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概要と使いどころ
Verifies build output integrity after code changes. Runs builds, validates artifact structure, checks for regressions in bundle size, asset references, and static export completeness. The last line of defense before a bad deploy ships.
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Create a self-contained, visually polished HTML showcase page for a topic or set of artifacts. Supply a mission (topic summary) and optional artifact paths explicitly — the skill never auto-scans the repo. Writes output to assets/showcase/<mission>/. Screenshots are optional (requires Puppeteer). Publishing is local-only by default; publish requests without a configured path fail clearly.
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Generate publish-grade SVG+PNG technical diagrams — architecture, data flow, flowchart, sequence, agent-memory, class, ER, state-machine, comparison, timeline, and more — across 8 visual styles. Writes output to tasks/visuals/ or an active plan's visuals/ directory. Requires rsvg-convert (librsvg) for PNG export; degrades gracefully to SVG-only when absent.
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Use when generating visual artifacts — explanations, diagrams, slides, or diff visualizations. Triggers on "explain X visually", "diagram this", "show as slides", "diff against main". NOT for rendering a plan as HTML (see mk:visual-plan), live media generation (see mk:multimodal), browser QA (see mk:qa), or plan critique (see mk:plan-ceo-review).
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Use when creating files and need the correct path, organizing project layout, or enforcing naming conventions. Two modes: advisory (return path) and organize (restructure).
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Coordinates staged or parallel jobs across live-verified coding-agent runtimes (Claude Code, Codex, Cursor, and other installed CLIs) and in-session toolkit subagents. Routes each job by capability and risk tier, isolates parallel writers in git worktrees, captures redacted output, resumes interrupted runs, and blocks completion until an independent arbiter verifies the results. Use when work should be split across multiple runtimes or subagents, run as staged or parallel jobs, and reviewed before handoff. NOT for a single-agent task or the in-session 7-phase flow (use mk:cook / mk:workflow-orchestrator).
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Use when refining a draft user prompt before sending it to a coding agent. Decomposes goal/context/constraints/acceptance/output-format, detects ambiguity and model-coupled framing, then emits a model-agnostic rewrite. Supports --analyze, --score, and --deep. NOT for prompts from scratch (mk:brainstorming), plans/reviews (mk:elicit), implementation plans (mk:plan-creator), or general codebase scouting (mk:scout).
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Structured second-pass reasoning after code review or plan evaluation. Offers named reasoning methods (pre-mortem, inversion, red team, Socratic, etc.) to re-examine findings through a specific lens. Use after /mk:review verdict or any time deeper analysis is needed on an existing output. NOT for initial review (see mk:review); NOT for creating implementation plans (see mk:plan-creator).
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Aggregate parallel agent results into concise output
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PostToolUse hook that compresses Playwright MCP tool output using Haiku summarization — Layer 4 of the token defense stack
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Execute CLI commands through RTK proxy for token-optimized output
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Parameterized evaluator-optimizer loop for quality-critical output with configurable rubrics
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Judge board subskill for simmer. Dispatches a panel of judges with different lenses, runs one deliberation round where they challenge each other's scores, then synthesizes consensus scores + single ASI. Drop-in replacement for simmer-judge that produces identical output format. Do not invoke directly — dispatched by the simmer orchestrator when JUDGE_MODE is board.
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Use when about to claim work is complete, fixed, or passing, before committing or creating PRs - requires running verification commands and confirming output before making any success claims; evidence before assertions always
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Adversarial dialectic tool inspired by GAN. Alternates between Generator (creative advocate) and Discriminator (adversarial critic). Supports forced role selection (g/d), intensity modes (hard/soft), and multi-language output. Use for stress-testing ideas, business plans, code, and spec designs.
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Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or tximeta, RSEM, 10X Genomics MTX/H5, AnnData H5AD, and RDS. Handles silent-miscounting traps (featureCounts -p v2.0.2 API break, STAR strandedness column choice, salmon NumReads-sum without tximport, RSEM non-integer expected_count, GENCODE _PAR_Y suffix, zero-length-transcript TPM divide-by-zero), and encodes the tximport countsFromAbundance decision tree with the "lengthScaledTPM is not TPM" warning. Use when assembling a gene-by-sample count matrix from aligner or quantifier output, importing salmon/kallisto for DESeq2 vs limma-voom, choosing strandedness column for STAR, debugging zero-count panics, or building tx2gene mapping.
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Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM), MeTPeak (HMM over sliding windows), MACS3/MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody methods cannot resolve, and orthogonal validation (miCLIP/GLORI/m6A-SAC-seq/m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set, reconciling differing peak sets across tools, validating MeRIP peaks against single-base methods, interpreting 5' peaks where m6Am contamination is possible, or recommending a consensus strategy.
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Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing correction choice (BH vs Storey q-value vs IHW vs lfsr), TREAT vs post-hoc fold-change filtering, p-value histogram diagnostics, gene annotation via org.db/biomaRt/mygene, GSEA preranked input, ORA background construction, replication reality (Schurch 2016 small-n result), and SABV/sex-stratified reporting. Use when extracting and interpreting DE results, troubleshooting padj=NA, choosing FDR method, preparing ranked lists for pathway analysis, annotating gene IDs, or comparing DESeq2 vs edgeR outputs.
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Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI, abritAMR, staramr, and species-specific callers (TB-Profiler, Mykrobe). Harmonises cross-tool output via hAMRonization, contextualises determinants with mobile-genetic-element annotation (MOB-suite, PlasmidFinder, MobileElementFinder, ICEberg), predicts phenotype against EUCAST or CLSI breakpoints, and translates calls into WHO GLASS reporting categories. Use when screening clinical or surveillance isolates for AMR, distinguishing acquired vs intrinsic vs point-mutation resistance, calling rpoB / katG / pncA / gyrA / mgrB mutations, reconciling AMRFinderPlus vs RGI vs ResFinder disagreement, contextualising carbapenemases or mcr alleles on plasmids, predicting susceptibility from genotype against the WHO Mtb 2nd-edition catalogue, or building a hAMRonized multi-lab AMR surveillance pipeline.
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Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).
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Designs and analyzes pooled prime-editor (PE) screens for installing precise genetic variants without bystander confounding. Covers pegRNA design with PRIDICT and PRIDICT2 for predicting per-pegRNA editing efficiency, pegRNA architecture (spacer + scaffold + PBS + RTT), PE2/PE3/PE3b/PEmax variants, MOSAIC in situ saturation mutagenesis, the PRIME pooled-screen methodology (Ren 2023; ~3,699 ClinVar variant screens), chromatin context as a major locus-level determinant of PE efficiency, scaffold-incorporation and indel byproduct quantification with CRISPResso2, and the cross-modal validation strategy of PE + base-editor screens for variant function. Use when designing a pegRNA library for variant installation, choosing between BE and PE for a specific edit, predicting pegRNA efficiency before library synthesis, analyzing PE screen output, distinguishing intended-edit from scaffold-incorporation, or scaling PE screens to thousands of variants.
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Build interactive HTML/web visualizations with plotly (Python/R), bokeh (Python), and gganimate/plotly frames for animation, with awareness of current Kaleido static-export model (post-orca-EOL), HTML file-size bloat, and the limits of interactive-only output for journal submission. Use when producing zoomable/hoverable plots for notebook EDA, supplementary HTML, dashboards, or animated time-course / iteration visualizations.
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Analyzes base-editing screens for variant function. Covers library design (Hanna 2021 ClinVar-scale CBE screen benchmarked on BRCA1/2, Cuella-Martin 2021 DDR saturation), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end; 4-7 for ABE7.10), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.
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Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.
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