Annotate Markdown documents with MIRA research objects and source-local relations. Use for md, smd, qmd, and myst files when identifying claims, evidence, questions, protocols, requests, typed claims, and relation attributes while preserving the original Markdown flavor and author wording. Not for general copyediting, prose rewriting, or extracting a separate knowledge graph without annotating the source.
Review MIRA annotations in Markdown documents for semantic correctness, Markdown dialect validity, preservation, and relation integrity. Use for md, smd, qmd, and myst files containing research objects such as claims, evidence, questions, protocols, requests, typed claims, ids, and relations. Produces actionable findings without modifying files by default.
Create, edit, or plan figures in Stencila Markdown — simple image figures, executable code figures, multi-panel subfigure layouts with grid arrangements, and SVG annotation overlays using overlay components. Use when asked to add or revise a figure, chart, plot, caption, subfigure grid, panel layout, overlay annotation, callout, scale bar, arrow, region-of-interest highlight, or figure design plan for a Stencila document.
Critically review an existing or proposed Stencila figure artifact for structural correctness, caption quality, layout, overlay annotation safety, cross-references, measurement validity, and approval readiness. Use when asked to review, critique, assess, audit, validate, or improve a figure block, multi-panel figure, subfigure grid, executable chart figure, caption, SVG overlay, ROI annotation, scale bar, panel labeling, or figure plan.
Create or update the [site] section of stencila.toml for published Stencila sites. Use when asked to configure site domain, title, author, logo, icons, labels, descriptions, socials, featured content, navigation, routes, access, layout presets and regions, glide, search, formats, reviews, uploads, remotes, actions, auto-index, or specimen. Covers reading existing TOML, generating valid configuration, editing while preserving comments and formatting, and snap-based visual verification.
Review a Stencila site configuration (stencila.toml) for correctness, completeness, best practices, and rendered appearance. Use when asked to review, audit, validate, check, or assess a site config, stencila.toml, site routes, redirects, site layout, layout presets, site nav, navigation, site access, access control, or site deployment readiness.
Create, update, or plan a Stencila theme for documents or published sites. Use when asked to choose a theme direction, write or patch theme.css, recommend semantic or module token families, customize site navigation or branding, tune PDF and print page tokens, align web, Python, and R plots with a Stencila design system, list available builtin tokens with `stencila themes tokens`, or validate a theme file with `stencila themes validate`.
Critically review an existing or proposed Stencila theme artifact for correctness, token usage, target coverage, cross-target portability, dark-mode handling, maintainability, and approval readiness. Use when asked to review, critique, assess, audit, or validate a theme.css file, theme patch, theme plan, site theme, document theme, plot theme, print or PDF theme, check design tokens, assess DOCX or email behavior, review dark mode support, or validate with stencila themes validate.