journal
End-of-day 5-minute checkin (Physical, Mind, Craft, Presence)
log-work
Log work activity to today's journal
md-to-html
Convert markdown to styled HTML for pasting into Google Docs. Use when the user wants to copy markdown (with tables, images, code blocks) into Google Docs or similar.
mermaid-erd
Generate a Mermaid ERD from SQL schema files
mermaid-monorepo
Generate a Mermaid diagram of monorepo package relationships
mermaid-to-png
Convert mermaid diagrams in markdown files to PNG images. Use when the user wants to export markdown with mermaid to formats that don't support mermaid (Google Docs, PDF, etc).
obsidian-save
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obsidian-todo
Manage topic-based todo lists in Obsidian vault
organize-feeds
Categorize uncategorized FreshRSS feeds by sampling content and inferring the best category. Use when user says "organize feeds", "categorize feeds", or wants to clean up uncategorized subscriptions.
paperless
Search and manage documents in Paperless-ngx document management system. Use when the user asks about documents, invoices, receipts, tax forms, bills, or wants to search their document library.
pr-activity-report
Quarterly PR Activity Report
proxmox
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qmd
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ralph-prep
Full Ralph preparation workflow - create spec skeleton, interview to flesh out, and generate docs PRD for Ralph story-loop execution. Triggers on "ralph prep", "prep ralph", "prepare for ralph", "set up ralph for".
react-useeffect
React useEffect best practices from official docs. Use when writing/reviewing useEffect, useState for derived values, data fetching, or state synchronization. Teaches when NOT to use Effect and better alternatives.
release
Cut a release (bump version, commit, tag, push)
resolve-merge-conflicts-all-prs
Resolve merge conflicts across all open GitHub PRs authored by the current user in the current repository by running resolve-merge-conflicts for each PR.
resolve-merge-conflicts
Resolve git merge conflicts for a GitHub PR. Accept a PR link/number when provided, otherwise infer the open PR for the current branch.
second-opinion
Get a peer review from the other AI agent. Claude invokes Codex, Codex invokes Claude. Automatically detects which agent is active.
spec-interview
Interview user to flesh out a spec file
questionably-ultrathink
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questionably-ultrathink-skill
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quarterly-review
Conduct a quarterly review of your overall research mission and direction. This is a user-level review stored in ~/.researchAssistant/. Use when the user types /quarterly_review, every 3 months, after major project milestones, or when questioning research direction.
write-background
Draft or update the background/introduction section based on literature in .research/literature/. Use when the user types /write_background, after completing literature review, or when background.md is empty but literature files exist.
write-results
Draft the results section from figures and their captions. Builds a coherent narrative from visual evidence. Use when the user types /write_results, when figures exist with captions, or after methods section is complete.
write-methods
Generate or update the methods section based on actual scripts in the pipeline. Links code directly to reproducible documentation. Use when the user types /write_methods, after completing scripts, when methods.md is out of sync with code, or before writing results.
plan-week
Create a focused weekly plan based on tasks, priorities, and your work patterns. Use when the user types /plan_week, after a weekly review, at the start of a new week, or when feeling overwhelmed by options.
peer-review
Systematic peer review and self-evaluation toolkit. Evaluate methodology, statistics, experimental design, reproducibility, ethics, and reporting standards. Use during the REVIEW phase to assess manuscript quality before submission, or when reviewing others' work.
review-script
Review a script for documentation quality, code standards, and reproducibility. Helps ensure code is ready for the methods section. Use when the user types /review_script, after writing a new script, before writing methods, or when passive checks flag undocumented scripts.
scientific-visualization
Create publication-quality scientific figures with matplotlib, seaborn, and plotly. Includes multi-panel layouts, error bars, significance markers, colorblind-safe palettes, and journal-specific export (PDF/EPS/TIFF). Use when creating figures for manuscripts, presentations, or any research visualization.
scientific-writing
Write scientific manuscripts with proper structure (IMRAD), citations (APA/AMA/Vancouver), figures/tables, and reporting guidelines (CONSORT/STROBE/PRISMA). Use when drafting any manuscript section, improving writing clarity, or preparing for journal submission.
statistical-analysis
Comprehensive statistical analysis toolkit for research. Conduct hypothesis tests (t-test, ANOVA, chi-square), regression, correlation, Bayesian stats, power analysis, assumption checks, and APA reporting. Use when the user asks about statistics, needs help analyzing data, or when writing methods sections that include statistical approaches.
summarize-meeting
Extract action items, decisions, and key points from meeting transcripts. Automatically routes items to tasks.md or GitHub Issues based on complexity. Use when the user types /summarize_meeting or after running /transcribe.
task
Rapid task capture without breaking flow. Use when the user types /task or wants to quickly add a todo item to tasks.md. Supports priority flags (!high, !low). Use this instead of /note for action items.
transcribe
Transcribe audio files from meetings into text documents using Whisper. Use when the user types /transcribe, has a new audio recording, or when RA detects new audio files in meetings/audio/. Supports speaker diarization with pyannote.
weekly-review
Conduct a weekly review of project progress and plan for the upcoming week. Use when the user types /weekly_review, when it's Monday and no review exists for this week, or at the end of the work week. Aggregates daily activity entries and identifies patterns.
wrap-up
End-of-day command to capture what happened, consolidate notes, and set up for tomorrow. Use when the user types /wrap_up, says "end of day", "wrapping up", or "done for the day". Gathers git activity, integrates /note entries, and creates a daily summary in activity.md.
note
Quick capture for thoughts, observations, or ideas during research sessions. Use when the user types /note or wants to capture a quick thought without context-switching. Logs timestamped notes to activity.md. Supports both explicit /note command and natural language like "make a note" or "jot down".
literature-review
Conduct comprehensive, systematic literature reviews using multiple databases (PubMed, bioRxiv, Semantic Scholar, OpenAlex). Creates documented searches, synthesizes findings thematically, verifies citations, and generates professional markdown reports with multiple citation styles (APA, Nature, Vancouver). Use when the user needs thorough literature research or types /deep_research.
hypothesis-generation
Generate testable scientific hypotheses from observations, data, or research questions. Develop competing explanations, design experiments, and formulate predictions. Use during the PLANNING phase or when developing research aims.
exploratory-data-analysis
Perform comprehensive exploratory data analysis on research data. Automatically analyze data structure, quality, distributions, and generate insights. Use when the user provides a dataset, asks to "explore data", "analyze this file", or needs to understand their data before formal analysis.
deep-research
Conduct a thorough literature search on a topic with verified citations. Use when the user types /deep_research, asks to "research a topic", "find papers on", or needs literature review. CRITICAL - Never fabricate citations. Every claim must have a verifiable source.
monthly-review
Conduct a monthly review of project alignment and progress toward aims. Use when the user types /monthly_review, at the start of a new month, after completing a major milestone, or when uncertain about project direction.
next
Assess current project state and suggest the most valuable next action. The primary entry point for users who aren't sure what to do. Analyzes context, checks for issues, and recommends specific skills or actions.
ai-sdk-core
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ai-sdk-ui
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ai-sdk-agents
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bun-dev
Definitive, rule-first Bun development/build/runtime guidance + automation. Use when adopting Bun, migrating a repo from Node.js, auditing/fixing Bun package management (bun.lockb, bun install), optimizing scripts/monorepos (bun run --parallel/--sequential, --workspaces/--filter), configuring Bun + TypeScript, using bun test/build, tuning performance, or deploying Bun workloads/Vercel Functions with the Bun runtime (bunVersion, limitations, Next.js ISR scripts).
codex-sdk
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supabase-ts
Production-ready Supabase integration patterns for Next.js/React/TypeScript applications. Use when working with Supabase for (1) SSR authentication with @supabase/ssr, (2) Database operations and migrations, (3) Row Level Security (RLS) policies, (4) Storage buckets and file uploads, (5) Realtime channels and presence, (6) Edge Functions with Deno, (7) pgvector embeddings and semantic search, (8) Vercel deployment and connection pooling, (9) CLI operations (type generation, migrations). Triggers on Supabase client setup, auth patterns, RLS policies, storage uploads, realtime subscriptions, Edge Functions, vector search, or Vercel+Supabase deployment.
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