review-toolkit}.md
│   │   ├── agents/templates/pr-review-toolkit.{toml,agent.md}
│   │   ├── templates/               # AGENTS, Claude, Cursor, context, config, CI/CD
│   │   └── bin/                     # project-preflight, project-init-templates, project-diff-rules, project-templates-path
│   ├── grant/                        # Grant proposal toolkit
│   │   ├── .claude-plugin/plugin.json
│   │   ├── .codex-plugin/plugin.json
│   │   ├── .github/plugin/plugin.json
│   │   ├── skills/{grant-writing,grant-review,grant-figure-qa}/
│   │   ├── agents/{grant-figure-qa,grant-review}.md
│   │   └── agents/templates/{grant-review,grant-figure-qa}.{toml,agent.md}
│   ├── manuscript/                   # Academic manuscript toolkit
│   │   ├── .claude-plugin/plugin.json
│   │   ├── .codex-plugin/plugin.json
│   │   ├── .github/plugin/plugin.json
│   │   ├── skills/{paper-review,manuscript-writing,manuscript-formatting,lit-review,humanizer}/
│   │   ├── agents/paper-review.md
│   │   └── agents/templates/paper-review.{toml,agent.md}
│   ├── opencite/                     # Literature search and citation management
│   │   ├── .claude-plugin/plugin.json
│   │   ├── .codex-plugin/plugin.json
│   │   ├── .github/plugin/plugin.json
│   │   └── skills/opencite/
│   ├── figures/                      # Publication-quality figures (v0.13.0)
│   │   ├── .claude-plugin/plugin.json
│   │   ├── .codex-plugin/plugin.json
│   │   ├── .github/plugin/plugin.json
│   │   ├── skills/{figure-bible,scientific-figure,transparent-icons,svg-figure,svg-primitives,ai-full-figure,plot-styling,figure-qa}/
│   │   ├── lib/{image_backend,prompting,theme}.py + schemas/theme.schema.json + tests/
│   │   ├── agents/figure-qa.md + figure-qa-scripts/{check_svg,check_raster,check_plot_script}.py
│   │   └── agents/templates/figure-qa.{toml,agent.md}
│   ├── presentation/                 # Interactive slide decks
│   │   ├── .claude-plugin/plugin.json
│   │   ├── .codex-plugin/plugin.json
│   │   ├── .github/plugin/plugin.json
│   │   └── skills/presentation-builder/
│   ├── neuroinformatics/             # Neuro data standards + experiments
│   │   ├── .claude-plugin/plugin.json
│   │   ├── .codex-plugin/plugin.json
│   │   ├── .github/plugin/plugin.json
│   │   ├── skills/{bids-conversion,experiment-design}/
│   │   └── agents/bids-validator.md + agents/templates/bids-validator.{toml,agent.md}
│   └── ml-training/                  # Cloud GPU provisioning for training/benchmarks
│       ├── .claude-plugin/plugin.json
│       ├── .codex-plugin/plugin.json
│       ├── .github/plugin/plugin.json
│       └── skills/runpod/ + references/ + templates/
├── .context/
    └── plan.md
└── .memory/
    ├── README.md
    └── INDEX.md

Read the full file on GitHub · 120 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 Changed · +17 tokens per session b509a5e472eb
  2. 10d ago Changed · +12 tokens per session 920a7e6efa53
  3. 12d ago Changed · +119 tokens per session 98fe8cce845a
  4. 13d ago Changed · +15 tokens per session 56aa1d9ba484
  5. 1mo ago Changed · +14 lines · +211 tokens per session 8d98be671ad8
  6. 1mo ago Changed · +1 lines · -73 tokens per session 5d41fdc97c93
  7. 1mo ago First seen · 105 lines · 3,264 tokens per session scan A fe3204255c51

Subscribe to this mod's changes

research-skills AGENTS.md is an instructions file published in the GitHub repository neuromechanist/research-skills (50 stars, last pushed 2d ago), licensed BSD-3-Clause. It adds 3,565 tokens to every session, about $0.0143 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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