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Resolve an in-progress git merge or rebase conflict end to end: read the conflict state, recover each side's original intent, resolve every hunk, run the project's checks, and prepare the merge/rebase for an explicitly approved finish. Use when asked to "resolve merge conflicts", "fix this rebase", "finish the merge", or when `git status` shows conflicted (unmerged) paths. NOT for the full ship pipeline that merges the base branch first (see mk:ship); NOT for debugging a runtime bug or test failure unrelated to a conflict (see mk:investigate / mk:fix).

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Multi-pass structural code review with adversarial analysis, scope-aware dispatch, adversarial persona passes, and forced-finding protocol. Supports input modes: branch diff (default), PR number (#123), commit hash, pending changes (--pending). Use when asked to "review this PR", "code review", "pre-landing review", "check my diff", or "review #123". Proactively suggest when the user is about to merge or land code changes. NOT for behavioral verification against a running build (see mk:evaluate); NOT for post-implementation simplification (see mk:simplify).

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Relentlessly interview the user about THEIR plan or design — one question at a time — resolving each branch of a decision tree until shared understanding. Claude is the interviewer; the user is the interviewee. Triggers on "grill me", "stress-test this plan", "get grilled on my design", "interrogate my plan". Checkpoints every answer to docs/knowledge/<slug>.md so progress survives a context-window reset. Flags knowledge the user cannot answer as a gap to chase. Do NOT use to PROPOSE solutions or compare approaches (→ mk:brainstorming). Do NOT use to validate "is this worth building?" (→ mk:office-hours). Do NOT use when Claude should ANSWER questions about the repo (→ mk:ask-me). Do NOT use for a one-shot review of an existing plan (→ mk:plan-ceo-review). Do NOT use to apply named reasoning lenses to findings (→ mk:elicit).

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。

DraftForge PR lifecycle workflow. Use when the user runs /pr, opens or pushes a pull request, or asks to monitor CI checks and Copilot review on a branch. Creates the PR (or reuses an existing one), polls GitHub Actions and Copilot up to ~15 min, then analyses CI failures and Copilot comments and reports findings grouped by file and skill.

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Rework a change as if the intended UX and architecture had existed from day one — deleting compatibility cruft, dead branches, and accidental complexity instead of patching around them. Use when refactoring, cleaning up after a feature lands, removing flags, collapsing legacy paths, or when the user says the code "should look like X from scratch".

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Review the current branch for bugs, intent fit, and test coverage; run or write tests; commit focused work; open or update a PR.

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。

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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Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast pairwise), AnchorWave (Song 2022 WGD-aware), and Mauve / progressiveMauve (bacterial). Operates the HAL toolkit (Hickey 2013) for downstream extraction including halSynteny, halLiftover, halBranchMutations, and hal2maf. Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.

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Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel 2020 ML reconciliation), AleRax (Morel 2024 co-estimation), Whale.jl (Bayesian DL+WGD), RANGER-DTL 2 parsimony, NOTUNG, ecceTERA, and Treerecs. Use when inferring ancestral gene-family content, distinguishing duplication from horizontal transfer from differential loss, rooting deep species trees from gene-content signals (STRIDE / Williams 2017 ALE-rooting), counting DTL events per branch, refining noisy gene trees against a species tree, modeling WGD events jointly with DTL, or producing publication-grade gene-family histories for phylogenomic / comparative analyses.

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Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011), f4-ratio and f-branch statistic (Malinsky 2018), TreeMix (Pickrell & Pritchard 2012), HyDe (Blischak 2018), QuIBL (Edelman 2019), sprime (Browning 2018), Twisst (Martin 2017), PhyloNet (Than 2008) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012). Distinguish introgression from incomplete lineage sorting (ILS), ancestral structure, ghost-lineage admixture, and rate variation. Use when testing inter-species gene flow, dating admixture events, identifying introgressed segments, building phylogenetic networks for reticulate evolution, or applying the ABBAclustering (Koppetsch-Malinsky-Matschiner 2024) framework for divergent-species gene flow.

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Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize something over many experiments without overfitting — e.g. "get my model's eval score up", "improve this agent/harness", "tune this pipeline", "beat the baseline on this benchmark", "run a search over approaches and keep the best", "do an MLE-bench / Kaggle-style optimization", or any long-horizon "make this artifact better and don't just memorize the dev set" task. Trigger it even when the user doesn't say "Arbor" or "hypothesis tree" but describes repeated experiment-and-evaluate loops, branching exploration of competing ideas, or worries about a dev/test gap. Runs Claude itself as the coordinator with subagent executors in isolated git worktrees; for the standalone `arbor` CLI tool see references/arbor-upstream.md.

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Workflow Phase 7 — Mechanical cleanup pass over the branch diff, followed by a `code-structure` review pass and a `verify` re-stamp. Shadows the global `simplify` skill at project scope; the cleanup pass is performed inline rather than via Skill self-call.

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。

Multi-agent collaboration plugin that spawns N parallel subagents competing on the same task via git worktree isolation. Agents work independently, results are evaluated by metric or LLM judge, and the best branch is merged. Use when: user wants multiple approaches tried in parallel — code optimization, content variation, research exploration, or any task that benefits from parallel competition. Requires: a git repo.

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。

Audit code changes on the current branch and update docs/ + .claude/rules/ to stay in sync. Run before /pr.

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。

Run a skeptical Claude review over the current diff or branch range.

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。

Review code changes for correctness defects, regressions, security risks, data-integrity problems, concurrency hazards, and missing meaningful tests. Use for pull requests, branches, commits, patches, or working-tree reviews; do not use for implementation unless the user separately requests fixes.

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Set up Claude Code hooks to block dangerous git commands (push, reset --hard, clean, branch -D, etc.) before they execute. Use when user wants to prevent destructive git operations, add git safety hooks, or block git push/reset in Claude Code.

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Interview the user relentlessly about a plan or design until reaching shared understanding, resolving each branch of the decision tree. Use when user wants to stress-test a plan, get grilled on their design, or mentions "grill me".

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Build a throwaway prototype to flush out a design before committing to it. Routes between two branches — a runnable terminal app for state/business-logic questions, or several radically different UI variations toggleable from one route. Use when the user wants to prototype, sanity-check a data model or state machine, mock up a UI, explore design options, or says "prototype this", "let me play with it", "try a few designs".

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Use when implementation is complete, all tests pass, and you need to decide how to integrate the work - guides completion of development work by presenting structured options for merge, PR, or cleanup

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。

GitHub PR lifecycle: branch, commit, open, CI, merge.

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Conducts multi-axis code review. Use before merging any change. Use when reviewing code written by yourself, another agent, or a human. Use when you need to assess code quality across multiple dimensions before it enters the main branch.

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Structures git workflow practices. Use when making any code change. Use when committing, branching, resolving conflicts, or when you need to organize work across multiple parallel streams.

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Decides how far ahead to plan, what to discount future payoffs by, and which backlog items can be dropped without analysis - using receding-horizon planning, an explicit discount factor, and branch-and-bound pruning against the incumbent. Use when building a roadmap, prioritising a backlog, arguing about short-term versus long-term, setting quarterly or annual plans, or when planning has become an end in itself.

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。