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Balances Hi-C contact matrices (ICE via cooler.balance_cooler, KR/SCALE/VC context), computes distance-decay expected with cooltools (expected_cis per-diagonal P(s), expected_trans scalar), builds observed/expected (O/E) matrices, and diagnoses polymer state from the P(s) log-derivative. Covers the within-matrix-vs-cross-sample distinction (balancing is NOT a normalizer), the equal-visibility assumption that CNV/aneuploidy violates (use raw counts for copy-number), cis-only balancing, mad_max/blacklist masking before balancing, multiplicative cooler weights vs divisive juicer weights, and the resolution-vs-depth budget. Use when balancing a .cool/.mcool, computing expected or P(s), making O/E matrices for compartments/loops, deciding ICE vs KR vs SCALE, choosing a resolution for a given depth, or troubleshooting NaN/all-NaN balanced matrices; route cross-sample comparison to hic-differential.

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Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).

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Run build, deploy, inspect, and fix loops for .NET MAUI apps that already have MAUI DevFlow integrated. USE FOR: launching MAUI apps, selecting devices or emulators, waiting for or recovering agent connections, broker/port/adb connectivity issues, visual tree inspection, screenshots, UI interaction, Blazor WebView CDP debugging, reading DevFlow logs, and iterative app debugging. DO NOT USE FOR: first-time DevFlow package setup (use maui-devflow-onboard), or generic desktop automation unrelated to MAUI. INVOKES: maui devflow CLI, dotnet CLI, Android adb/android tools, and Apple simctl tools.

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Use when a dispatcher, operations manager, or owner asks how to plan loads to minimize empty (deadhead) miles, sequence freight efficiently, balance regional capacity, design dedicated loops, or build a load-pairing strategy across customers. Covers loaded-ratio math, lane balance, region-pair pricing, and software-supported optimization.

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Analyze undirected cycle structure within a valid DAG using the source paper's orientation and contraction method. Use for cycle-basis analysis with explicit graph and reduction choices. NOT for directed feedback loops, workflow deadlocks, or runtime resilience claims.

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Decides HOW to mutate a DAG when a node fails, quality is below threshold, or new information changes the plan. Selects from mutation strategies (add node, replace agent, fork paths, loop back, downgrade model) based on failure type, cost budget, and execution history. Activate on "DAG failed how to fix", "mutation strategy", "replan on failure", "adaptive DAG", "recovery strategy", "what to do when node fails". NOT for detecting failures (use dag-quality), executing mutations (use dag-planner), or runtime execution (use dag-runtime).

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Diagnose when intuitive judgment, agent confidence, or expert routing can be trusted by classifying environment validity, feedback quality, and task-boundary fit. Use for confidence calibration, agent routing, expertise audits, and escalation design. NOT for deterministic implementation tasks, pure syntax debugging, or domains with explicit verifiable answers.

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Diagnose when intuitive judgment, agent confidence, or expert routing can be trusted by classifying environment validity, feedback quality, and task-boundary fit. Use for confidence calibration, agent routing, expertise audits, and escalation design. NOT for deterministic implementation tasks, pure syntax debugging, or domains with explicit verifiable answers.

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Runs an iterative, conversational product-discovery process with a founder/stakeholder: structured interview, live low-fi wireframing, a linked feature/page node-graph built up as you go, a founder-confirmed lock-in checkpoint, then a generated PRD, a Mermaid-rendered sitemap, and a mockup with a full design system (palette, typography, dark mode). Use when building or operating an AI product-discovery chatbot, or when running founder/stakeholder discovery by hand and you need the structure (interview script, node-graph schema, PRD template, design-system handoff order). NOT for implementing the spec'd product once locked — hand off to feature-specific skills (ideal-web-app-builder, tailwind-v4-expert, color-theory-palette-harmony-expert, typography-expert, dark-mode-design-expert) for that. NOT for one-shot PRD generation without an interview loop — if the founder already has a written spec, this process is unnecessary overhead.

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Choose, compare, and decompose work into the right coordination topology: dag, workflow, manager-driven team, swarm, blackboard, team-builder, or recurring loop. Use when the coordination shape is unclear, when you need topology-native breakdown instructions instead of a generic DAG, or when planning topology and runtime topology may differ. NOT for actual execution, node-level skill matching, or framework/tool installation.

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Use when designing a background-job system, choosing between BullMQ / Sidekiq / RQ / Temporal / SQS, deciding queue-vs-workflow, sizing concurrency vs rate limits, building dead-letter queues, or making handlers idempotent. Triggers: jobs running twice on retry, lost jobs after worker crash, DLQ filling up, Redis OOM from job backlog, exactly-once requested, "do we need Temporal?", visibility timeout / lockDuration confusion, exponential backoff vs jitter, fan-out fan-in workflows. NOT for outbound webhook publishing (different concerns), receiver-side webhook handling (different concerns), event-streaming/Kafka topology, or in-process async (event loop only).

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Expert in 3D computer vision labeling tools, workflows, and AI-assisted annotation for LiDAR, point clouds, and sensor fusion. Covers SAM4D/Point-SAM, human-in-the-loop architectures, and vertical-specific training strategies. Activate on '3D labeling', 'point cloud annotation', 'LiDAR labeling', 'SAM 3D', 'SAM4D', 'sensor fusion annotation', '3D bounding box', 'semantic segmentation point cloud'. NOT for 2D image labeling (use clip-aware-embeddings), general ML training (use ml-engineer), video annotation without 3D (use computer-vision-pipeline), or VLM prompt engineering (use prompt-engineer).

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Apply cognitive task analysis to expert work that depends on perceptual cues, branching judgment, and recurring monitoring loops. Use when decomposing expert capability into agent structure, simulation design, or validation interviews. NOT for ordinary step-by-step SOP capture or simple pipelines with no tacit cue layer.

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Design RL simulation sandboxes, trajectory datasets, QLoRA/LoRA adaptation plans, eval harnesses, and rollback unhooks for agents learning specific coding behaviors beyond the base model. Use when building or reviewing tool-use training loops, offline trajectories, reward functions, self-improvement harnesses, or Port Daddy agent behavior curricula. NOT for generic ML tutorials, full model training operations, or production deployment without eval gates and safety unhooks.

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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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Apply AlphaGo-style patterns: learned priors plus search, mixed evaluators, self-play, and asynchronous fast/slow loops. Use for intractable search and compute allocation. NOT for basic supervised learning, tractable optimization, or domains without search bottlenecks.

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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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FLOW framework integration: evidence-led SEO using the Find → Leverage → Optimize → Win loop. Surfaces stage-specific AI prompts from the FLOW knowledge base (41 prompts, CC BY 4.0). Use when user says "FLOW", "FLOW framework", "seo flow", "evidence-led SEO", "find leverage optimize win", or wants stage-specific SEO prompts.

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Doctrine for all Supabase realtime: postgres_changes, broadcast, presence. Use before writing a `.channel(`/useChannel subscription, echo suppression, reconnect logic, an autosave loop beside realtime, or replacing polling with live updates, or when the tab freezes, messages duplicate, or a subscription delivers nothing.

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The one skill for taking a page to done: its agent surface and its UI/UX, in one pass. Use when assigned pages or routes to pass, on `/page-pass <route>`, or when a campaign brief says 'do the page pass'. NOT for certification ledger writes (use surface-certification-loop).

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Redux Toolkit selector rules against re-renders, recalculation warnings, and render loops. Use when writing useSelector/useAppSelector or createSelector, deriving state in a connected component, or seeing 'Selector returned a different result when called with the same parameters'.

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Continuous localhost UI iteration loop with Arman, through full surface certification. Use when he asks to fix, refine, review, or iterate on a page, route, panel, overlay, or other UI while he may inspect localhost. NOT for a report-only UI audit.

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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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The watch-fix-rerun method for making an existing platform agent or automated process efficient and correct: baseline its ledger, run one unit yourself, fix the class behind every wasted call, rerun, record. Use when asked to improve, optimize, watch, or 'make efficient' an agent, a sandbox session, a sync job, or any recurring automated process.

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