Use when you need to detect drift between an existing paper-book companion and a revised version of its source paper, then sync the mechanical pieces (new bib entries, new/changed figures) and report the substantive drift (renamed sections, changed numbers, new theorems, new contributions) for the user to triage. Counterpart to /init-paper-book. Read-only by default; --apply flag opts in to mechanical fixes.

Cross-reference \cite{} keys against .bib files or embedded \bibitem entries. Finds missing, unused, and typo'd citation keys. Deep verification mode spawns parallel agents for DOI/metadata validation at scale. Fix mode auto-adds missing entries to Paperpile.

Use when you need to review and understand old code, data, or analysis files.

> Interactive project setup: answer questions, get a ready-to-use research project directory.

Use when you need to scaffold a NEW educational companion book for a LaTeX paper. Reads the paper, drafts 8 substantive chapters into the vault at ~/Research-Vault/books/<slug>/, copies bib + figures, registers the book, and verifies atlas serves it. Source-of-truth is the paper PDF/tex; the book is a reading companion, never a re-statement of new claims. For syncing an existing book to a paper revision, use /audit-paper-book.

Use when you need to bootstrap a university course or module folder.

Use when you need to bootstrap a lightweight project with minimal structure.

Use when you need to bootstrap a full research project with directory scaffold and Overleaf symlink.

Use when you need to compile a LaTeX document — includes autonomous error resolution, citation audit, and quality scoring.

Use when you need to compile LaTeX with autonomous error resolution and citation audit.

Use when you need to prune duplicates and merge overlapping entries in MEMORY.md files.

Use when you need to explore a research question from multiple independent perspectives.

Use when you need to process referee comments from a reviews PDF into tracking files.

Use when you need to map scripts to their inputs, outputs, and paper figures/tables.

Use when you need to process referee comments from a reviews PDF into tracking files.

Use when you need to set up safety rules and folder structures for a research project.

Use when you need to save information from the current conversation to the context library.

Use when you need to download, split, and deeply read an academic PDF that is NOT in Paperpile (for Paperpile items, prefer paperpile get-pdf-text directly).

Use when you receive referee comments for a paper (R&R, revise-and-resubmit) and need a DAG-validated revision master plan — atomic task extraction, dependency mapping, computational critical-path analysis, execution blocks, venue strategy. Merges /parse-reviews ingestion with Sihvonen's strategic-revision architecture.

Use when you need to run parallel audits across skills, hooks, agents, rules, and conventions.