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Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.

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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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Manage feature manifests for code traceability. Use when creating new features, updating existing features, checking feature health, or exploring the feature-to-code relationship. Activates for manifest validation, feature creation, changelog updates, and traceability queries.

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Manage database schema with Drizzle ORM and SQLite migrations. Use when adding tables, modifying columns, creating indexes, or running migrations. Activates for database schema changes, migration generation, and Drizzle query patterns.

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Matches natural language task descriptions to appropriate skills using semantic similarity, ranks candidates by fit and performance history, and maintains the skill catalog. Use when assigning skills to DAG nodes, searching for the right skill for a task, ranking competing skills, or browsing the skill catalog. Activate on "find skill", "match skill", "which skill", "skill for this task", "skill catalog", "rank skills", "best skill". NOT for executing DAGs (use dag-runtime), creating skills (use skill-architect), or grading skills (use skill-grader).

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Marketing and promotion specialist for Claude ecosystem technology - MCP servers, skills, plugins, and agents. Expert in community engagement, registry submissions, content marketing, and developer relations. Activate on 'promote MCP', 'share skill', 'market plugin', 'launch agent', 'developer marketing', 'MCP registry'. NOT for creating MCPs/skills (use agent-creator), general marketing (use content-marketer), or SEO optimization (use seo-visibility-expert).

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Design decisions for when and what sounds to use in web apps, mobile apps, and desktop native apps — plus how to create them with AI. Covers UI sound vocabulary (confirms, alerts, transitions, errors), platform conventions (iOS, macOS, Material), creating sounds with AI tools (ElevenLabs, AudioCraft, Stable Audio), Web Audio API for procedural sounds, haptic-audio pairing, and the psychology of satisfying vs. annoying UI sounds. Activate on 'app sounds', 'UI sounds', 'notification sound', 'sound design app', 'earcons', 'sonic branding', 'interaction sounds', 'feedback sounds', 'app audio', 'satisfying sounds'. NOT for professional audio engineering (use sound-engineer), Windows 3.1 retro sounds specifically (use win31-audio-design), music composition (use sound-engineer).

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Design low-friction UX, interaction patterns, and comeback loops for AI coding assistant apps, agent consoles, background coding agents, and Port Daddy swarm/operator surfaces. Use when creating flows like prompt-to-diff, context attach, plan/apply/review, checkpoint rollback, background-agent dashboards, visual proof, or multi-agent invocation. NOT for generic landing pages, static dashboards, or implementation-only changes without product flow.

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Discipline an AI agent needs to work an issue/task tracker (Jira, Linear, GitHub Issues) as the shared source of truth: pull the right next item instead of inventing work, search before creating to avoid duplicates, write actionable items with checkable acceptance criteria, keep status transitions honest, and link work to items via branches/PRs/commits so progress is legible. Use when an agent picks up tracker work, files a new issue, updates status, or closes an item. NOT for authoring the PR itself (use agent-pr-authoring), roadmap-level planning and prioritization (use legible-roadmap-with-sidequests), or the mechanics of multiple agents coordinating on the same codebase (use multi-agent-coordination).

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Fundamental patterns for effective agentic behavior. Teaches decomposition, tool orchestration, error recovery, context management, quality self-assessment, and knowing when to stop. Model-agnostic principles that make any agent more effective regardless of domain. Activate on: "how should I structure this agent", "agentic workflow", "agent patterns", "multi-step task", "tool orchestration", "/agentic-patterns", "decompose this", "agent best practices", "chain of actions", "when should the agent stop", "agent loop design". NOT for: creating agent infrastructure (use agent-creator), building DAGs (use jury_rig-architect), specific tool implementation.

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Recipe for creating or changing a floating window. Use when adding a window, editing a window component, declaring restore or ephemeral behavior, wiring a ?panels= link or the Tools grid, or a window fails to restore after reload. NOT for drag/resize/tray internals (use window-panels).

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Lifecycle for AI Matrx agent-aware UI surfaces. Use when creating a surface in features/surfaces/manifests/, or completing or repairing one that is partial, stubbed, unregistered, missing runtime context or context menus, or not agent-wired. NOT for certifying a surface (use surface-check).

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One-route pattern: public marketing landing plus signed-in workspace. Use when creating or fixing a landing page or a feature's front door, guests see an error, 'make /X work signed out', signed-in users land on a pitch, or ModuleLanding / AuthedWorkspaceCTA. NOT for (public) share viewers or free tools.

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Filesystem auto-discovery of App Router pages into navigable index pages. Use when creating an index/listing page, adding route directories, converting hard-coded route configs to auto-discovery, or adding a route-listing display variant.

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Rules for SKILL.md files that trigger, fit, and are proven. Use when creating a SKILL.md, rewriting its description, splitting an oversized SKILL.md, or editing one because an agent ignored, misread, or never fired it.

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SSR-first Next.js App Router doctrine with zero layout shift. Use when creating a page or data-fetching UI, fixing CLS, layout shift, or hydration mismatches, placing 'use client', Suspense, or skeleton boundaries, awaiting params/searchParams/cookies, adding server-only guards or cache() dedup, or choosing Route Handlers vs Server Actions.

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Runbook for creating or majorly growing an @ai-matrx TypeScript npm package. Use when invoked as /new-package <name or capability>, or for a new @ai-matrx/* package, extracting code into one, or a major growth wave. NOT for a routine fix inside an existing package (THE SAME-SESSION LAW).

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No-loss protocol for changing an existing mandate's output contract. Use when changing what an agent or mandate emits or how it is typed: binding a kind, declaring output_kind, kind-backfill batches, provision reconciliation, or any make-this-contract-honest sweep. NOT for creating a new agent (use create-agent).

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Scaffold recipe for a new authenticated route: SSR shell, DB-derived types, Redux hydration, view sub-pages. Use when creating a new route or page, adding a feature with a sidebar/main layout, adding view modes to a route, or feature types don't match database.types.ts.

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Permanent-delete grooming for leftover Docker builds, agent worktrees, and .next caches. Use when creating or finishing a git worktree, after a local docker build, when the disk is full, or when /tmp or .wt trees were left behind.

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The provision for a call site: the exhaustive menu of values that place in the code can realistically produce. Use before creating or fixing a mandate or agent that reasons about more than its own input, when deciding whether an agent can answer at all with what it is sent, or when its output 'looks right' but nobody checked it could be. NOT for building the agent (use create-agent).

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The procedure for every doc change in common-docs or a repo's CLAUDE.md, FEATURE.md or SKILL.md. Use when creating, editing, moving or deleting a doc, finding duplicate or disagreeing docs, planting a repo pointer, consolidating a node, or on /docs and the daily docs-steward run.

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Redux state for agent execution and firing agent shortcuts. Use when editing features/agents/redux/, building agent UI, creating a conversation, touching assembleRequest or NDJSON stream state, wiring agent-state selectors, adding a per-conversation capability, or triggering a shortcut from a button, menu, or code (useShortcutTrigger, launchAgentExecution).

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Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).

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