Build a single self-contained HTML dashboard of all captured ideas and every paper's pipeline progress — per-section completion, conference name, deadline, and days-left, with click-to-sort columns. Use when the user says "show my dashboard", "overview of my ideas and papers", "which paper is due first", or triggers /dashboard.
Design and run experiments bound to a GitHub repo. Tracks the bound repo's URL + SHA, records versioned execution attempts (semver), and mirrors structured results locally so /paper can consume them when writing. Use when the user wants to design, log, sync, or analyze experiments. Triggered by /experiment.
Generate research figures — structural SVG (architecture / pipeline / concept) or data matplotlib plots — plus curate a reference-figure library. Each figure goes through a 6-step interactive flow (intent → kind → refs → size → palette → render) and lands in the correct paper or experiment scope. Triggered by /figure.
Socratic research-direction tool — walk the user through Socratic discussion, scout the last 3 years of arXiv + WebSearch, score value/feasibility, recommend venues, emit a brain-library index, hand off to /paper. Each idea is persisted as an on-disk manifest under outputs/idea-checks/<slug>/ and mirrored to AgentDB ideas/<slug>. Also retains the legacy horizontal-matrix and vertical-lineage modes. Use when the user says "help me find a research direction", "is this idea novel", "compare these N papers", "what should I learn for this idea", "where does this idea come from", or triggers `/idea-check`.
Summarize research papers (PDF or arXiv) into structured markdown (problem / method / results / contribution / limitations) and index each summary into the AgentDB `papers/` namespace for later semantic search. Use when the user drops PDFs into `inputs/papers/` or pastes an arXiv URL.
Bundle per-user state into a zip for cross-machine migration and restore it on the new machine without overwriting existing files. Excludes externally-reproducible artifacts (HuggingFace base models, etc.) registered via per-experiment external-artifacts.md. Triggered by /migrate.
Multi-stage paper output flow — venue setup, direction discussion, paper scouting, problem focusing, motivation experiment design, section drafting. Organizes everything under outputs/papers/<venue>/<direction>/. Use when the user is starting or working on a paper for a specific venue. Triggered by /paper.
Manage references (BibTeX merge, cite-as-you-write resolution) and convert documents between Markdown / LaTeX / docx via pandoc. Use when the user says "build my bib file", "resolve [@cite] placeholders", "convert this draft to LaTeX / Word".