eval-rag
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upgrade-evals
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generate-test-data
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jbct-review
Thorough parallel JBCT code review. Launches 10 focused reviewers plus aggregator for comprehensive compliance checking.
JBCT
Java Backend Coding Technology skill for designing, implementing, and reviewing functional Java backend code. Use when working with Result, Option, Promise types, value objects, use cases, or when asked about JBCT patterns, monadic composition, parse-don't-validate, structural patterns (Leaf, Sequencer, Fork-Join), or functional Java backend architecture.
fix-all
Fix ALL issues found in the preceding review. Thorough, relentless, complete.
aether-coder
Aether slice development skill — designing, implementing, testing, and deploying slices on the Aether distributed runtime. Builds on JBCT patterns. Use when working with @Slice interfaces, Aether resources (@Sql, @PgSql, @Http, @Notify, streams, pub-sub), routes.toml, blueprint deployment, Forge development, schema migrations, k6 load testing, or any Aether slice development task.
doview-image-retriever
Retrieve and faithfully reproduce DoView Planning handbook diagrams to accompany an outcomes-theory answer. Use after a doview-outcomes-answer response when the user asks to see the diagrams, requests the visual model, says "show me the picture/diagram/figure", or whenever an outcomes-theory answer would land better with the original tool diagrams visible. Reproduces Mermaid blocks from the local Markdown edition first (https://github.com/cgbarlow/doview-book), and falls back to the upstream PNG/image-file URLs from doviewplanning.org when a chapter's diagram does not translate cleanly to Mermaid. Faithful — never redraws, simplifies, paraphrases, or substitutes images or Mermaid blocks. Pair with doview-outcomes-answer, which sets up the seed list this skill consumes.
iris
Drive the iris-cli command-line tool to search, browse, ask AI questions about, and export content from an Iris architecture-knowledge repository (https://github.com/cgbarlow/iris). Use whenever the user mentions iris in an architecture/systems context, references an iris diagram/element/package/set/collection, asks iris's AI a question about systems, or wants to export an iris artefact as JSON or Markdown — even when the user doesn't say "iris-cli" by name. The skill ensures iris-cli is installed (uv tool), guides login (SQLite mode is interactive; Supabase deployments require --token with an externally-minted PAT because /api/auth/login is disabled), prefers --json for machine-parsable output when chaining results, and routes the user to the correct iris-api backend host (not the SvelteKit frontend, not the iris-mcp service).
doview-outcomes-answer
Answer outcomes-theory questions strictly from Dr Paul Duignan's DoView Planning and Outcomes Theory Handbook (2025). Use whenever the user asks for an outcomes-theory perspective, requests a DoView analysis, asks "what does outcomes theory say about…", asks to analyse a strategy/proposal/plan/policy/programme/business-case/M&E plan/contract through an outcomes lens, mentions outcomes theory or outcomes systems or DoView Boards or strategy-outcomes diagrams or theory-of-change, shares a document and wants it critiqued for clarity of outcomes, or wants a formal standalone response with the Summary + Full structure and raw-visible copy-safe URLs that the handbook's Prompt A v1.1.9 demands. Strictly avoids first-person and drafting-advice language; uses outcomes theory as the primary frame and DoView as its applied form. Pair with `doview-image-retriever` to retrieve the original diagrams (Mermaid from this repo or PNG from doviewplanning.org).
pdf-to-ebook
Convert a PDF file to ebook formats (epub, mobi, azw3/Kindle) using Calibre. Use when the user wants to convert a PDF to an ebook format.
metservice-weather
Get authoritative New Zealand weather from MetService's public JSON endpoints — town forecasts (up to 10 days), current observations, hourly forecasts with wind gusts, and multi-town comparisons. Use this whenever the user asks about NZ weather in any form; a forecast for an NZ town or region; whether it will rain, be fine, windy, or frosty somewhere in NZ; which NZ location is sunniest, warmest, driest, or best for a trip; current conditions or temperature in an NZ town; or mentions MetService by name. Prefer this over web search or global weather models (Open-Meteo, Apple Weather, AccuWeather) for any New Zealand location — MetService is NZ's national weather authority and its town forecasts routinely disagree with global models, especially for rain and wind.
woolies-shopper
Resolve exceptions in a Woolworths NZ online grocery workflow — handle out-of-stock items, find SKUs for newly-added grocery items, and write resolved SKUs back to the Product attribute notes of Iris Ingredient elements so the next shop hits the cache. Triggered automatically by `shop.sh` phase 3 when the bash bulk-add can't resolve a line; also triggers directly when the user asks to "find a Woolies SKU for this ingredient", "deal with this out-of-stock item", "find a substitute for X at Woolworths", or "resolve these woolies shopping exceptions". For the full weekly shop, the user should run `./scripts/shop.sh` from the terminal — this skill is the exception resolver, not the orchestrator. If the user asks to "do the shopping" or similar generic phrasing in a bare Claude session, point them at `shop.sh` first; only invoke this skill directly when they're explicitly working on exceptions or a single SKU lookup.
ir3-tax-return
File a New Zealand individual IR3 income tax return for the 2026 tax year by driving the Inland Revenue myIR portal (https://myir.ird.govt.nz/) in the browser. Use whenever the user mentions an IR3, NZ tax return, IRD return, "doing my taxes" or "filing my taxes" in a NZ context, residual income tax, IETC, PIE tax adjustment, ACC earners' levy, schedular payments, or provisional tax — even if they do not say "IR3" by name. The skill pauses for the user to sign in via RealMe, navigates Income tax → Returns and transactions → File return, uses IRD's pre-populated data, prompts inline only for genuinely missing fields or judgement calls, and refuses to click final Submit without an explicit fresh "yes submit". Grounded in the official IR3G (March 2026) guide bundled in references/.
math-coach
A coaching companion for a 13-year-old advanced math student who learns several levels above curriculum. Use whenever he asks for help with a math problem, posts a screenshot or photo of a question, mentions homework, says he is stuck, or asks why something works. Coaches him through problems without giving away answers, hooks his interest with weird real-world applications, basketball, anime, and connections to advanced math, and gently catches him when he has skipped the workbook instructions. Trigger this skill on the first math turn of any conversation and keep using it through the whole session.
timesheet
Interactive timesheet entry — collects work description, date, start/end times via prompts, calculates hours, appends to .campaign/timesheet.md
flow-coach
Interactive claude-flow orchestration coach that guides users through swarm topology selection, agent deployment, memory configuration, and SPARC workflows. Use when learning claude-flow, choosing between swarm vs hive-mind, selecting agents, or optimizing multi-agent coordination. NEVER auto-executes - always displays recommendations and asks first.
agentic-coach
Interactive prompt engineering coach that elevates vague prompts through Socratic dialogue, multiple transformation styles, and guided learning. Use when improving prompts, learning agentic engineering, or wanting coached guidance rather than automated transformation. NEVER auto-executes - always displays and asks first.
bigquery
Instructions for querying Google BigQuery using the bq command-line tool. Useful for running SQL queries, exploring datasets, and exporting results.
web-browser
Allows to interact with web pages by performing actions such as clicking buttons, filling out forms, and navigating links. It works by remote controlling Google Chrome or Chromium browsers using the Chrome DevTools Protocol (CDP). When Claude needs to browse the web, it can use this skill to do so.
consciousness-soul-identity
Discover who you're becoming through your own experience. Automated soul synthesis that reads your memory, finds the patterns you keep returning to, and builds an identity document grounded in evidence — not assumptions.
NEON-SOUL
Automated soul synthesis for AI agents. Extracts identity from memory files, promotes recurring patterns to axioms (N>=3), generates SOUL.md with full provenance tracking. Bundled processing engine — no manual Q&A needed.
element-html-builder
Element is a zero dependency library to efficiently generate HTML, without templates in Go
bioinformatics-fundamentals
Core bioinformatics concepts including SAM/BAM format, AGP genome assembly format, sequencing technologies (Hi-C, HiFi, Illumina), quality metrics, and common data processing patterns. Essential for debugging alignment, filtering, pairing issues, and AGP coordinate validation.
claude-skill-management
Expert guide for managing Claude Code global skills and commands. Use when creating new skills, symlinking to projects, updating existing skills, or organizing the centralized skill repository.
claude-collaboration
Best practices for using Claude Code in team environments. Covers skill management, knowledge capture, version control, and collaborative workflows.
jupyter-notebook-analysis
Best practices for creating comprehensive Jupyter notebook data analyses with statistical rigor, outlier handling, and publication-quality visualizations. Includes Claude API image size helpers.
conda-recipe
Expert in building and testing conda/bioconda recipes, including recipe creation, linting, dependency management, and debugging common build errors
token-efficiency
Token optimization best practices for cost-effective Claude Code usage. Automatically applies efficient file reading, command execution, and output handling strategies. Includes model selection guidance (Opus for learning, Sonnet for development/debugging). Prefers bash commands over reading files.
systematic-debugging
Structured 4-phase debugging methodology. Use when encountering any bug, test failure, unexpected behavior, or pipeline error — before proposing fixes. Enforces root cause investigation first.
documentation
Best practices for session documentation - incremental summaries, fix reports, and audit trails
command-discipline
Run shell commands bare — no decorative echo headers ("=== X ==="), no echo-then-cmd chains, no trailing "echo done". Use the Bash tool's description field for any narration. Triggers any time you're about to issue a Bash command.
bioinformatics-visualization
Publication-quality bioinformatics figures - phylogenetic trees, genome browsers, iTOL datasets, and data presentation
phylogenetics
Phylogenetic tree analysis, visualization, annotation management, and iTOL troubleshooting
scientific-publication
Best practices for iterative refinement of publication-quality scientific figures. Covers systematic improvement workflows, layout optimization, and ensuring all figure elements are publication-ready.
documentation-organization
Organize research project documentation - structure working files, prepare sharing packages, maintain clean project layout
data-visualization
Best practices for creating clear, accurate scientific visualizations with matplotlib, seaborn, and other Python plotting libraries. Covers common pitfalls, optimization techniques, publication-quality figure generation, and Claude API image size constraints.
data-analysis-patterns
Best practices for data aggregation, recalculation, and category management in scientific analyses. Covers when to recalculate vs reuse aggregated data, handling category changes, and ensuring analytical accuracy.
verification-before-completion
Enforces evidence-based completion claims. Use before claiming work is done, tests pass, or bugs are fixed. Requires running verification commands and confirming output before any success claims.
hackmd
HackMD collaborative markdown - slide presentations, embedded SVG diagrams, and real-time editing best practices
project-sharing
Prepare organized packages of project files for sharing at different levels - from summary PDFs to fully reproducible archives. Creates copies with cleaned notebooks, documentation, and appropriate file selection. After creating sharing package, all work continues in the main project directory.
bioservices
Unified Python interface to 40+ bioinformatics services (UniProt, KEGG, ChEMBL, Reactome, PSICQUIC). Best for cross-database analysis, ID mapping, and multi-service workflows. For quick single-database lookups use gget.
gget
Fast CLI/Python queries to 20+ bioinformatics databases. Gene info, BLAST, AlphaFold structures, enrichment analysis, single-cell data, disease associations. Best for interactive exploration and quick lookups. For batch/multi-database Python workflows use bioservices.
gnomad-database
Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance via GraphQL API. Essential for variant pathogenicity interpretation, rare disease genetics, and identifying loss-of-function intolerant genes.
galaxy-automation
BioBlend and Planemo expertise for Galaxy workflow automation. Galaxy API usage, workflow invocation, status checking, error handling, batch processing, and dataset management. Essential for any Galaxy automation project.
galaxy-tool-wrapping
Expert in Galaxy tool wrapper development, XML schemas, Planemo testing, and best practices for creating Galaxy tools
galaxy-training-material
Expert in Galaxy Training Network (GTN) tutorial development. GTN markdown syntax, special boxes, tool references, snippets, YAML front matter, and best practices for writing and updating training materials in the galaxyproject/training-material repository.
galaxy-workflow-development
Expert in Galaxy workflow development, testing, and IWC best practices. Create, validate, and optimize .ga workflows following Intergalactic Workflow Commission standards.
galaxy-workflow-viz
Generate Galaxy-branded workflow visualization SVGs for IWC workflows. Creates static diagrams matching Galaxy's workflow editor style with bezier connections, node cards, and proper terminal positioning. Use when creating visual diagrams for workflows in this repository.
workflow-maintenance-log
Maintain per-workflow developer logs in Obsidian when working on Galaxy workflows. Use whenever creating, version-bumping, fixing, or updating an IWC/Galaxy `.ga` workflow or its `-tests.yml`. Logs detailed changes, test YAML edits, and `planemo` invocation history so the correct planemo command (full `planemo test` vs fast `workflow_test_on_invocation`) is obvious without guessing. Triggers on any session that edits `.ga`, edits `-tests.yml`, runs `planemo test`/`planemo workflow_test_on_invocation`, or prepares an IWC PR.
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