research-papers-plugin

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 account; requires credentials in a gitignored .secrets/bookshare.json.

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 channels fail. Enable this skill only if the install has institutional access configured.

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 waterfall.

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 is enabled (sci-hub by default, or institutional).

Read scientific papers and extract implementation-focused notes. Converts PDFs to page images, then reads them. Papers <=300pp are read directly by the assigned worker; papers >300pp use a chapter-aligned chunk protocol (preferred) or 50-page chunks (fallback) and synthesize a master notes.md that links to per-chapter files. Creates structured notes in papers/ directory.

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.

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.

Grade a drafted literature review against the cited papers' notes. For each cited @key, read that paper's notes.md/abstract.md and grade whether the citing sentence is faithful. Fans out one subagent per cited paper.

Retrieve a paper, read it, and run the full per-paper propstore ingestion flow through nested skills. Give it a URL, DOI, or title.

Check paper directories for completeness, format compliance, and index consistency. Run on a single paper or --all for the entire collection.

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 subagents (default: sequential).

Author the DeLP rule artifacts (strict, defeasible, proper_defeater, blocking_defeater) encoding a paper's stated argument structure. Runs after register-predicates.

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.

Extract inter-claim stances and author them through pks source propose-stance.

Rebuild a knowledge store from a paper collection by running paper-process per paper, then doing one final build and optional stance backfill.

Extract propositional claims from a paper directory into the propstore source branch using pks source propose-claim.

Register concepts from a paper into its propstore source branch using pks source propose-concept.

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.

Enrich existing source-branch claims by updating them through pks source propose-claim.

Extract intra-paper justification structure and author it through pks source propose-justification.

Reconcile source-branch concept vocabularies across a paper collection and report collision groups.

Initialize a propstore source branch for an extracted paper directory and write notes plus metadata into that source branch.

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 CONTEXT_PHI_NODE records that accumulate when multiple per-paper contexts share concepts with no authored bridges.

Add tags to papers that are missing them. Reads notes.md and description.md to pick 2-5 tags, preferring tags already in use. Run on a single paper directory or use --all for the entire collection.

Process all unprocessed PDFs in papers/ through the full paper-process workflow.

Promote a fully prepared propstore source branch for one paper directory into master.

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.

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.