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.
npx skills add jinleiphys/research_LLM_wiki --skill literature-wikigit clone --depth 1 https://github.com/jinleiphys/research_LLM_wikiWrote 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.
[](https://agentmods.dev/skills/jinleiphys/research_llm_wiki/literature-wiki)<a href="https://agentmods.dev/skills/jinleiphys/research_llm_wiki/literature-wiki"><img src="https://agentmods.dev/badge/skills/jinleiphys/research_llm_wiki/literature-wiki/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.
<a href="https://agentmods.dev/skills/jinleiphys/research_llm_wiki/literature-wiki"><img src="https://agentmods.dev/badge/skills/jinleiphys/research_llm_wiki/literature-wiki.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00233 | $0.04642 |
| Opus 5 | $0.00117 | $0.02321 |
| Sonnet 5 | $0.00047 | $0.00928 |
| Haiku 4.5 | $0.00023 | $0.00464 |
Grade A, and why
literature-wiki 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 12d 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.
How it starts
The opening of the file, as written. The whole thing — 298 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Literature Wiki Maintenance (Schema v2)
This file is the canonical operational protocol. Harness-neutral. The skill ships parallel SKILL.md (Claude Code) and AGENTS.md (Codex CLI) bodies kept in sync by hand. If you edit one, edit the other.
Schema v2 (current) introduces controlled vocabulary on the source frontmatter and an update-index operation that augments each concept page (methods/.md, systems/.md, etc.) with an auto-generated "Papers using this" appendix. Pre-v2 wikis can run migrate to backfill.
v2.1 addition: every source page opens with a ## For future agents gist (see "Source page gist" below). Pre-v2.1 source pages get backfilled on next touch or flagged by lint.
Why this skill exists
Most LLM-document workflows look like RAG: every question re-discovers knowledge from raw PDFs. Nothing accumulates. For a researcher reading dozens of papers a year on related topics, this is wasted compounding.
This skill maintains a persistent, structured wiki of markdown files. When the user reads a new paper, the skill reads it, extracts what matters, and integrates it into existing entity / method / system pages — updating cross-references, flagging where new data contradicts old claims, strengthening the evolving synthesis. The wiki is the compiled artifact; the raw PDFs sit beside it but are not the primary lookup layer.
The user curates and asks. The skill writes and maintains.
The pattern is field-independent. Default category names suit physical-science research; users in other fields rename in their <wiki>/CLAUDE.md.
Wiki location
Resolution order:
LITERATURE_WIKI_PATHenv var.~/.literature-wiki-path(single-line absolute path).- Default:
~/research-wiki/.
If absent, ask before creating.
Wiki layout
<wiki>/
├── CLAUDE.md / AGENTS.md # ⭐ vocabulary + per-wiki style overrides (v2)
├── index.md # navigation hub (manual)
├── log.md # chronological log of ingests/queries/lints
├── raw/ # source PDFs/markdown, IMMUTABLE
│ └── assets/ # downloaded figures
├── sources/ # one page per paper, summary + key numbers + tags
├── entities/ # author / group / experiment / code-package pages (manual + AUTO appendix)
├── methods/ # method-level pages (manual + AUTO appendix)
├── systems/ # system-level pages (manual + AUTO appendix)
├── observables/ # quantity-level pages (manual + AUTO appendix)
├── debates/ # explicit pages for who-disagrees-with-whom
└── synthesis/ # cross-cutting themes, working theses
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.
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.
- 12d ago First seen · 298 lines · 0 tokens per session scan A a72615c3399e
literature-wiki is a skill published in the GitHub repository jinleiphys/research_LLM_wiki (10 stars, last pushed 2mo ago), licensed MIT. It adds 233 tokens to every session and 4,642 once invoked, about $0.0012 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.
Other skills, from other repositories
reconcile
Cross-reference a paper against the collection. Finds which cited papers are already collected, which are new leads, which collection papers cite this one, and reconciles all cross-references bidirectionally. Run on a single paper directory or use --all for the entire collection.
adjudicate
Systematically adjudicate disagreements across a paper collection. Produces ruthless verdicts on who was wrong, what supersedes what, and what the best current understanding is. Organized by topic clusters with actionable replacement values for implementation.
author-context
Create a propstore context for one paper with CEL assumptions, parameters, and perspective. Every claim extracted from the paper will reference this context. Required before extract-claims if the paper does not already have one.
author-rules
Author the DeLP rule artifacts (strict, defeasible, properdefeater, blockingdefeater) encoding a paper's stated argument structure. Runs after register-predicates.
extract-claims
Extract propositional claims from a paper directory into the propstore source branch using pks source propose-claim.
paper-retriever
Retrieve a scientific paper PDF given an arxiv URL, DOI, or paper title. Downloads to papers/ directory. Handles open-access retrieval (arxiv direct, Chrome print-to-pdf for publisher-direct HTML, Unpaywall, title-based open-repository search); for paywalled papers it hands off to whichever paper-retriever- access…