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Automate Bitbucket repositories, pull requests, branches, issues, and workspace management via Rube MCP (Composio). Always search tools first for current schemas.

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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 DTL+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 (Solis-Lemus 2017) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012; Lipson 2013). 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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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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Find and identify the CCSPlayerPawn_SnapViewAngles function in CS2 server binary using IDA Pro MCP. Use this skill when reverse engineering CS2 server.dll or libserver.so to locate the non-virtual SnapViewAngles method, anchored on the "setang" console-command usage string and its non-teleport call branch. Emits a unique IDA-style byte signature and a func YAML. Trigger: CCSPlayerPawn_SnapViewAngles, SnapViewAngles

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Analyzes PHP codebase for test coverage gaps. Detects untested classes, methods, branches, exception paths, and edge cases. Provides actionable recommendations.

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[21] UNDERSTAND. Deep research workflow for this project using 150% scope (100% core + 50% boundary), evidence-based reasoning, and structured investigation notes. Use when the task requires investigation, root-cause analysis, or mapping unknown areas. Always maintain a research log file that captures findings, hypotheses, and next branches; use web.run when external verification is needed.

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コミットやPR作成の前に、作業ブランチが適切かどうかを確認・切り替えるスキル。git-commit や create-pr からサブルーチンとして呼び出される。

Automate Bitbucket repositories, pull requests, branches, issues, and workspace management via Rube MCP (Composio). Always search tools first for current schemas.

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。

Performs a comprehensive security review of code changes in a GitHub PR or issue. Checks out the branch, analyzes changed files against a 9-category security checklist, and produces PASS/WARNING/FAIL verdicts. Use when reviewing pull requests for security vulnerabilities, hardcoded secrets, injection flaws, auth bypasses, or insecure configurations. Trigger keywords - security review, code review, appsec, vulnerability assessment, security audit, review PR security.

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Full pull request lifecycle — create branches, commit changes, open PRs, monitor CI status, auto-fix failures, and merge. Works with gh CLI or falls back to git + GitHub REST API via curl.

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The PRIMARY development workflow for the Archon project (remote-coding-agent). Use this skill instead of any PRP skills when working on Archon code. Routes to 10 specialized cookbooks based on what the user is trying to do: RESEARCH — "how does the orchestrator work?", "where is session state defined?", "trace the workflow execution flow", "what is IWorkflowStore?" INVESTIGATE — "should we use Drizzle or Prisma?", "what's the best way to add WebSockets?", "can we migrate to Turso?", "how do other projects handle rate limiting?" PRD — "write a PRD for dark mode", "spec out the notification feature", "product requirements for webhook retry" PLAN — "plan the auth refactor", "design the caching layer", "create an implementation plan for #42" IMPLEMENT — "implement the plan", "execute .claude/archon/plans/auth.plan.md", "build the feature from the plan", "code this up" REVIEW — "review PR #123", "review my changes", "code review the diff" DEBUG — "debug the failing test", "why is streaming broken?", "root cause analysis on the timeout issue" COMMIT — "commit these changes", "commit the auth refactor" PR — "create a PR", "open a pull request for this branch" ISSUE — "report this to gh", "create a gh issue", "log it in github", "file a bug for this", "create a feature request" This skill triggers on ANY development task: researching, investigating, planning, building, reviewing, debugging, committing, or shipping code. NOT for: Running Archon CLI workflows in worktrees (use /archon instead).

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Create a release from dev branch. Generates changelog entries from commits, bumps version, and creates a PR to main. TRIGGERS - Use this skill when user says: - "/release" - create a patch release (default) - "/release minor" - create a minor release - "/release major" - create a major release - "make a release", "cut a release", "ship it", "release to main"

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 a PR or branch diff using the knowledge graph for full structural context. Outputs a structured review with blast-radius analysis.

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。

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

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Use when working with the fjo CLI or Forgejo/Gitea instances: repositories, issues, pull requests, releases, branches, comments, Actions, or authentication. Provides safe host-aware read/write workflows. Not for GitHub — use `using-gh-for-github` there.

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Review code changes from the current branch, staged changes, a git ref, or a diff/patch file. Pure git-native — no platform/PR awareness. Trigger when user says "review this", "review diff", "/aiwork:code-review-diff", or provides a git ref or diff path. Read-only — never posts comments.

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 from current branch, an Azure DevOps PR, a git ref, or a diff/patch file. Trigger when user says "review this", "code review", "/df:code-review", or provides a PR id/URL, ticket URL, git ref, or diff path. Read-only — never posts comments.

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。

Azure DevOps pull requests, for repos whose git remote is on dev.azure.com or *.visualstudio.com. Covers comment threads, which `az repos pr` cannot read or post. Use to create a PR for the current branch, check out, list or complete PRs, post code comments on a PR, reply to threads, and assess whether review feedback was addressed. Trigger on "create PR", "checkout PR 123", "list PRs", "complete PR", "comment on the PR", "post these review findings", "check PR feedback", "/dev-azdo: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。

All changes to code must follow the guidance documented in the repository. Before any issue is filed, branch is made, commits generated, or pull request (or PR) created, a search must be done to ensure the right steps are followed. Whenever asked to create an issue, commit messages, to push code, or create a PR, use this skill so everything is done correctly.

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。

Investigate and fix CI failures on a pull request. Use when CI checks fail on a PR branch — covers finding the PR, identifying failed checks, downloading logs and artifacts, extracting the failure cause, and iterating on a fix. Requires the `gh` CLI.

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。

Best practices for git workflow automation including atomic commits, branch naming, conventional commit format, and changelog generation.

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。

Migration and code evolution instructions generator for GitHub Copilot. Analyzes differences between two project versions (branches, commits, or releases) to create precise instructions allowing Copilot to maintain consistency during technology migrations, major refactoring, or framework version upgrades.

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。