Jabkit

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jabkit

Jabkit is an Agent Skill for documents published in the JabRef/jabref repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.

JabRef's Swiss Army knife CLI for BibTeX/biblatex - fetches entries online, converts DOIs to BibTeX, extracts references from PDFs, checks libraries, generates citation keys, writes XMP metadata, and searches .bib files.

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How to use this skill

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Inspect the Agent Skill at https://github.com/JabRef/jabref/blob/HEAD/skills/users/jabkit/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/jabkit, but wait for my approval before writing files or running scripts.

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jabkit — JabRef's CLI Toolkit

jabkit exposes JabRef's BibTeX/biblatex handling as a command-line application.

Installation

jabkit runs via JBang — no JDK setup needed. Install JBang if missing:

curl -Ls https://sh.jbang.dev | bash -s - app setup   # Linux/macOS

iex "& { $(iwr -useb https://ps.jbang.dev) } app setup"   # Windows

Then install jabkit on the PATH (the same command also updates it):

jbang app install --fresh --force jabkit@jabref

One-off run without installation:

jbang --fresh jabkit@jabref --help

Global flags

Place before the subcommand:

-p, --porcelain — script-friendly output (no banners/progress)
-d, --debug — debug logging
-v, --version — version info

Commands

Command	Purpose
`check [FILE]`	Run consistency and integrity checks on a library; subcommands `consistency` and `integrity` run one of them
`citationkeys generate`	Generate citation keys for entries in a `.bib` file
`convert`	Convert between bibliography formats (including PDF → BibTeX)
`doi-to-bibtex DOI...`	Convert one or more DOIs to BibTeX entries
`fetch`	Query an online provider (ArXiv, Crossref, ...) and output matching entries
`generate-bib-from-aux`	Extract the subset of a library cited in a LaTeX `.aux` file
`get-cited-works DOI`	List the works cited by a publication
`get-citing-works DOI`	List the works citing a publication
`pdf update`	Write XMP metadata and/or embedded BibTeX into linked PDFs
`preferences reset\|import\|export`	Manage jabkit preferences
`pseudonymize`	Replace identifying data in a library (writes a key file for reversal)
`search`	Search in a library using JabRef's search syntax

Input files are passed positionally or via --input; both forms are equivalent. --input-format "*" auto-detects the input format.

Examples

# DOI to BibTeX
jabkit doi-to-bibtex 10.1145/3149935.3149942

# Fetch from an online catalogue into a file
jabkit fetch --provider ArXiv --query "test driven development" --output tdd.bib

# PDF paper to BibTeX entry (see the pdf-to-bibtex skill for details)
jabkit convert --input paper.pdf --input-format pdfMerged --output paper.bib

# Validate in CI (errorformat output, non-zero exit on findings)
jabkit -p check library.bib --output-format github-actions

# Citation keys with a custom pattern
jabkit citationkeys generate library.bib --pattern "[auth][year]" --output library.bib

# Write BibTeX + XMP metadata into the PDFs linked from an entry
jabkit pdf update --citation-key Smith2020 --input library.bib --input-format bibtex

# Library subset actually cited in a LaTeX document
jabkit generate-bib-from-aux --aux paper.aux --input full-library.bib --output paper.bib

Notes for agents

Always use -p/--porcelain when parsing output programmatically.
fetch --provider matches JabRef's web-search fetcher names case-insensitively; on an unknown name, jabkit reports Could not find fetcher.
URLs are accepted as input: jabkit convert --input https://example.org/refs.ris --input-format ris.