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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CTCF-only/DNase-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.

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Drafting and iterating sections of The Federated Harbor whitepaper — the third paper in the Curiositech sequence after Anchor (local identity) and Bonded Commons (local coordination), extending coordination across machines and administrative domains. Use when authoring a section, rewriting a section after a redteam/whitehat round, or composing a new chapter. NOT for marketing copy, NOT for the other two papers, NOT for production threat response.

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Adversarial reviewer for The Federated Harbor whitepaper — the third paper in the Curiositech sequence after Anchor and Bonded Commons. Probes federation-specific threats: trust transitivity, cross-harbor token forgery, federated revocation under partition, cross-harbor Sybil, cross-domain settlement, equivocation, bond-pool draining, cold-start joining, federation-operator Sybil. Use during a versioned red-vs-white round; pairs with federated-harbor-whitehat. NOT for incident response, NOT for the Anchor or Bonded papers (use redteam-review).

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Domain-Driven Design methodology using bounded contexts, ubiquitous language, and strategic/tactical patterns

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Treat tokens as a coding swarm's cost-of-goods-sold and legibility engine while accounting for finite subscription allowance when per-call price is unknown. Covers provider windows, remaining-usage evidence, burn forecasts, preemptive checkpoint/model switching, per-agent budgets, compaction, shared digests, context degradation, and spend metering. Activate on: "token budget", "context budget", "compaction strategy", "briefing as compression", "context rot", "summarization collapse", "COGS for agents", "subscription usage remaining", "five-hour or weekly limit", "burn forecast", "model switch before limit", or "/context-economics-for-agent-swarms". NOT for: memory architecture (use always-on-agent-architecture), single-prompt wording (use prompt-engineer), mechanism-design proofs (use nisan-et-al-2007-algorithmic-game-theory), physical containment (use sandboxed-adversarial-test-harness), or production rebodiment and fencing (use agent-resurrection-and-body-continuity).

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Use when wrangler deploys silently fail or produce wrong artifacts, secrets upload as empty strings, custom domain DNS is not resolving, route assignment broke after rename, observability/tail logs are needed, D1/KV/R2 bindings are missing, OAuth scope errors block a command, cookies on a redirect are not attaching, or the worker exceeds CPU time. Triggers: "Tenant or user not found", "Authentication error" on wrangler d1 push, secret length is 0 after upload, route returns origin not worker, "compatibility_date too old", 1101 errors, custom_domain assignment lost on script rename. NOT for AWS Lambda / Vercel Edge / Deno Deploy (different runtimes), Cloudflare Zero Trust, or R2-specific tuning.

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Backlink profile analysis: referring domains, anchor text distribution, toxic link detection, competitor gap analysis. Works with free APIs (Moz, Bing Webmaster, Common Crawl) and DataForSEO extension. Use when user says backlinks, link profile, referring domains, anchor text, toxic links, link gap, link building, disavow, or backlink audit.

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The standing order for local git state in every AI Matrx repo — zero worktrees, zero local branches, zero dirty files, zero open PRs, everything merged to origin/main, and no code ever lost. Use when you find a worktree, a local branch, a stale checkout, an unpushed commit, or a dirty tree in any repo under /Users/armanisadeghi/code, when asked to "clean up", "unify", "merge everything", or when you are tempted to create a worktree or branch. Works without any access to Arman.

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One-time recovery when a shared checkout has drifted far from GitHub main: hundreds ahead/behind, stacked worktrees and PRs, a dirty tree nobody owns. Use when tempted to reset or force-push. NOT for the ordinary 30-minute release loop (operations/INTEGRATION_MAINTAINER.md).

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スキルを作成・更新・プロンプト改善するためのメタスキル。 **collaborative**モードでユーザーと対話しながら共創し、 抽象的なアイデアから具体的な実装まで柔軟に対応する。 **orchestrate**モードでタスクの実行エンジン（Claude Code / Codex / 連携）を選択。 Anchors: • Continuous Delivery (Jez Humble) / 適用: 自動化パイプライン / 目的: 決定論的実行 • The Lean Startup (Eric Ries) / 適用: Build-Measure-Learn / 目的: 反復改善 • Domain-Driven Design (Eric Evans) / 適用: ユビキタス言語 / 目的: 一貫した語彙 • Design Thinking (IDEO) / 適用: ユーザー中心設計 / 目的: 共感と共創 • Microservices Patterns (Richardson) / 適用: サービス委譲 / 目的: 疎結合な連携 Trigger: 新規スキルの作成、既存スキルの更新、プロンプト改善を行う場合に使用。 スキル作成, スキル更新, プロンプト改善, skill creation, skill update, improve prompt, Codexに任せて, assign codex, Codexで実行, GPTに依頼, 実行モード選択, どのAIを使う

Consult Claude Code from Codex for a second opinion while Codex remains responsible for implementation and verification. Use when the user asks Codex to collaborate with Claude, consult Claude, ask Claude for a plan, get a Claude review, delegate analysis to Claude, or says "Claudeと一緒に", "Claudeに相談", "Claudeにレビューしてもらう", "Claudeの意見も聞く", or "Claudeと計画を立てる". Also use when an explicit independent planning or review pass from Claude would materially reduce risk on a complex coding task.

Set up, resume or troubleshoot cmail custom-domain email (domain at any registrar → Cloudflare Email Routing → any inbox; optional GoDaddy automation and Gmail send-as): runs cmail setup itself, asking only for missing input, secrets or risky approvals. Don't use for mail migrations or campaigns.

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Find and buy a domain for the current Convex app through Convex, then bind it (labs; spend action).

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Generates DDD Repository interfaces and implementation stubs for PHP 8.5. Creates domain interfaces in Domain layer, implementation in Infrastructure.

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Analyzes PHP code for immutability violations. Checks Value Objects, Events, DTOs for readonly properties, no setters, final classes, and wither patterns. Ensures domain objects maintain invariants.

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Generates DDD Domain Services for PHP 8.5. Creates stateless services for business logic that doesn't belong to entities or value objects. Includes unit tests.

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Generates DDD Domain Events for PHP 8.5. Creates immutable event records with metadata, past-tense naming. Includes unit tests.

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Extract structured domain knowledge from AI models in-session or from local open-source models via Ollama. No API key needed.

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Master proven backend architecture patterns including Clean Architecture, Hexagonal Architecture, and Domain-Driven Design to build maintainable, testable, and scalable systems.

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Runs the morning maintainer standup for NemoClaw. Triages the backlog, determines the day's target version, labels selected items, surfaces stragglers from previous versions, and outputs the daily plan. Use at the start of the workday. Trigger keywords - morning, standup, start of day, daily plan, what are we shipping today.

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Cut a new semver release — bump all version strings via bump-version.ts, open a release PR, and after merge tag main and push. Use when cutting a release, tagging a version, shipping a build, or preparing a deployment. Trigger keywords - cut tag, release tag, new tag, cut release, tag version, ship it.

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Runs the end-of-day maintainer handoff for NemoClaw. Checks version target progress, bumps stragglers to the next patch version, generates a QA handoff summary, and cuts the release tag. Use at the end of the workday. Trigger keywords - evening, end of day, EOD, wrap up, ship it, cut tag, handoff, done for the day.

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Sync delta specs from a change to main specs. Use when the user wants to update main specs with changes from a delta spec, without archiving the change.

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Generates creative domain name ideas for your project and checks availability across multiple TLDs (.com, .io, .dev, .ai, etc.). Saves hours of brainstorming and manual checking.

日本語の概要は準備中です。原文の説明を表示しています。