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Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. 'ggtree' and using functions from 'ape' and 'phangorn'. It extends the 'ggtree' package [@Yu2017] to allow the visualization of phylogenetic networks using the 'ggplot2' syntax. It offers an alternative to the plot functions already available in 'ape' Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633> and 'phangorn' Schliep (2011) <d

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VPS 安全加固自动化 Skill。通过 SSH 登录 VPS 并执行完整的安全策略配置。 触发场景： - "加固VPS安全"、"VPS安全配置"、"新VPS初始化" - "配置SSH安全"、"修改SSH端口"、"禁用root密码登录" - "VPS安全加固"、"服务器安全设置"、"hardening" 功能（7招安全加固）： 1. 创建 sudo 用户，禁用 root 密码登录 2. 修改 SSH 端口（支持 Ubuntu 不同版本） 3. Fail2ban 自动安装配置 4. SSH 密钥登录支持 5. SSH 登录通知（可选） 6. UFW 防火墙配置 7. Docker 安全提醒 Author: github.com/wlzh Version: 1.0.0

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Root cause analysis and debugging

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Writes a single failing test that reproduces a bug after its root-cause analysis is complete, before any fix is written. TRIGGER when: a bug has a completed root-cause analysis and you need the failing reproduction test, writing a test that proves a bug exists, the second step of the bug-fixing pipeline. DO NOT TRIGGER when: still triaging or diagnosing the bug → opsmill-dev-analyzing-bugs; implementing the fix once the test exists → opsmill-dev-fixing-bugs; general feature test-first work → superpowers test-driven-development.

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Performs root-cause analysis of a bug — from a GitHub issue, an issue URL, or a free-text description — before any reproduction or fix is written. TRIGGER when: triaging or diagnosing a bug, investigating why something misbehaves, an issue number/URL handed over for analysis, needing the root cause before touching code. DO NOT TRIGGER when: a failing reproduction test already exists and you are ready to fix → opsmill-dev-fixing-bugs; writing that reproduction test → opsmill-dev-test-driving-bugs; capturing a new bug as a ticket → opsmill-dev-creating-issues.

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Use a repo-root `.editorconfig` to configure free .NET analyzer and style rules. Use when a .NET repo needs rule severity, code-style options, section layout, or analyzer ownership made explicit. USE FOR: the repo needs a root .editorconfig; analyzer severity and style ownership are unclear; the team wants one source of truth for rule configuration. DO NOT USE FOR: choosing analyzers with no config change; formatting-only execution with no config ownership question. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.

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Audit iOS and Android mobile applications against OWASP MASVS / MASTG — insecure storage, weak crypto, certificate pinning, deeplinks, IPC, jailbreak/root detection, reverse-engineering resistance. Use when the user mentions 'mobile security,' 'iOS security,' 'Android security,' 'mobile audit,' 'mobile pentest,' 'MASVS,' 'MASTG,' 'certificate pinning,' 'jailbreak detection,' 'root detection,' 'deeplink,' 'URL scheme,' 'app transport security,' 'keychain,' 'keystore,' 'mobile reverse engineering,' or has a mobile app to review.

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Model-guided autonomous root-cause analysis over a UModel object-graph semantic layer. Use with `umodel-query` when diagnosing service degradation, SLO breach, latency/error spikes, incidents, outages, or questions like why a service is slow, degraded, erroring, or timing out. The skill guides evidence collection across object graph, metrics, logs, topology, runbooks, deployments, config changes, business traffic, and runtime capacity; it is especially useful for ruling out red herrings such as recent but unrelated deployments. Triggers: root cause, RCA, incident, SLO breach, outage, postmortem, latency spike, error spike, timeout, 根因分析, 故障排查, 告警定位, 为什么慢, SLO 击穿.

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Validate consistency across SEED Design component documentation layers (design guidelines in ./docs/content/docs/components, Rootage specs in ./packages/rootage/components, and React docs in ./docs/content/react/components). Use when auditing documentation completeness, before releases, or validating new component docs.

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Production incident response automation. Reads logs, checks recent deploys, identifies root cause, suggests fixes, drafts incident comms, creates post-mortem templates. Severity classification (SEV1-4), escalation paths, status page updates. Generates incident-report.md with timeline, root cause, impact assessment, remediation steps, and prevention measures.

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Triage a raw, vague issue or bug report into a structured document that names what is known, what is missing, and what to do next. Use when an incoming issue, bug report, or problem description is too vague or incomplete for investigation or planning, and recommend the right next han skill. Does not investigate root causes or trace code paths — use investigate for debugging, diagnosis, and root cause analysis. Does not plan features or build solutions — use plan-a-feature or plan-implementation for that.

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Evidence-based investigation of issues, bugs, API calls, integrations, and other aspects of software development that need a deep dive to find the root cause and solutions. Use when you need to debug, troubleshoot, diagnose, or figure out why something is broken. Does not review code for quality or style — use code-review for auditing changes or post-code-review-to-pr for posting review feedback to GitHub. Does not assess architectural health or structural risk — use architectural-analysis for architectural concerns. Does not research open-ended options, prior art, or how something works when nothing is broken — use research for that. Does not plan the structural change a root cause calls for — use plan-a-change. Does not map bounded contexts or domain boundaries — use ddd-analysis. Does not capture feedback on Han's own skills — use han-feedback for that.

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Fix Gorse recommendation engine pods crashing with "user: unknown userid 65532" error. Use when: (1) Gorse master/server/worker pods show CrashLoopBackOff or Error status, (2) Logs show "failed to get user directory" with unknown userid, (3) Running gorse containers with runAsNonRoot security context and custom UID. The gorse images call os.UserHomeDir() at startup which requires the UID to exist in /etc/passwd.

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Analyze vulnerable code to identify underlying root causes such as violated assumptions, incorrect invariants, missing validation checks, or unsafe component interactions. Use when investigating security vulnerabilities, CVEs, exploit code, or security audit findings. Infers why the vulnerability exists beyond surface symptoms, identifies systemic issues, and explains the chain of failures that enable exploitation.

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Locate root causes of failing regression tests by analyzing code changes, error messages, and test dependencies. Use when regression tests start failing after code changes, investigating test failures in CI/CD, debugging flaky tests, or understanding why previously passing tests now fail. Analyzes git diffs, stack traces, test output, and dependency changes to produce structured markdown reports ranking likely causes. Triggers when users ask to find why tests are failing, debug regression failures, investigate test breakage, or analyze failing test suites.

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Apply when debugging. Trace each symptom to its root cause and fix it there; reproduce first, ask why until you reach it, resist nil-check guards that silence crashes.

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Expert in running effective incident postmortems. Covers blameless analysis, root cause investigation, action item prioritization, and building a learning culture. Understands that incidents are opportunities to improve systems, not punish people. Use when "postmortem, incident review, what went wrong, root cause, blameless, outage, post-incident, " mentioned.

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Expert in real-time game animation systems including skeletal animation, blend trees, state machines, inverse kinematics, root motion, procedural animation, and animation retargeting. Specializes in creating fluid, responsive character animation that balances visual quality with performance constraints. Use when "animation system, state machine, blend tree, skeletal animation, inverse kinematics, IK system, root motion, animation blending, character animation, animator controller, motion matching, animation retargeting, foot IK, look at IK, aim offset, animation montage, animation notify, additive animation, animation layers, procedural animation, animation, game-dev, character, state-machine, unity, unreal, godot, skeletal, rigging, motion" mentioned.

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Finds the cause of a hard bug by running several read-only subagents in parallel, each attacking it from a different angle (change history, code path, data and state, environment, reproduction), then checking their evidence, ranking the hypotheses and naming the one experiment that would confirm the leader. It diagnoses and does not fix. Use when someone says "hunt this bug with multiple agents", "swarm on this regression", "investigate in parallel", "find the root cause", or when a failure is intermittent, crosses components, or has resisted a first look.

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The lifecycle gate for a local Codespace-equivalent sandbox. Routed to when the user invokes /ca-sandbox:sandbox to pull an untrusted repo into an ephemeral, host-FS-isolated Docker container, or any of the interaction commands (/ca-sandbox:sandbox-shell, /ca-sandbox:sandbox-exec, /ca-sandbox:sandbox-cp, /ca-sandbox:sandbox-destroy) against an existing box. Five gated phases — pre-flight, clone+build, isolated run, interact, teardown. The load-bearing invariant is structural: untrusted code in the box can never reach the host filesystem (no bind mount, no docker socket, never --privileged, cap-drop ALL, non-root, read-only root). Network defaults to offline; egress out is host-initiated only. Every object is labeled ca.sandbox=1 and torn down on exit.

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Uncover root causes through recursive Why questioning and consequence exploration. Use before acting on problems.

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Use when a task in code_review was sent back before (an earlier need_revision comment exists) - verify every prior point was fixed at its root

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Root-cause debugging discipline. Use when a test, build or pipeline fails, behaviour does not match expectations, a bug task arrives, or a task comes back in need_revision — before proposing any fix.

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Investigates a bug, failing test, build error, regression, flaky behavior, performance symptom, or unexpected result by reproducing it, minimizing the case, testing ranked hypotheses, tracing the first incorrect state, and locking the root cause with a regression check. Use before proposing a fix. Not for planning a new feature or reviewing a healthy diff.

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