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Reference guide for the Twelve-Factor App methodology — 15 principles (12 original + 3 modern extensions) for building portable, resilient, cloud-native applications. Use when evaluating application architecture, designing cloud-native services, reviewing codebases for methodology compliance, advising on configuration, scaling, observability, security, and deployment patterns. Incorporates the 2025 open-source community evolution and cloud-native reinterpretations of each factor.

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Organization-grade cloud and supply-chain attack-surface discovery: S3/GCS/Azure Blob bucket discovery via observed-name mining (CNAME/cert-SAN/Wayback) and bounded two-class permutation (6 prefixes x 15 suffixes on trusted tokens, bounded target-bound expansion on subdomain stems), existence (HEAD/GET) vs public-listing confirmation, object-key triage into 9 value tiers (database dumps, credentials, IaC state, kubeconfig, VCS dirs, config, archives, PII, logs), dangling-CNAME bucket-takeover detection, and the ownership-gated severity model that stops an unattributable public bucket from becoming a false CRITICAL; the fully offline AWS-account-ID recovery from a leaked AKIA/ASIA/AROA access key (base32 decode, runnable stdlib Python, canonical test vector, AWS-documentation-example-ID screening); dependency-confusion confirmation for npm/PyPI (internal-signal classifier -- private-registry binding vs org-namespace match -- paired with a read-only public-registry 404 check and the npm scope-claimability nuance the public search API misses); and passive cloud-native/container/Kubernetes/CI control-plane fingerprinting (Lambda URLs, API Gateway, Cloud Run, App Service, kubelet/etcd/K8s API/dashboard, Jenkins/GitLab/Argo CD) as an org-attribution and exposure surface. Passive/discovery only -- no exploitation, no credential submission, no active control-plane confirmation (a stage-6 validate_cloud active tier is described but out of scope). Use when enumerating a target's cloud storage footprint, recovering an AWS account ID from a leaked key, confirming a supply-chain dependency-confusion vector, or fingerprinting cloud-native/K8s/CI infrastructure for an authorized external recon engagement.

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World-class Java and Spring Boot development skill for enterprise applications, microservices, and cloud-native systems. Expertise in Spring Framework, Spring Boot 3.x, Spring Cloud, JPA/Hibernate, and reactive programming with WebFlux. Includes project scaffolding, dependency management, security implementation, and performance optimization.

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Expert Kubernetes architect specializing in cloud-native infrastructure, advanced GitOps workflows (ArgoCD/Flux), and enterprise container orchestration. Masters EKS/AKS/GKE, service mesh (Istio/Linkerd), progressive delivery, multi-tenancy, and platform engineering. Handles security, observability, cost optimization, and developer experience. Use PROACTIVELY for K8s architecture, GitOps implementation, or cloud-native platform design.

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Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR (Python) implicit transpose, AnnData (cells-rows) <-> SingleCellExperiment (cells-cols) orientation flip, HDF5/h5ad vs Zarr cloud-native shift, HDF5SummarizedExperiment + DelayedArray for out-of-memory bulk, scanpy backed mode for large h5ad, the ~10-15% density crossover where dense beats sparse, 10X format proliferation (MTX vs CellRanger H5 vs h5ad), the dense-conversion memory blow-up, and Dask + Zarr for consortium-scale matrices. Use when choosing sparse format, working with single-cell-sized matrices, importing/exporting 10X, debugging R/Python interop transposes, processing matrices too large for RAM, or building cloud-native pipelines.

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Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR (Python) implicit transpose, AnnData (cells-rows) <-> SingleCellExperiment (cells-cols) orientation flip, HDF5/h5ad vs Zarr cloud-native shift, HDF5SummarizedExperiment + DelayedArray for out-of-memory bulk, scanpy backed mode for large h5ad, the ~10-15% density crossover where dense beats sparse, 10X format proliferation (MTX vs CellRanger H5 vs h5ad), the dense-conversion memory blow-up, and Dask + Zarr for consortium-scale matrices. Use when choosing sparse format, working with single-cell-sized matrices, importing/exporting 10X, debugging R/Python interop transposes, processing matrices too large for RAM, or building cloud-native pipelines.

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Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR (Python) implicit transpose, AnnData (cells-rows) <-> SingleCellExperiment (cells-cols) orientation flip, HDF5/h5ad vs Zarr cloud-native shift, HDF5SummarizedExperiment + DelayedArray for out-of-memory bulk, scanpy backed mode for large h5ad, the ~10-15% density crossover where dense beats sparse, 10X format proliferation (MTX vs CellRanger H5 vs h5ad), the dense-conversion memory blow-up, and Dask + Zarr for consortium-scale matrices. Use when choosing sparse format, working with single-cell-sized matrices, importing/exporting 10X, debugging R/Python interop transposes, processing matrices too large for RAM, or building cloud-native pipelines.

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Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR (Python) implicit transpose, AnnData (cells-rows) <-> SingleCellExperiment (cells-cols) orientation flip, HDF5/h5ad vs Zarr cloud-native shift, HDF5SummarizedExperiment + DelayedArray for out-of-memory bulk, scanpy backed mode for large h5ad, the ~10-15% density crossover where dense beats sparse, 10X format proliferation (MTX vs CellRanger H5 vs h5ad), the dense-conversion memory blow-up, and Dask + Zarr for consortium-scale matrices. Use when choosing sparse format, working with single-cell-sized matrices, importing/exporting 10X, debugging R/Python interop transposes, processing matrices too large for RAM, or building cloud-native pipelines.

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Expert Kubernetes architect specializing in cloud-native infrastructure, advanced GitOps workflows (ArgoCD/Flux), and enterprise container orchestration. Masters EKS/AKS/GKE, service mesh (Istio/Linkerd), progressive delivery, multi-tenancy, and platform engineering. Handles security, observability, cost optimization, and developer experience. Use PROACTIVELY for K8s architecture, GitOps implementation, or cloud-native platform design.

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Run molecular property predictions, explore molecular shapes, and estimate how compounds bind to proteins through a cloud Python API. Process compound batches and connect modeling steps without maintaining local high-performance computing infrastructure.

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• Predicting properties across a compound library
• Exploring molecular shapes and tautomeric forms
• Estimating how compounds bind to proteins

Set up decoy credentials, storage, and secrets across AWS, Azure, and GCP to detect suspicious access. Connect audit logs to security alerts, verify detection, and document permissions, resource inventories, and maintenance plans.

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• Detecting use of leaked cloud credentials
• Monitoring suspicious access to decoy storage and secrets
• Extending on-premises deception coverage to cloud environments

Respond to security incidents across AWS, Azure, and GCP by investigating audit logs, containing compromised identities, isolating resources, and preserving evidence. Organize recovery and follow-up security measures for credential leaks, unauthorized permission changes, and attacks spanning cloud services.

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• Responding to leaked cloud credentials
• Investigating unauthorized permission or resource changes
• Preserving audit logs and disk snapshots

Set up Microsoft Sentinel to collect security logs from AWS, Azure, and GCP. Build detection queries, investigate historical activity, and create automated response workflows for a centralized security operations team.

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• Centralizing security monitoring across multiple clouds
• Migrating from an existing SIEM platform
• Automating responses to suspicious cloud activity

Write complex SQL, improve slow queries, and design database schemas for transaction processing and analytics. Uses schema details and query execution plans to guide indexing, validate results, and assess performance with realistic data volumes.

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• Investigate and improve slow analytical queries
• Design a database schema for a SaaS application
• Write customer retention and cohort analysis queries

Design and implement systems that collect, transform, validate, and store data for analysis. Covers scheduled and real-time processing, data warehouses, quality checks, monitoring, and cost tuning using tools such as Apache Spark, dbt, and Airflow.

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• Building scheduled data collection and transformation workflows
• Designing a data warehouse for analysis
• Synchronizing database changes in real time

Build .NET 8 APIs and backend services using C# 12, with clear separation of application responsibilities. The skill covers database access, authentication, API documentation, compilation checks, and integration tests that verify components working together.

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• Building endpoints with minimal APIs
• Adding database access with Entity Framework Core
• Separating application responsibilities with MediatR

Build and debug Java applications with Spring Boot 3.x. This skill guides application design, API implementation, database query tuning, authentication, and testing, including WebFlux applications that process requests without blocking.

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• Build APIs with Spring Boot
• Improve slow JPA queries
• Configure OAuth2/JWT authentication

Assess Kubernetes security from an existing pod or API access point. Covers permission checks, exposed node services, secrets, host access, and cloud metadata to explain how configuration weaknesses can expand access across a cluster.

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• Review service account permissions and RBAC settings
• Assess host access and secrets exposure from pods
• Trace access paths from a cluster to cloud infrastructure

Assess web applications and APIs for SQL injection, where input changes database queries. The skill covers finding vulnerable inputs, testing different database systems, automating checks, and documenting findings with remediation suggestions.

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• Assessing web application inputs for SQL injection
• Reviewing GraphQL and WebSocket injection risks
• Combining SQLmap automation with manual verification

Assess AWS, Azure, and GCP environments by identifying identities, permissions, and paths to broader access or data exposure. Covers cloud storage, secrets, cross-account trust, and CI/CD, the automated systems used to build and deploy software.

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• Planning an AWS, Azure, or GCP security assessment
• Tracing privilege escalation from current permissions
• Reviewing CI/CD credentials and OIDC trust settings

Hunt cloud / infrastructure misconfigurations. AWS: public S3 buckets (s3:GetObject anonymous), permissive bucket policies (PutObjectAcl public-write), exposed CloudFront origin, public Lambda function URL, public RDS snapshot, IAM credentials in JS bundles, AWS metadata accessible via SSRF. GCP: public GCS buckets, exposed Cloud Run services, leaked service account JSON. Azure: public blob containers, exposed Function App. (Kubernetes/Docker exposure is owned by hunt-k8s; CI/CD pipeline attacks by hunt-cicd; post-credential IAM escalation by cloud-iam-deep.) Detection: targeted dorking, certificate transparency, JS bundle secret extraction, port scan for known service ports. Validate: actual data read / write / RCE. Use when hunting cloud-native storage and compute misconfig (S3/GCS/Blob, IMDS-via-SSRF, serverless, public managed services).

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Master modern SQL with cloud-native databases, OLTP/OLAP optimization, and advanced query techniques. Expert in performance tuning, data modeling, and hybrid analytical systems. Use PROACTIVELY for database optimization or complex analysis.

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Master Java 21+ with modern features like virtual threads, pattern matching, and Spring Boot 3.x. Expert in the latest Java ecosystem including GraalVM, Project Loom, and cloud-native patterns. Use PROACTIVELY for Java development, microservices architecture, or performance optimization.

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Build scalable data pipelines, modern data warehouses, and real-time streaming architectures. Implements Apache Spark, dbt, Airflow, and cloud-native data platforms. Use PROACTIVELY for data pipeline design, analytics infrastructure, or modern data stack implementation.

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