Reaper

Reaper (REAd PapER) — an AI-native scientific research pipeline. A composable set of AI agent skills that takes a research goal — optionally with a research paper — and autonomously conducts rigorous, multi-step academic research. Runs on any agent that supports the SKILL.md convention (Cursor, Codex CLI, Cline, Continue, Gemini CLI, Copilot, Windsurf, Claude Code, and 40+ more).

What Reaper Does

Give Reaper a research question — with or without a PDF. It reads the paper (if provided), searches for related work, formalizes hypotheses, investigates them in parallel, critiques its own findings, and delivers a structured research report — all without manual prompting between steps.

# Without a paper — pure goal-driven research
/reaper "explore the feasibility of post-quantum threshold signatures"

# With a paper
/reaper "determine if the security proof in Section 4 holds under asynchrony" path/to/paper.pdf

How you invoke a skill depends on the host agent. The /<skill> form above is the canonical display convention used throughout these docs — it works directly on slash-command hosts (e.g. Claude Code), and on auto-discovery hosts (Cursor, Codex CLI, Cline, Continue, Gemini CLI, Copilot, Windsurf, …) you simply ask the agent to "run the /reaper skill on …" by its bare name.

Key capabilities:

• Autonomous multi-stage pipeline — goal clarification, paper analysis, literature review, hypothesis formalization, parallel investigation, critique, and synthesis all chain automatically
• Parallel investigation with keep-or-discard discipline — multiple hypotheses are investigated concurrently; only genuine progress advances the working state, while dead ends stay logged
• Built-in academic search — paper search, PDF download, citation graph tracing, and venue resolution across arXiv, IACR ePrint, Semantic Scholar, DBLP, and OpenAlex
• Domain-agnostic design — ships with cryptography and distributed systems references, but swap the reference files to adapt to any research domain
• Multi-model AI consultation — optionally consult Codex, Gemini, DeepSeek, or local models for a second opinion at every pipeline stage
• Composable skills — each pipeline stage is an independent skill you can run standalone
• Host-agnostic — distributed as plain SKILL.md folders that work across 45+ AI coding agents

How It Works

Reaper executes a multi-stage pipeline where investigation runs in parallel batches and critique provides feedback from multiple sources:

                     ┌── /analyze-paper (if paper) ──┐
/clarify-goal ─────> │                               ├─> /formalize-problem
                     └── /review-literature ─────────┘          │
                           │ (parallel)                         v
                           │                    ┌──────────> /brainstorm
                           └── calls            │                │
                               /analyze-paper   │                │
                               per downloaded   │    ┌─ /investigate ─────────────────┐
                               paper            │    │  plan batch                    │
                                                │    │    ├──> agent H1 ─┐            │
                                                │    │    ├──> agent H2 ─┼──> merge   │
                                                │    │    └──> agent H3 ─┘     │      │
                                                │    │          next batch or done    │
                                                │    └────────────────────────────────┘
                                                │                    │
                                                │    ┌─ /critique ────────────────────┐
                                                │    │  --self  --codex  "feedback"   │
                                                │    └────┬───────────────────┬───────┘
                                                │         │                   │
                                                │   deepen/explore    rewrite/done ──> /synthesize ──> report.md
                                                └─────────┘

Skills

Each skill can be used independently or composed by the orchestrator. Invoke by skill name using your host's native skill-loading mechanism.

Skill	What it does
/reaper	Full pipeline: clarify → analyze → literature → formalize → brainstorm → investigate ↔ critique → synthesize
/clarify-goal	Ask targeted clarifying questions to sharpen a vague research goal
/analyze-paper	Extract structured information from a research paper
/review-literature	Search and summarize related academic work
/formalize-problem	Produce precise, testable hypotheses from a research question
/brainstorm	Generate, prioritize, and refine research ideas based on current state
/investigate	Run investigation cycles with keep-or-discard discipline
/critique	Provide critique via human feedback, Codex consultation, or self-review (can trigger more investigation)
/synthesize	Generate a structured research report from investigation results
/search-paper	Find papers, download PDFs, trace citation graphs, and resolve publication venues across arXiv, IACR ePrint, Semantic Scholar, DBLP, and OpenAlex

The /<skill> form is the canonical display convention used throughout these docs. Slash-command hosts (Claude Code) invoke them directly that way (e.g. /clarify-goal). Auto-discovery hosts (Cursor, Codex CLI, Cline, Continue, Gemini CLI, Copilot, Windsurf, …) invoke them by the bare skill name — drop the leading / when asking the agent to run a skill.

Installation

Prerequisites

The search skills require Python packages:

pip install arxiv requests beautifulsoup4

Note: npx skills only copies SKILL.md files, Python scripts, and reference files into your agent's skills folder. It does not install Python dependencies, register MCP servers, or create the reaper-workspace/ directory. Install Python deps yourself with the command above; register the Codex MCP server separately if you want --codex (see Optional: Multi-model AI consultation below); the workspace directory is created automatically the first time the pipeline runs.

Install via npx skills (recommended — works on 45+ agents)

Reaper is distributed as standard SKILL.md folders. The cross-agent installer vercel-labs/skills shallow-clones this repository and copies all 10 skill directories — including Python scripts and reference files — into your agent's conventional skills folder.

# Latest from the default branch
npx skills add SebastianElvis/reaper

# Pinned to a specific release (recommended for reproducibility)
npx skills add SebastianElvis/reaper#v0.4.0

# Install into a specific agent (defaults to all detected)
npx skills add SebastianElvis/reaper --agent cursor

Supported targets include Cursor, OpenAI Codex CLI, Cline, Continue, Gemini CLI, GitHub Copilot, Windsurf, OpenCode, Warp, Goose, Replit, Claude Code, and a universal target at .agents/skills/. See npx skills list-agents for the full list.

Reminder: npx skills add copies files only. Python deps and MCP server registration are separate steps — see Prerequisites above and Optional: Multi-model AI consultation below.

Install on Claude Code (as a plugin)

Claude Code can also consume Reaper via its native plugin marketplace mechanism, which bundles the same skills with slash-command routing:

/plugin marketplace add SebastianElvis/reaper
/plugin install reaper@SebastianElvis-reaper

Or clone and add as a local marketplace:

git clone https://github.com/SebastianElvis/reaper.git
/plugin marketplace add ./reaper
/plugin install reaper@reaper

See the Claude Code plugin docs for more details.

Invocation across hosts

• Slash-command hosts (Claude Code): /reaper "<goal>", /analyze-paper <path>, etc. Each skill is available as a top-level slash command.
• Auto-discovery hosts (Cursor, Codex CLI, Cline, Continue, Gemini CLI, Copilot, Windsurf, …): the agent loads SKILL.md files from its skills folder and invokes them by name when the task matches the skill's description. Ask the agent to run the skill, e.g. "use the reaper skill to research X".
• Manual invocation: any host can be pointed at a specific SKILL.md if its native discovery doesn't pick it up.

A few skill features are host-specific:

• The --codex flag enables external-model consultation via MCP. It currently requires a host with MCP support (Claude Code, OpenCode, etc.) and silently falls back to self-review elsewhere.
• Frontmatter keys user-invocable, argument-hint, hooks, and context: fork are Claude-Code-specific. They are preserved in the SKILL.md files but no-op on other hosts.

Optional: Multi-model AI consultation

Pass --codex to enable pipeline-wide AI consultation — every skill gains a checkpoint where it can consult an external model for a second opinion. The orchestrator controls when consultations happen and routes to the best-suited model (see skills/reaper/references/codex-consultation.md for the protocol).

Supported backends:

Model	Setup	Strength
OpenAI Codex/o3	Register codex-mcp-server in your host's MCP config	Adversarial review, stress-testing arguments
Google Gemini	(coming soon)	Long-context review across full paper corpora
DeepSeek R1	(coming soon)	Proof checking, formal reasoning
Local models	(coming soon — via ollama)	Offline/private use, cost control

Example registration on Claude Code:

claude mcp add codex-cli -- npx -y codex-mcp-server

Other MCP-capable hosts use their own equivalent registration. If no model backends are configured, AI consultation is silently skipped and the pipeline continues with self-review only.

Workspace

When Reaper runs, it creates a reaper-workspace/ directory:

reaper-workspace/
├── notes/                          # Evolving — edited inline to reflect latest state
│   ├── clarified-goal.md           # Refined goal, scope, assumptions, Q&A
│   ├── paper-summary.md            # Structured paper extraction
│   ├── literature.md               # Related work survey
│   ├── problem-statement.md        # Formalized problem (model, properties, metrics)
│   ├── ideas.md                    # Research ideas/hypotheses (edited inline on revisit)
│   ├── current-understanding.md    # "Branch tip" — advances only on keep
│   └── results.md                  # One row per hypothesis, updated inline on revisit
├── investigations/                 # Evolving — reuse directory on revisit, edit inline
│   └── NNN-<name>/                 # One directory per hypothesis
│       ├── analysis.md             # Reasoning, attempts, dead ends, insights
│       └── proof.md                # Formal proofs (theorems, lemmas, corollaries)
├── feedbacks/                      # Append-only — one file per event, never modified
│   ├── round-N.md                  # Human feedback classified by type
│   └── codex-consultation-N.md     # Codex critique (alternates devil's advocate / inspiration)
├── logs/                           # Append-only — one file per cycle, never modified
│   └── cycle-NNN-<slug>.md         # One log per investigation cycle (snapshot at cycle end)
└── report.md                       # Final synthesized output

The workspace contract is host-agnostic — any agent that can read and write files in the working directory produces the same workspace structure.

Evaluation

Skills ship with a layered evaluation system following Anthropic's Demystifying Evals for AI Agents methodology. The judge is the local claude CLI — no API key, just your existing subscription.

Layer	Grader	Cadence	Scope
L1 Structural	Code (evals/graders/)	Every PR (CI)	Required sections, lengths, broken refs, keep-or-discard cycle invariant
L2 Skill rubric	claude -p with structured-output JSON schema (evals/judge/)	Locally / nightly	Per-skill quality dimensions: groundedness, specificity, completeness
L3 End-to-end	Both	Pre-release	Full /reaper pipeline against canonical cases

# L1 only (no LLM) — same thing CI runs
python3 -m evals.run_evals --layer structural

# L1 + L2 (uses your local claude CLI)
python3 -m evals.run_evals --layer all --skill analyze-paper

Each fixture pairs a gold-standard reference with planted negatives — one targeting L1 (drops a required section) and one targeting L2 (fabricated theorem statements, generic content) — so a permissive grader fails CI as visibly as a missed regression. See evals/README.md for the full design and how to add a fixture.

Methodology

Reaper's research loop follows six principles:

1. Separation of Concerns — AI writes to workspace, human provides the goal, skill definitions are fixed
2. Fixed Evaluation Signal — Clarify the goal, establish baseline via paper analysis and literature review, then formalize into precise hypotheses with trust assumptions, security properties, and impossibility screening
3. Structured Results Log — Every hypothesis gets one row in notes/results.md with action, outcome, confidence, and keep/discard status; revisits update the row inline rather than appending duplicates
4. Keep-or-Discard Loop — current-understanding.md only advances on genuine progress; dead ends stay logged but don't pollute working state
5. Never Stop — Run all cycles without asking permission to continue; if stuck, re-read the paper, question assumptions, combine discarded results, search for more related work, or try a radically different approach
6. Clarity and Simplicity — One "ping" per finding, refutable claims, fewer assumptions = better; write early to crystallize understanding, not just to report it

See dev/ROADMAP.md for the full methodology and development roadmap.

Development Status

See dev/ROADMAP.md for the full roadmap.

• Horizon 1 (The Pipeline): Core skills, orchestrator, and layered eval system (L1 structural graders + L2 Claude-CLI judges with rubrics, calibrated against planted negatives) — complete; LaTeX report output and broader rubric coverage across all skills planned
• Horizon 2 (The Library): arXiv/ePrint search via Python scripts + citation graph + venue resolution (Semantic Scholar / DBLP / OpenAlex) — complete
• Horizon 3 (The Committee): Multi-model critique via the /critique skill's --codex mode — Codex complete, Gemini/DeepSeek/local planned
• Horizon 3.5 (The Polyglot): Cross-agent distribution via npx skills and host-agnostic skill prose — complete; per-host orchestration polish ongoing
• Horizon 4 (The Academy): Broader topic search (Scholar/DBLP), author-centric and venue-centric search — planned
• Horizon 5 (The Apprentice): Evidence quality taxonomy, evidence-aware critique — planned
• Horizon 6 (The Examiner): Proactive reformulation trigger, claim provenance, formal verification — planned

Acknowledgements

Reaper's methodology draws from the following sources:

• karpathy/autoresearch — Loop discipline: constrain the loop so the AI can iterate autonomously with a clear signal of progress. The structured results log, keep-or-discard mechanism, and never-stop policy are direct adaptations.
• Richard Hamming, "You and Your Research" — The importance filter ("Why are you not working on the important problems?") and the technique of inverting blockages into insights.
• Zhiyun Qian, "How to Look for Ideas in Computer Science Research" — Systematic idea generation patterns (fill-in-the-blank, start-small-then-generalize, build-a-hammer) for formulating research ideas.
• Simon Peyton Jones, "How to Write a Great Research Paper" — Writing as a primary mechanism for doing research, not just reporting it. Shapes the report structure: one clear "ping," explicit refutable contributions, examples before generality.
• S. Keshav, "How to Read a Paper" (ACM SIGCOMM CCR, 2007) — The three-pass method for reading papers: first pass for the big picture, second pass to grasp content without details, third pass to virtually re-derive the work and challenge every assumption. Structures how the literature review skill reads downloaded papers at increasing depth.
• Mathew Stiller-Reeve, "How to Write a Thorough Peer Review" (Nature, 2018) — Three-reading review method (aims → scientific substance → presentation) and the mirror technique. Structures the per-paper notes in the literature review skill: mirror the paper's claims, classify issues as major/minor/fatal, evaluate whether conclusions answer the introduction's questions.
• vercel-labs/skills — The cross-agent skills convention and CLI installer that makes Reaper portable across 45+ AI coding agents.

License

This project is open source. Licensed under the Apache License 2.0.