research-setup

research-setup is a skill for Claude Code from a2ngerer/claude_onboarding_agent. It costs 53 tokens per session (2,641 once invoked), scanned A, original, MIT.

A configuration setup for the input side of academic research, including literature reviews, paper screening, summaries, references, annotated bibliographies, and reading notes. It is for preparing and organizing research, not drafting the final manuscript.

In plain words
What is it for?
Use it to review academic literature, screen papers, summarize sources, manage references with Zotero, and create annotated bibliographies or reading notes.
Why use it?
It gives research work a defined process and keeps reading, screening, and reference-management tasks together instead of mixing them with manuscript writing.

Skill for Claude Code

Written for Claude Code: PreToolUse hook event. Also seen: reads .claude/ paths; mentions CLAUDE.md; mentions Claude Code.

Part of the claude-onboarding-agent plugin — 16 skills, 4 agents, 1 hook shipped together

Good fit Use it to review academic literature, screen papers, summarize sources, manage references with Zotero, and create annotated bibliographies or reading notes.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/a2ngerer/claude_onboarding_agent/research-setup
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.

Any agent
npx skills add a2ngerer/claude_onboarding_agent --skill research-setup
Clone the repo
git clone --depth 1 https://github.com/a2ngerer/claude_onboarding_agent

Made for: Claude Code.

Or install claude-onboarding-agent, the plugin that ships this one along with the rest of its 16 skills, 4 agents, 1 hook.

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 research-setup

README.md
[![agentmods](https://agentmods.dev/badge/skills/a2ngerer/claude_onboarding_agent/research-setup/github.svg)](https://agentmods.dev/skills/a2ngerer/claude_onboarding_agent/research-setup)
Your own site
<a href="https://agentmods.dev/skills/a2ngerer/claude_onboarding_agent/research-setup"><img src="https://agentmods.dev/badge/skills/a2ngerer/claude_onboarding_agent/research-setup/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.

agentmods 80×15 button for research-setup

Your own site · 80×15
<a href="https://agentmods.dev/skills/a2ngerer/claude_onboarding_agent/research-setup"><img src="https://agentmods.dev/badge/skills/a2ngerer/claude_onboarding_agent/research-setup.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 53 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,641 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector warn 7 Sept 2026
SkillSpector: 2 findings, up to medium

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

  • medium Agent Snooping · line 151
    Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.
    Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
  • medium Agent Snooping · line 201
    Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.
    Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
How audits are shown
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 $0.00053 $0.02641
Opus 5 $0.00026 $0.01321
Sonnet 5 $0.00011 $0.00528
Haiku 4.5 $0.00005 $0.00264

Measured 9d ago against content hash aedcc38d21b3, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-08, from the pricing page.

Security

Grade A, and why

research-setup 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 9d 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.

skills/research-setup/SKILL.md · 240 lines

How it starts

The opening of the file, as written. The whole thing — 240 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Research Setup

This skill configures Claude for academic and research work.

Handoff context: Read skills/_shared/consume-handoff.md and run it with the handoff block (if any). The helper guarantees the following locals: detected_language, existing_claude_md, inferred_use_case, repo_signals, graphify_candidate. Use detected_language for all user-facing prose; generated file content stays in English.

Existing CLAUDE.md: If existing_claude_md: true, DO NOT overwrite it. Append a new delimited section at the end of the file:

<!-- onboarding-agent:start setup=research skill=research-setup section=claude-md -->
## Claude Onboarding Agent — Research Setup
...generated content...
<!-- onboarding-agent:end -->

If the delimited block already exists from a previous run, replace only the content between the markers; leave the rest untouched. Wrap generated .gitignore entries in # onboarding-agent: research — start / — end markers so /upgrade-setup can refresh them non-destructively.

Supporting Files

Read these on-demand at the step that invokes them. Do not read eagerly.

  • skills/_shared/consume-handoff.md — orchestrator handoff parse + inline fallback (preamble, before Step 1)
  • skills/_shared/offer-superpowers.md — canonical Superpowers opt-in (Step 1)
  • skills/_shared/offer-graphify.md — canonical Graphify opt-in (Step 5)

Step 1: Install Dependencies

Read skills/_shared/offer-superpowers.md and run it with skill_slug: research-setup, mandatory: false, capability_line: "A widely used free Claude Code skills library. Brainstorming and planning skills work well for structuring research arguments and planning complex documents." The helper asks the user, delegates to skills/_shared/installation-protocol.md on yes, and sets superpowers_installed, superpowers_scope, superpowers_method.

Step 2: Context Questions

Ask one at a time:

  1. "What is your research domain? (e.g., machine learning, economics, molecular biology, history, philosophy)"

Read the full file on GitHub · 240 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. 9d ago First seen · 240 lines · 53 tokens per session scan A aedcc38d21b3

Subscribe to this mod's changes

research-setup is a skill published in the GitHub repository a2ngerer/claude_onboarding_agent (5 stars, last pushed today), licensed MIT. It adds 53 tokens to every session and 2,641 once invoked, about $0.0003 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 2026-08-31.

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