Ingest a research paper into the project's two-folder reading library. Use when the user hands you a paper — a PDF path, a DOI, or a URL — and wants it read, summarized, and indexed. The skill writes a project-agnostic summary (with a cropped main figure) to the library's bibliographic-management/ folder, upserts a row in that folder's index.csv, judges whether the paper is relevant to the project's narrative (from CLAUDE.md
Write a structured Markdown record of the current session — the requests, the analyses run, the files touched, decisions made, and open next steps — to the project's session-logs dir (one dated file per invocation), then propagate any durable result/decision into the wiki knowledge vault. This is a working record for the user, not a scientific artifact and not a status/sync report. Reconstructs content faithfully from the actual conversation; never invents. Use at the end of (or partway through) a session, or when the user types /save-session-log.
Session-orientation workflow — read the project's Markdown corpus (CLAUDE.md, the outline, project MEMORY, the wiki landing page), build a genuine understanding of the study, then report a concise project summary and an honest current-status snapshot. Read-only with zero side effects — no exports, no memory edits, no report files, no analysis runs. Runs in light mode (cheap, core files only — the default for auto-trigger) or full mode (full corpus sweep). Use at the start of a session to reproduce the effect of "understand this project", or when the user types /session-start.
When a project artifact whose filename carries a version — the canonical outline or the figure deck — is bumped (e.g. v4→v5, ver7→ver8), propagate the new filename into every file that references the old one (CLAUDE.md, command/skill files, agent memories, manuscript anchors, export scripts) so no downstream tool points at a stale file, then offer to delete genuinely-obsolete archive files (never auto-delete). Reads the previously-current values from CLAUDE.md
Three-step pipeline from a Keynote (.key) or PowerPoint (.pptx) deck to manuscript + outline. Func 1 exports vector PDFs per slide; func 2 crops them (vector preserved) and renders an outline-grade PNG from the same cropped artifact; func 3 copies PDFs into the LaTeX manuscript figures dir and PNGs into the outline.md figures dir, then inserts/updates image links after each result heading.
Drive one figure from design idea to manuscript-ready vector PDF + outline-ready PNG. Loops `@figure-descriptor` → `@analysis-implementer` → `@reviewer` against a single fig-id in `figures.json`, with the `cropfig` skill auto-invoked at the end of each implement phase to keep manuscript + outline artifacts in lockstep. The third Phase 2 engine — a 3-agent loop, more complex than `/iterate-revision`'s 2-agent loop, and the only Phase 2 engine that executes real code per iteration. Safe to re-run; safe to resume after BLOCKED or HALT.
Revise one manuscript section against the reviewer team until DONE, BLOCKED, or HALT. Loops `@paper-writer` ↔ `@reviewer` with a venue-specific reviewer brief, recording every iteration's issues + verdict to `reviews.json` and updating `paper.json.sections[name]` status / iter. The first OMCR engine — a worked example of how to compose `skills/orchestrate/phases/*` primitives into a domain-specific loop. Safe to re-run; safe to resume after BLOCKED or HALT.
Find, summarize, and verify N papers on a topic, then drop verified entries into `references.bib` and the literature summary CSV. Dispatches `@literature-curator` (one or many instances) over a CrossRef/OpenAlex candidate list, runs every survivor through the `verify-citation` skill, and writes the run summary to `citations.json.last_sweep`. Sequential by default; opt-in `--parallel N` (1 ≤ N ≤ 4) fan-out for speed. Safe to re-run; idempotent against duplicate DOIs (existing BibTeX entries are skipped, not double-added).