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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Prepare, execute and verify authorized Fusion CAD changes using resolved entities, explicit units and state-bound plans. Use for reviewed parameter, sketch, feature, assembly or configuration operations.

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Expert-level nanotechnology covering nanomaterials, nanofabrication, characterization methods, nanoelectronics, nanomedicine, and self-assembly.

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Use when planning the migration of a legacy system or monolith — analyzes the source codebase (current repo, or a repo URL cloned to a temp dir) and produces an evidence-based Strangler Fig migration plan with per-domain SPECs. Default target is .NET (Blazor WebAssembly, .NET MAUI, ASP.NET Core); other stacks allowed by user decision. Do NOT use to implement code or when approved SPECs already cover the migration.

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Builds and improves task-specific decision artifacts from application requirements and labeled records. Use for data assembly, primitive and base-model selection, fitting, export/reload, inference policy, or bounded data/model/program improvement. Includes rules and no-training outcomes; does not require a rung ladder or training a general Jev.

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Design SS14 components as serialized state in the correct assembly.

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Place contracts and behavior across authority, prediction, presentation, localization, and assembly boundaries.

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Prove repository ownership, module ownership, assembly boundaries, edit-marker rules, extension points, and test placement.

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Build repeatable data-to-Docs pipelines from Sheets and Drive sources. Use for automated status reports, template-based document assembly, and scheduled publishing workflows.

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Reverse-engineers and debugs macOS and iOS binaries with Hopper Disassembler and LLDB: ObjC/Swift symbols, dyld loading, framework internals, and crash investigation from disassembly. Use when private API behavior or a runtime crash needs to be understood at the binary level.

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Implement or extend a CPU architecture, processor variant, instruction set, addressing modes, registers, interrupts, bus transactions, disassembly, timing, and processor tests in EMULATORS. Use when adding a processor not yet emulated, deriving a CPU from F6500, FZ80, or another family, filling missing opcodes, correcting instruction semantics or cycles, or creating exhaustive instruction and interrupt tests.

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Reverse engineer Go-compiled malware using Ghidra with specialized scripts for function recovery, string extraction, and type reconstruction in stripped Go binaries.

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Use when designing, evaluating, documenting, modernizing, reviewing, refactoring, or implementing software architecture and code-level structure, including requirements, context, architecture style selection, microservices patterns, WebAssembly/WASI/Component Model, UMA portable capabilities, runtime contracts, capability graphs, governed MCP/agent orchestration, clean code, code smells, Rust crate/library API architecture, Cargo feature/MSRV/SemVer policy, unsafe/FFI/no_std/library testing, modularity, views, NFR tactics, IAM/auth, security patterns, cost estimation, architecture-as-code fitness functions, ADR/RFC work, and engineering execution plans.

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Turn an approved topic into a narrated, non-presenter video using a script, voice asset, visual coverage, assembly, and captions.

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Turn one approved topic into a curiosity-led 3D educational short with character sheets, ordered keyframes, motion clips, narration, captions, and an auditable assembly plan.

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Turn approved video clips, audio, captions, and timing decisions into an ordered, reviewable draft while preserving a reproducible timeline.

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Develop a short scripted micro-drama from an idea or approved script through character sheets, storyboard frames, animated shots, and a reviewable assembly.

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Diagnose MSBuild build performance bottlenecks using binary log analysis. Only activate in MSBuild/.NET build context. USE FOR: identifying why builds are slow by analyzing binlog performance summaries, detecting ResolveAssemblyReference (RAR) taking >5s, Roslyn analyzers consuming >30% of Csc time, single targets dominating >50% of build time, node utilization below 80%, excessive Copy tasks, NuGet restore running every build. Covers timeline analysis, Target/Task Performance Summary interpretation, and 7 common bottleneck categories. Use after build-perf-baseline has established measurements. DO NOT USE FOR: establishing initial baselines (use build-perf-baseline first), fixing incremental build issues (use incremental-build), parallelism tuning (use build-parallelism), non-MSBuild build systems. INVOKES: binlog MCP server tools (overview, errors, search, items, properties); falls back to dotnet msbuild binlog replay + grep/cat when the MCP is unavailable.

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Guide for modernizing and migrating MSBuild project files to SDK-style format. Only activate in MSBuild/.NET build context. USE FOR: converting legacy .csproj/.vbproj with verbose XML to SDK-style, migrating packages.config to PackageReference, removing Properties/AssemblyInfo.cs in favor of auto-generation, eliminating explicit <Compile Include> lists via implicit globbing, consolidating shared settings into Directory.Build.props. Indicators of legacy projects: ToolsVersion attribute, <Import Project="$(MSBuildToolsPath)">, .csproj files > 50 lines for simple projects. DO NOT USE FOR: projects already in SDK-style format, non-.NET build systems (npm, Maven, CMake), .NET Framework projects that cannot move to SDK-style. INVOKES: dotnet try-convert, upgrade-assistant tools.

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VibeFarsi blocks/templates/sites: production-level assembly, responsiveness and content. Use when implementing, reviewing or testing vibefarsi blocks/templates/sites for React, Vite, Next.js or Perfect_AI projects.

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Master binary analysis patterns including disassembly, decompilation, control flow analysis, and code pattern recognition. Use when analyzing executables, understanding compiled code, or performing...

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Scaffold, build, and package SwiftPM-based macOS apps without an Xcode project. Use when you need a from-scratch macOS app layout, SwiftPM targets/resources, a custom .app bundle assembly script, or signing/notarization/appcast steps outside Xcode.

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Produce intentional, responsive, accessible UI work and perform visual QA instead of generic component assembly.

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Comprehensive patterns and techniques for analyzing compiled binaries, understanding assembly code, and reconstructing program logic.

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