init

A workflow for building a research wiki from papers, notes, and optional web sources. bioRxiv, papers, and other research sources are collected, prepared, and turned into linked wiki pages.

In plain words
What is it for?
It prepares user-provided sources, optionally discovers more, selects the final paper set, ingests papers in parallel, and updates the wiki structure and visual graph.
Why use it?
It organizes a scattered research collection into a repeatable set of notes, topics, concepts, and connections.

Skill for Claude CodeCodex

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/skyllwt/autosci/init
Any agent
npx skills add skyllwt/AutoSci --skill init
Clone the repo
git clone --depth 1 https://github.com/skyllwt/AutoSci

Made for: Claude Code, Codex.

Per session 19 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 4,365 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 $0.00019 $0.04365
Opus 5 $0.00010 $0.02183
Sonnet 5 $0.00004 $0.00873
Haiku 4.5 $0.00002 $0.00436

Measured 3d ago against content hash 681c4c42ed05, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

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 3d 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.

.claude/skills/init/SKILL.md · 283 lines

How it starts

The opening of the file, as written. The whole thing — 283 lines — stays where its author put it; the contents beside it link to each section on GitHub.

/init

Build a wiki from raw/ with deterministic source preparation, planner-guided discovery, provisional notes/web scaffolding, and parallel /ingest fan-out/fan-in.

Use these local references on demand:

  • references/prepare-and-discovery.md — prepare flow, final selection, fetch, and source-manifest rules
  • references/planner-policy.md — planner behavior and LLM trim expectations
  • references/parallel-ingest.md — worktree isolation, subagent prompt contract, merge, and cleanup

Inputs

  • topic (optional): research direction keywords; omit when raw/ already defines the seed set
  • --no-introduction (optional): disable external discovery; use only when the user explicitly requests it
  • User-owned sources under raw/papers/, raw/notes/, raw/web/

Outputs

  • wiki/ scaffold and provisional pages (Summary, topics, ideas, concepts)
  • raw/tmp/ and raw/discovered/ prepared sources
  • Final paper pages via parallel /ingest subagents
  • .checkpoints/init-*.json manifests for resume and replay
  • Updated wiki/index.md, wiki/log.md, wiki/graph/*
  • Refreshed visualization artifacts: wiki/.obsidian/graph.json (per-entity-type color groups) and wiki/canvases/*.canvas (best-effort, see Step 6). The interactive web Graph view is served by tools/serve.py (SPA), not regenerated as a standalone file.

Wiki Interaction

Reads

  • raw/papers/, raw/notes/, raw/web/
  • .checkpoints/init-prepare.json and .checkpoints/init-sources.json for resume, planning, and fan-out
  • wiki/index.md plus existing wiki/topics/, wiki/ideas/, wiki/concepts/, wiki/methods/ for duplicate avoidance and scaffold alignment

Writes

  • wiki/ scaffold and provisional pages
  • raw/tmp/ and raw/discovered/
  • wiki/index.md, wiki/log.md, wiki/graph/*
  • .checkpoints/init-prepare.json, .checkpoints/init-plan.json, .checkpoints/init-sources.json, and init-session checkpoint metadata

Graph edges created

  • /init itself creates only scaffold-level edges when provisional pages need them
  • all paper-driven edges are delegated to /ingest

Read the full file on GitHub · 283 lines

Files

What ships with it

3 files 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. 3d ago First seen · 283 lines · 19 tokens per session scan A 681c4c42ed05

Subscribe to this mod's changes

init is a skill published in the GitHub repository skyllwt/AutoSci (1,659 stars, last pushed 3d ago), licensed MIT. It adds 19 tokens to every session and 4,365 once invoked, about $0.0001 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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