paper-init

paper-init is a skill for Claude Code from oprogramadorreal/optimus-claude. It costs 102 tokens per session (4,671 once invoked), scanned A, original, MIT.

A preparation tool that collects a research paper and organizes the information needed to implement it. It creates a local bundle with the paper, figures, references, datasets, reported results, and unresolved questions.

In plain words
What is it for?
Use it before coding a paper-based project to gather source files, transcribe the paper, document figures and data origins, and write an implementation specification.
Why use it?
It prevents implementation work from depending on scattered sources or conversation history and highlights when reproducing the paper's results may be difficult.

Skill for Claude Code

Written for Claude Code: disable-model-invocation in frontmatter. Also seen: mentions CLAUDE.md; names the AskUserQuestion tool.

Installs and runs on its own, but its text points at files inside its plugin — anything it tells you to read at a ${CLAUDE_PLUGIN_ROOT} path is only there once the plugin is installed. Installing the plugin gets both.

Part of the optimus plugin — 19 skills, 15 agents, 3 hooks shipped together

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 skills/oprogramadorreal/optimus-claude/paper-init
Any agent
npx skills add oprogramadorreal/optimus-claude --skill paper-init
Clone the repo
git clone --depth 1 https://github.com/oprogramadorreal/optimus-claude

Made for: Claude Code.

Or install optimus, the plugin that ships this one along with the rest of its 19 skills, 15 agents, 3 hooks.

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 paper-init

README.md
[![agentmods](https://agentmods.dev/badge/skills/oprogramadorreal/optimus-claude/paper-init.svg)](https://agentmods.dev/skills/oprogramadorreal/optimus-claude/paper-init)
Your own site
<a href="https://agentmods.dev/skills/oprogramadorreal/optimus-claude/paper-init"><img src="https://agentmods.dev/badge/skills/oprogramadorreal/optimus-claude/paper-init.svg" alt="Measured on agentmods" height="20"></a>
Per session 102 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 4,671 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 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 5.1 $0.00102 $0.04671
Opus 5 $0.00051 $0.02336
Sonnet 5 $0.00020 $0.00934
Haiku 4.5 $0.00010 $0.00467

Measured 2d ago against content hash 689ddbf524cd, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-05, from the pricing page.

Security

Grade A, and why

paper-init 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.

skills/paper-init/SKILL.md · 345 lines

How it starts

The opening of the file, as written. The whole thing — 345 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Paper Init

Build the local context bundle a later session needs to implement a research paper: the paper itself, its figures and references, what it specifies, what it leaves open, and its data. Context only — no implementation code, no stack setup. Everything the implementer needs must end up on disk; nothing may depend on this conversation's context.

The bundle

One paper/ directory at the project root holds everything paper-derived:

  • paper/README.md — bundle index: what this is, the read-first order, current status. Under ~50 lines.
  • paper/source/ — pristine originals only: the PDF (supplementary material included) plus the best machine-readable form available (EPUB, HTML, XML, arXiv LaTeX source), exactly as acquired. Derived files (text dumps, extracted markup) never live here.
  • paper/source/metadata.json — the provenance record (step 2).
  • paper/paper.md — the faithful working transcription (step 3).
  • paper/tables.md — overflow tables, only when the transcription takes its escape hatch (step 3).
  • paper/figures/ + paper/figures/README.md — every figure, one README line each (file, dimensions, caption) with known defects — duplicates, missing diagrams — at the top.
  • paper/references.md — every reference, annotated: role (dataset, baseline, method), resolved link, and fetch priority.
  • paper/cited/ — pristine sources of the works the paper, or a fetched work in turn, defers load-bearing content to (step 3), when any were fetched. Nothing derived lives here.
  • paper/spec.md — what the paper actually specifies (step 3), ending with the targets the implementation is later judged against.
  • paper/open-questions.md — what the paper leaves open (step 3).
  • paper/dataset.md — dataset provenance and re-acquisition, when the paper uses datasets (step 6).
  • paper/reference-code/ — vendored existing code, when it exists (step 4); gitignored, its provenance tracked in metadata.json.
  • data/ — the datasets themselves, gitignored, when any were acquired (step 6).

Read the full file on GitHub · 345 lines

Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

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 · +12 lines 689ddbf524cd
  2. 6d ago First seen · 333 lines · 102 tokens per session scan A 8a070b8c34d4

Subscribe to this mod's changes

paper-init is a skill published in the GitHub repository oprogramadorreal/optimus-claude (73 stars, last pushed yesterday), licensed MIT. It adds 102 tokens to every session and 4,671 once invoked, about $0.0005 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 2026-08-30.

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