Protein Solubility Optimization - Optimize protein solubility: calculate properties, predict solubility, predict hydrophilicity, and suggest mutations. Use this skill for protein engineering tasks involving calculate protein sequence properties predict protein function ComputeHydrophilicity zero shot sequence prediction. Combines 4 tools from 3 SCP server(s).

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Help address review/issue comments on the open GitHub PR for the current branch using gh

Use when a user asks to debug or fix failing GitHub PR checks that run in GitHub Actions;

Use when the task requires automating a real browser from the terminal (navigation, form

Use when the user explicitly asks for a desktop or system screenshot (full screen, specific

Perform language and framework specific security best-practice reviews and suggest improvements.

Repository-grounded threat modeling that enumerates trust boundaries, assets, attacker capabilities,

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Audits Solidity codebases for smart contract vulnerabilities using a four-phase workflow (cheatsheet loading, codebase sweep, deep validation, reporting) covering 36 vulnerability classes. Use when auditing Solidity contracts for security issues, performing smart contract vulnerability scans, or reviewing Solidity code for common exploit patterns.

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Analyze the git diff between the current branch and main from multiple perspectives (duplication, correctness, security, performance, testing, architecture, scope) using parallel subagents, then produce a remediation plan for issues found. Use when reviewing branch changes before merge, after implementation, or when the user asks to critique or review current code changes.

Prepare code for review by running quality checks, creating conventional commits, and opening pull requests. Use when the user wants to commit changes, create a PR, prepare for code review, or asks to commit their work.

Process all unaddressed PR review comments in parallel. Each comment gets a dedicated subagent that either applies the fix or replies with technical reasoning for disagreement.

Use when you need to generate a checklist document with Java system prompts, following the embedded template exactly and producing INVENTORY-SKILLS-JAVA.md in the project root. Part of the skills-for-java project

Use when you need to generate a checklist document with embedded agents inventory, following the embedded template exactly and producing INVENTORY-AGENTS-JAVA.md in the project root. Part of the skills-for-java project

Guides the creation of agile epics with comprehensive definition including business value, success criteria, and breakdown into user stories. Use when the user wants to create an agile epic, define large bodies of work, break down features into user stories, or document strategic initiatives. Part of the skills-for-java project

Guides the creation of detailed agile feature documentation from an existing epic. Use when the user wants to split an epic into feature files, derive features with scope and acceptance criteria, or plan feature documentation for stakeholders or engineering. Part of the skills-for-java project

Guides the creation of agile user stories and Gherkin feature files. Use when the user wants to create a user story, write acceptance criteria, define Gherkin scenarios, or author BDD feature files. Part of the skills-for-java project

Use when you need to generate Architecture Decision Records (ADRs) for a Java project through an interactive, conversational process that systematically gathers context, stakeholders, options, and outcomes to produce well-structured ADR documents. Part of the skills-for-java project

Facilitates conversational discovery to create Architectural Decision Records (ADRs) for non-functional requirements using the ISO/IEC 25010:2023 quality model. Use when the user wants to document quality attributes, NFR decisions, security/performance/scalability architecture, or design systems with measurable quality criteria. Part of the skills-for-java project

Use when you need to generate Java project diagrams — including UML sequence diagrams, UML class diagrams, C4 model diagrams, UML state machine diagrams, and ER (Entity Relationship) diagrams — through a modular, step-based interactive process that adapts to your specific visualization needs. Part of the skills-for-java project

Use when creating a plan using Plan model and enhancing structured design plans in Cursor Plan mode for Java implementations. Use when the user wants to create a plan, design an implementation, structure a development plan, or use plan mode for outside-in TDD, feature implementation, or refactoring work. Part of the skills-for-java project

Use when you need to take a `*.plan.md` file and turn it into OpenSpec change artifacts by validating OpenSpec installation, initializing or reusing an OpenSpec project, and creating or updating a change proposal/spec/tasks flow. Includes a concrete workflow based on `examples/requirements-examples/problem1/requirements/openspec`. Part of the skills-for-java project

Use when you need to review, improve, or troubleshoot a Maven pom.xml file — including dependency management with BOMs, plugin configuration, version centralization, multi-module project structure, build profiles, or any situation where you want to align your Maven setup with industry best practices. Part of the skills-for-java project

Use when you need to add or evaluate Maven dependencies that improve code quality — including nullness annotations (JSpecify), static analysis (Error Prone + NullAway), functional programming (VAVR), or architecture testing (ArchUnit) — and want a consultative, question-driven approach that adds only what you actually need. Part of the skills-for-java project

Use when you need to add or configure Maven plugins in your pom.xml — including quality tools (enforcer, surefire, failsafe, jacoco, pitest, spotbugs, pmd), security scanning (OWASP), code formatting (Spotless), version management, container image build (Jib), build information tracking, and benchmarking (JMH) — through a consultative, modular step-by-step approach that only adds what you actually need. Part of the skills-for-java project

Use when you need to create a DEVELOPER.md file for a Maven project — combining a fixed base template with dynamic sections derived from the project pom.xml, including a Plugin Goals Reference, Maven Profiles table, and Submodules table for multi-module projects. Part of the skills-for-java project

Use when you need to review, improve, or refactor Java code for object-oriented design quality — including applying SOLID, DRY, and YAGNI principles, improving class and interface design, fixing OOP concept misuse (encapsulation, inheritance, polymorphism), identifying and resolving code smells (God Class, Feature Envy, Data Clumps), or improving object creation patterns, method design, and exception handling. Part of the skills-for-java project

Use when you need to review, improve, or refactor Java code for type design quality — including establishing clear type hierarchies, applying consistent naming conventions, eliminating primitive obsession with domain-specific value objects, leveraging generic type parameters, creating type-safe wrappers, designing fluent interfaces, ensuring precision-appropriate numeric types (BigDecimal for financial calculations), and improving type contrast through interfaces and method signature alignment. Part of the skills-for-java project

Use when you need to apply Java exception handling best practices — including using specific exception types, managing resources with try-with-resources, securing exception messages, preserving error context via exception chaining, validating inputs early with fail-fast principles, handling thread interruption correctly, documenting exceptions with @throws, enforcing logging policy, translating exceptions at API boundaries, managing retries and idempotency, enforcing timeouts, attaching suppressed exceptions, and propagating failures in async/reactive code. Part of the skills-for-java project

Use when you need to apply Java secure coding best practices — including validating untrusted inputs, defending against injection attacks with parameterized queries, minimizing attack surface via least privilege, applying strong cryptographic algorithms, handling exceptions securely without exposing sensitive data, managing secrets at runtime, avoiding unsafe deserialization, and encoding output to prevent XSS. Part of the skills-for-java project

Use when you need to apply Java concurrency best practices — including thread safety fundamentals, ExecutorService thread pool management, concurrent design patterns like Producer-Consumer, asynchronous programming with CompletableFuture, immutability and safe publication, deadlock avoidance, virtual threads, scoped values, backpressure, cancellation discipline, and observability for concurrent systems. Part of the skills-for-java project

Use when you need to review, improve, or refactor Java code for generics quality — including avoiding raw types, applying the PECS (Producer Extends Consumer Super) principle for wildcards, using bounded type parameters, designing effective generic methods, leveraging the diamond operator, understanding type erasure implications, handling generic inheritance correctly, preventing heap pollution with @SafeVarargs, and integrating generics with modern Java features like Records, sealed types, and pattern matching. Part of the skills-for-java project

Use when you need to apply testing strategies for Java code — RIGHT-BICEP to guide test creation, A-TRIP for test quality characteristics, or CORRECT for verifying boundary conditions. Part of the skills-for-java project

Use when you need to review, improve, or write Java unit tests — including migrating from JUnit 4 to JUnit 5, adopting AssertJ for fluent assertions, structuring tests with Given-When-Then, ensuring test independence, applying parameterized tests, mocking dependencies with Mockito, verifying boundary conditions (RIGHT-BICEP, CORRECT, A-TRIP), leveraging JSpecify null-safety annotations, or eliminating testing anti-patterns such as reflection-based tests or shared mutable state. Part of the skills-for-java project

Use when you need to set up, review, or improve Java integration tests — including generating a BaseIntegrationTest.java with WireMock for HTTP stubs, detecting HTTP client infrastructure from import signals, injecting service coordinates dynamically via System.setProperty(), creating WireMock JSON mapping files with bodyFileName, isolating stubs per test method, verifying HTTP interactions, or eliminating anti-patterns such as Mockito-mocked HTTP clients or globally registered WireMock stubs. Part of the skills-for-java project

Use when you need to implement acceptance tests from a Gherkin .feature file for framework-agnostic Java (no Spring Boot, Quarkus, Micronaut) — finding @acceptance scenarios, happy path with RestAssured, Testcontainers for DB/Kafka, WireMock for external REST. Requires .feature file in context. Part of the skills-for-java project

Use when you need to refactor Java code to adopt modern Java features (Java 8+) — including migrating anonymous classes to lambdas, replacing Iterator loops with Stream API, adopting Optional for null safety, switching from legacy Date/Calendar to java.time, using collection factory methods, applying text blocks, var inference, or leveraging Java 25 features like flexible constructor bodies and module import declarations. Part of the skills-for-java project

Use when you need to apply functional programming principles in Java — including writing immutable objects and Records, pure functions, functional interfaces, lambda expressions, Stream API pipelines, Optional for null safety, function composition, higher-order functions, pattern matching for instanceof and switch, sealed classes/interfaces for controlled hierarchies, Stream Gatherers for custom operations, currying/partial application, effect boundary separation, and concurrent-safe functional patterns. Part of the skills-for-java project

Use when you need to apply functional exception handling best practices in Java — including replacing exception overuse with Optional and VAVR Either types, designing error type hierarchies using sealed classes and enums, implementing monadic error composition pipelines, establishing functional control flow patterns, and reserving exceptions only for truly exceptional system-level failures. Part of the skills-for-java project

Use when you need to apply data-oriented programming best practices in Java — including separating code (behavior) from data structures using records, designing immutable data with pure transformation functions, keeping data flat and denormalized with ID-based references, starting with generic data structures converting to specific types when needed, ensuring data integrity through pure validation functions, and creating flexible generic data access layers. Part of the skills-for-java project

Use when you need to set up JMeter performance testing for a Java project — including creating the run-jmeter.sh script from the exact template, configuring load tests with loops, threads, and ramp-up, or running performance tests from the project root with custom or default settings. Part of the skills-for-java project

Use when you need to set up Java application profiling to detect and measure performance issues — including automated async-profiler v4.0 setup, problem-driven profiling (CPU, memory, threading, GC, I/O), interactive profiling scripts, JFR integration with Java 25 (JEP 518, JEP 520), or collecting profiling data with flamegraphs and JFR recordings. Part of the skills-for-java project

Use when you need to analyze Java profiling data collected during the detection phase — including interpreting flamegraphs, memory allocation patterns, CPU hotspots, threading issues, systematic problem categorization, evidence documentation with profiling-problem-analysis and profiling-solutions markdown files, or prioritizing fixes using Impact/Effort scoring. Part of the skills-for-java project

Use when you need to refactor Java code based on profiling analysis findings — including reviewing docs/profiling-problem-analysis and docs/profiling-solutions, identifying specific performance bottlenecks, and implementing targeted code changes to address CPU, memory, or threading issues. Part of the skills-for-java project

Use when you need to verify Java performance optimizations by comparing profiling results before and after refactoring — including baseline validation, post-refactoring report generation, quantitative before/after metrics comparison, side-by-side flamegraph analysis, regression detection, or creating profiling-comparison-analysis and profiling-final-results documentation. Part of the skills-for-java project