agents/
├── analysis/        (3 files) - Code analysis and metrics
├── architecture/    (4 files) - System architecture and design
├── consensus/       (6 files) - Byzantine, Raft, Gossip consensus
├── core/            (6 files) - Coder, Researcher, Planner, Reviewer, Tester
├── data/            (3 files) - Data processing and transformation
├── development/     (4 files) - Full-stack development specialists
├── devops/          (3 files) - CI/CD and deployment automation
├── documentation/   (3 files) - Documentation generation
├── flow-nexus/      (6 files) - Cloud platform integration
├── github/          (8 files) - Repository management and automation
├── goal/            (4 files) - Goal-oriented action planning (GOAP)
├── hive-mind/       (4 files) - Queen-worker collective intelligence
├── neural/          (3 files) - Neural network training and patterns
├── optimization/    (5 files) - Performance and resource optimization
├── reasoning/       (3 files) - Advanced reasoning algorithms
├── sparc/           (5 files) - SPARC methodology specialists
├── specialized/     (2 files) - Domain-specific experts
├── swarm/           (6 files) - Swarm coordination and topology
├── templates/       (1 file)  - Template generation
└── testing/         (1 file)  - Quality assurance specialists

commands/
├── agents/          (4 files)
│   ├── agent-capabilities.md
│   ├── agent-coordination.md
│   ├── agent-spawning.md
│   └── agent-types.md
│
├── analysis/        (2 files)
│   ├── token-efficiency.md
│   └── token-usage.md
│
├── automation/      (6 files)
│   ├── auto-agent.md
│   ├── self-healing.md
│   ├── session-memory.md
│   ├── smart-agents.md
│   ├── smart-spawn.md
│   └── workflow-select.md
│
├── coordination/    (6 files)
│   ├── agent-spawn.md
│   ├── init.md
│   ├── orchestrate.md
│   ├── spawn.md
│   ├── swarm-init.md
│   └── task-orchestrate.md
│
├── github/          (5 files)
│   ├── code-review.md
│   ├── github-swarm.md
│   ├── issue-triage.md
│   ├── pr-enhance.md
│   └── repo-analyze.md
│
├── hive-mind/       (6 files)
│   ├── hive-mind-consensus.md
│   ├── hive-mind-init.md
│   ├── hive-mind-memory.md
│   ├── hive-mind-metrics.md
│   ├── hive-mind-spawn.md
│   └── hive-mind-status.md
│
├── hooks/           (6 files)
│   ├── post-edit.md
│   ├── post-task.md
│   ├── pre-edit.md
│   ├── pre-task.md
│   ├── session-end.md
│   └── setup.md
│
├── memory/          (4 files)
│   ├── memory-persist.md
│   ├── memory-search.md
│   ├── memory-usage.md
│   └── neural.md
│
├── monitoring/      (5 files)
│   ├── agent-metrics.md
│   ├── agents.md
│   ├── real-time-view.md
│   ├── status.md
│   └── swarm-monitor.md
│
├── optimization/    (5 files)
│   ├── auto-topology.md
│   ├── cache-manage.md
│   ├── parallel-execute.md
│   ├── parallel-execution.md
│   └── topology-optimize.md
│
├── sparc/           (16 files)
│   ├── analyzer.md
│   ├── architect.md
│   ├── batch-executor.md
│   ├── coder.md
│   ├── debugger.md
│   ├── designer.md
│   ├── documenter.md
│   ├── innovator.md
│   ├── memory-manager.md
│   ├── optimizer.md
│   ├── researcher.md
│   ├── reviewer.md
│   ├── swarm-coordinator.md
│   ├── tdd.md
│   ├── tester.md
│   └── workflow-manager.md
│
├── swarm/           (6 files)
│   ├── swarm-background.md
│   ├── swarm-init.md
│   ├── swarm-modes.md
│   ├── swarm-monitor.md
│   ├── swarm-status.md
│   └── swarm.md
│
├── training/        (5 files)
│   ├── model-update.md
│   ├── neural-patterns.md
│   ├── neural-train.md
│   ├── pattern-learn.md
│   └── specialization.md
│
└── workflows/       (5 files)
    ├── development.md
    ├── research.md
    ├── workflow-create.md
    ├── workflow-execute.md
    └── workflow-export.md

skills/
├── agentdb-memory-patterns/SKILL.md
│   Memory patterns and caching strategies for distributed agents
│
├── agentdb-vector-search/SKILL.md
│   Semantic search and RAG implementation with vector databases
│
├── flow-nexus-neural/SKILL.md
│   Distributed neural network training in cloud sandboxes
│
├── flow-nexus-platform/SKILL.md
│   Platform management: sandboxes, app store, payments, challenges
│
├── flow-nexus-swarm/SKILL.md
│   Cloud swarm deployment and workflow automation
│
├── github-code-review/SKILL.md
│   Multi-agent code review with PR coordination
│
├── github-multi-repo/SKILL.md
│   Cross-repository synchronization and coordination
│
├── github-project-management/SKILL.md
│   Issue tracking, project boards, and team coordination
│
├── github-release-management/SKILL.md
│   Automated release coordination and deployment
│
├── github-workflow-automation/SKILL.md
│   GitHub Actions workflow automation and CI/CD
│
├── hive-mind-advanced/SKILL.md
│   Queen-led hierarchical coordination with consensus
│
├── hooks-automation/SKILL.md
│   Intelligent hooks for coordination, formatting, learning
│
├── pair-programming/SKILL.md
│   AI-assisted pair programming with modes and sessions
│
├── performance-analysis/SKILL.md
│   Bottleneck detection and performance optimization
│
├── reasoningbank-intelligence/SKILL.md
│   Advanced reasoning with WASM-powered memory and intelligence
│
├── skill-builder/SKILL.md
│   Create new Claude Code skills with proper structure
│
├── sparc-methodology/SKILL.md
│   Complete SPARC development workflow
│
├── stream-chain/SKILL.md
│   Stream-JSON pipeline processing and automation
│
├── swarm-advanced/SKILL.md
│   Advanced swarm orchestration patterns and examples
│
├── swarm-orchestration/SKILL.md
│   Swarm coordination patterns and best practices
│
└── verification-quality/SKILL.md
    Truth scoring, verification, and quality assurance

{
  "files": [
    ".claude/",
    "bin/",
    "dist/",
    "src/"
  ]
}

# Test the init process
npx claude-flow init --force

# Expected output:
# ✅ Copied 76 agent files
# ✅ Copied 81 command files
# ✅ Copied 21 skill files
# ✅ Skill system setup complete
# ✅ Agent system setup complete with 64 specialized agents