Reference · 47 slash commands

Slash commands

Every command is typed inside Claude Code. It resolves the active library from ~/.config/ref-manager/config.json and fails loudly, pointing at /ref:init, when none is configured. Commands that work on a set of papers share one selector grammar; see selectors.

Reading the reference. Each entry lists its arguments, the steps it runs, which files it reads and writes, a terminal example, and the script or subagent behind it. Chips mark the build phase, external dependencies (PubMed, Papers.app), subagent use, and read-only commands.

Bring papers in

/ref:init <path>: create a library where you choose and record it in the config file
/ref:add <pmid…>: core ingest path: resolve metadata via PubMed, dedupe by PMID, allocate a stable citekey
/ref:add-pdf <path…>: identify PDFs by DOI/PMID clues, add PubMed records, then attach the files
/ref:add-fetch <pmid…>: convenience wrapper: add missing records, then fetch full text for records that exist
/ref:add-url <url…>: identify articles by URL (DOI/PMID/PMCID clues or page metadata), add records, then fetch
/ref:import <item…>: source-aware front door: routes a mix of PMIDs, URLs, PDFs/folders, DOIs, or BibTeX/CSL-JSON into add/fetch/attach
/ref:fetch <pmid…>: acquire full text in priority order and convert it to source.md, per-PMID results
/ref:fetch-pdf <pmid…>: download free PMC OA PDFs and attach them through the PDF pipeline
/ref:attach <pmid> <path> …: attach PDFs you already have, after an identity check
/ref:read <pmid…>: render a local HTML reading copy from the current full-text version and figures
/ref:extract <pmid…>: full claim extraction, one ref-extractor subagent per paper
/ref:describe-figure <pmid> <figure-id>: on-demand, cached model description of one figure

Find

/ref:search: search the library's evidence, or your personal notes, with distinct labels
/ref:ask <question>: retrieve evidence and write one grounded answer with [^pmid] citations
/ref:pubmed-query <question>: translate a prompt or PICO into a PubMed query without running it
/ref:search-pubmed: turn a question into a PubMed query and save the run immutably
/ref:search-add-fetch: search PubMed, save the run, add selected PMIDs, then fetch full text
/ref:update-queries <slug>: manually re-run a saved query and append a new run
/ref:related <pmid>: snowball backward through references and forward via PubMed

Organize & review

/ref:project: projects, questions, membership, and relevance
/ref:queue: reading state, priority, and why-saved notes within a project
/ref:screen: record a project-specific include/exclude/pending decision with a reason
/ref:note <pmid>: append your own dated notes to notes.md
/ref:verify: accept, edit, or reject claims, identity matches, and grant links as overlays
/ref:study: group publications into studies; record datasets and methods

Write & compare

/ref:compare <selector>: evidence matrix with source-linked cells
/ref:methods <selector>: protocols, instruments, datasets, and software with locators
/ref:summarize <selector>: prose narrative across a set, or a single paper
/ref:review: appraised synthesis, or --prisma flow record for a project's search
/ref:check-citations: check a paragraph's assertions against library evidence
/ref:brief: save an answer and its evidence snapshot; refresh explicitly
/ref:cite <pmid>: print the stable @citekey
/ref:export <selector>: BibTeX and CSL-JSON for a frozen set
/ref:export-papers <selector>: Papers-dialect BibTeX plus PDF copies for import into Papers.app

Explore the graph

/ref:weave: build and review concepts and relations, regenerate OKF views
/ref:concept: find, create, and alias concept nodes
/ref:gaps <selector>: fragile single-study claims, open conflicts, coverage gaps
/ref:hypothesize --concept <slug>: Swanson ABC candidates, each checked against PubMed

People, grants & reports

/ref:person: researcher identity: name variants, ORCID, matches
/ref:publications --person <id>: authorship roles, or a coauthor declaration for a window
/ref:grant: funders, awards, aliases, and publication links
/ref:discover --person <id>: explicit PubMed search for portfolio candidates
/ref:report --person <id>: reproducible publication report for a date window

Maintain

/ref:audit: re-check retraction/errata status; --citations records dated PMC cited-by counts
/ref:index --rebuild: rebuild catalog.sqlite from committed records
/ref:status: show the configured library and catalog counts
/ref:open <pmid>: open the acquired PDF in Papers.app
/ref:pull-annotations <pmid>: import your Papers highlights and margin notes, read-only