Build the manuscript to PDF/DOCX/HTML, create figures and diagrams, manage cross-references, and run writing-quality checks (lint, grammar, readability).
Search academic literature, manage the search queue, download papers, and verify sources. Use when the user wants to find papers, when working search-queue.md, or when adding references.
Pre-submission checks, bibliography verification, and peer-review responses. Use when the manuscript nears submission, when verifying references, or when responding to reviewers.
Create writing plans, section drafts, and manuscript prose. Use when drafting or editing any part of the paper, building evidence chains from notes, or planning the writing.
Conventions for projects that generate their own results — running models, labeling data, computing statistics. Use when writing or running experiment code, or when drafting sections that report original results.
Plain-language Git for a non-technical user — snapshots, backups, undo, and disaster recovery. Use for any Git operation beyond a routine commit, and whenever the user says save, back up, undo, or go back.
Extract text from papers, summarize them, and create reading notes. Use when reading or summarizing a paper, and automatically after downloading one.
First-time setup and fixing missing tools. Use when a command fails with "not found", when starting a brand-new project, or when the user says something seems broken.