Research paper collection management plugin for Claude Code, Codex CLI, and Gemini CLI
Skill Claude CodeCodex
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.
Skill Claude CodeCodex
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.
Skill Claude CodeCodex
Author DeLP/McCarthy context lifting rules between existing context YAMLs so cross-context claim reasoning can proceed. Collection-level, runs after all papers are ingested. Targets the CONTEXTPHINODE records that accumulate when multiple per-paper contexts share concepts with no authored bridges.
Skill Claude CodeCodex
Author the DeLP rule artifacts (strict, defeasible, properdefeater, blockingdefeater) encoding a paper's stated argument structure. Runs after register-predicates.
Skill Claude CodeCodex
Enrich existing source-branch claims by updating them through pks source propose-claim.
Skill Claude CodeCodex
Extract propositional claims from a paper directory into the propstore source branch using pks source propose-claim.
Skill Claude CodeCodex
Extract intra-paper justification structure and author it through pks source propose-justification.
Skill Claude CodeCodex
Extract inter-claim stances and author them through pks source propose-stance.
Skill Claude CodeCodex
Rebuild a knowledge store from a paper collection by running paper-process per paper, then doing one final build and optional stance backfill.
Skill Claude CodeCodex
Process all unprocessed PDFs in papers/ through the full paper-process workflow.
Skill Claude CodeCodex
Check paper directories for completeness, format compliance, and index consistency. Run on a single paper or --all for the entire collection.
Skill Claude CodeCodex
Retrieve a paper, read it, and run the full per-paper propstore ingestion flow through nested skills. Give it a URL, DOI, or title.
Skill Claude CodeCodex
Read scientific papers and extract implementation-focused notes. Converts PDFs to page images, then reads them. Papers at most 300pp are read directly by the assigned worker; papers greater than 300pp use a chapter-aligned chunk protocol (preferred) or 50-page chunks (fallback) and synthesize a master notes.md that…
Skill Claude CodeCodex
Credentialed-source backend for retrieving books from Bookshare (bookshare.org) into the papers/ collection. Given a book title or ISBN and a target directory name, it searches Bookshare and downloads the EPUB via the published bookshare CLI. Download-only (produces book.epub). Enable only if you have a Bookshare…
Skill Claude CodeCodex
Paywalled-access backend for paper-retriever. Retrieves a paywalled paper's PDF through an institutional / library subscription (a library proxy such as EZproxy or OpenAthens, or an institutional login), given an identifier (DOI/URL) and the target paper directory name. Invoked by paper-retriever when open-access…
Skill Claude CodeCodex
Paywalled-access backend for paper-retriever. Retrieves a paywalled paper's PDF via sci-hub browser automation, given an identifier (DOI/URL) and the target paper directory name. Invoked by paper-retriever when open-access channels fail; enabled by default. Disable this skill to remove sci-hub from the retrieval…
Skill Claude CodeCodex
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…
Skill Claude CodeCodex
Extract all "New Leads" from the paper collection and process them via paper-process. Retrieves and reads papers that other papers in your collection cite but you don't have yet. Use --all to process everything, or pass a number to limit (e.g., "10" for first 10). Add --parallel N to process N leads concurrently via…
Skill Claude CodeCodex
Process all unprocessed PDF files in the papers/ root directory. If subagents are available, parallelize across papers immediately after listing them; otherwise process sequentially. Any PDF in papers/ root is unprocessed by convention (processed papers live in subdirectories). Invokes paper-reader on each PDF.
Skill Claude CodeCodex
Reconcile source-branch concept vocabularies across a paper collection and report collision groups.
Skill Claude CodeCodex
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.
Skill Claude CodeCodex
Register concepts from a paper into its propstore source branch using pks source propose-concept.
Skill Claude CodeCodex
Author the DeLP/Datalog predicate declaration artifacts a paper's rules will use. Required before author-rules if the paper's rules reference predicates not yet declared.
Skill Claude CodeCodex
Research a topic using web search and create structured findings. Use when you need to investigate approaches, find papers, compare implementations, or gather knowledge on a topic. Creates structured notes in reports/ directory.