homepage-add
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home-assistant-manager
Expert-level Home Assistant configuration management with efficient deployment workflows (git and rapid scp iteration), remote CLI access via SSH and hass-cli, automation verification protocols, log analysis, reload vs restart optimization, and comprehensive Lovelace dashboard management for tablet-optimized UIs. Includes template patterns, card types, debugging strategies, and real-world examples.
handoff
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clean-permissions
Clean up Claude Code permissions allowlist
claude-review
Perform a senior-level peer review of staged changes, then implement warranted fixes
bd
Manage beads (issues) based on conversation context
bd-next
Find best candidates for next task
bd-load
Parse context and create beads from it
bd-clean
Review and consolidate beads issues
bd-add
Create a new bead with provided arguments
aws-use-sso
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draft-pr
Commit, push, and open a draft PR
add-newsletter
Subscribe to an email newsletter via Kill the Newsletter and add the resulting feed to FreshRSS with auto-categorization. Use when user wants to subscribe to a newsletter, says "add newsletter", or provides an email-based newsletter to follow.
add-vessia-project
Add a project to vessia.net projects page
address-pr-feedback
Address all open PR comments on current branch autonomously
init-ralph
Set up Ralph autonomous agent structure in a repository
dump-context
Summarize current context and write to a markdown file
add-feed
Add an RSS feed to FreshRSS with auto-categorization. Use when user provides a feed URL and wants it added to FreshRSS, or says "add feed", "subscribe to", "add rss".
done
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diataxis-documentation
Use when writing, restructuring, or reviewing technical documentation and you need to decide between tutorial, how-to, reference, and explanation styles.
deslop
Review text or code comments for AI writing tropes and suggest fixes. Use when writing prose, documentation, PR descriptions, or commit messages.
commit-message
Generate a conventional commit message for staged changes
commit-and-push
Commit changes and push to remote
commit-all
Stage all changed files and create a commit
codex-review
Send staged changes to Codex for independent peer review, then evaluate and implement warranted feedback
cli-design
Design and build agent-first CLIs with HATEOAS JSON responses, context-protecting output, and self-documenting command trees. Use when creating new CLI tools, adding commands to existing CLIs, or reviewing CLI design for agent-friendliness. Triggers on 'build a CLI', 'add a command', 'CLI design', 'agent-friendly output', or any task involving command-line tool creation.
cleanup
Audit codebase for tech debt and improvements
questionably-ultrathink
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questionably-ultrathink-skill
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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.
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.
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.
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.
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.
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.
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-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.
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.
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.
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".
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.
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.
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.
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.
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