// Initialize architecture analysis swarm
mcp__claude-flow__swarm_init { topology: "mesh", maxAgents: 4 }
mcp__claude-flow__agent_spawn { type: "analyst", name: "Structure Analyzer" }
mcp__claude-flow__agent_spawn { type: "architect", name: "Repository Architect" }
mcp__claude-flow__agent_spawn { type: "optimizer", name: "Structure Optimizer" }
mcp__claude-flow__agent_spawn { type: "coordinator", name: "Multi-Repo Coordinator" }

// Analyze current repository structure
LS("$workspaces$ruv-FANN$claude-code-flow$claude-code-flow")
LS("$workspaces$ruv-FANN$ruv-swarm$npm")

// Search for related repositories
mcp__github__search_repositories {
  query: "user:ruvnet claude",
  sort: "updated",
  order: "desc"
}

// Orchestrate structure optimization
mcp__claude-flow__task_orchestrate {
  task: "Analyze and optimize repository structure for scalability and maintainability",
  strategy: "adaptive",
  priority: "medium"
}

// Create standardized repository template
mcp__github__create_repository {
  name: "claude-project-template",
  description: "Standardized template for Claude Code projects with ruv-swarm integration",
  private: false,
  autoInit: true
}

// Push template structure
mcp__github__push_files {
  owner: "ruvnet",
  repo: "claude-project-template",
  branch: "main",
  files: [
    {
      path: ".claude$commands$github$github-modes.md",
      content: "[GitHub modes template]"
    },
    {
      path: ".claude$commands$sparc$sparc-modes.md", 
      content: "[SPARC modes template]"
    },
    {
      path: ".claude$config.json",
      content: JSON.stringify({
        version: "1.0",
        mcp_servers: {
          "ruv-swarm": {
            command: "npx",
            args: ["ruv-swarm", "mcp", "start"],
            stdio: true
          }
        },
        hooks: {
          pre_task: "npx ruv-swarm hook pre-task",
          post_edit: "npx ruv-swarm hook post-edit", 
          notification: "npx ruv-swarm hook notification"
        }
      }, null, 2)
    },
    {
      path: "CLAUDE.md",
      content: "[Standardized CLAUDE.md template]"
    },
    {
      path: "package.json",
      content: JSON.stringify({
        name: "claude-project-template",
        version: "1.0.0",
        description: "Claude Code project with ruv-swarm integration",
        engines: { node: ">=20.0.0" },
        dependencies: {
          "ruv-swarm": "^1.0.11"
        }
      }, null, 2)
    },
    {
      path: "README.md",
      content: `# Claude Project Template

## Quick Start
\`\`\`bash
npx claude-flow init --sparc
npm install
npx claude-flow start --ui
\`\`\`

## Features
- 🧠 ruv-swarm integration
- 🎯 SPARC development modes  
- 🔧 GitHub workflow automation
- 📊 Advanced coordination capabilities

## Documentation
See CLAUDE.md for complete integration instructions.`
    }
  ],
  message: "feat: Create standardized Claude project template with ruv-swarm integration"
}

// Synchronize structure across related repositories
const repositories = [
  "claude-code-flow", 
  "ruv-swarm",
  "claude-extensions"
]

// Update common files across repositories
repositories.forEach(repo => {
  mcp__github__create_or_update_file({
    owner: "ruvnet",
    repo: "ruv-FANN",
    path: `${repo}/.github$workflows$integration.yml`,
    content: `name: Integration Tests
on: [push, pull_request]
jobs:
  test:
    runs-on: ubuntu-latest
    steps:
      - uses: actions$checkout@v3
      - uses: actions$setup-node@v3
        with: { node-version: '20' }
      - run: npm install && npm test`,
    message: "ci: Standardize integration workflow across repositories",
    branch: "structure$standardization"
  })
})

[Single Message - Repository Architecture Review]:
  // Initialize comprehensive architecture swarm
  mcp__claude-flow__swarm_init { topology: "hierarchical", maxAgents: 6 }
  mcp__claude-flow__agent_spawn { type: "architect", name: "Senior Architect" }
  mcp__claude-flow__agent_spawn { type: "analyst", name: "Structure Analyst" }
  mcp__claude-flow__agent_spawn { type: "optimizer", name: "Performance Optimizer" }
  mcp__claude-flow__agent_spawn { type: "researcher", name: "Best Practices Researcher" }
  mcp__claude-flow__agent_spawn { type: "coordinator", name: "Multi-Repo Coordinator" }
  
  // Analyze current repository structures
  LS("$workspaces$ruv-FANN$claude-code-flow$claude-code-flow")
  LS("$workspaces$ruv-FANN$ruv-swarm$npm") 
  Read("$workspaces$ruv-FANN$claude-code-flow$claude-code-flow$package.json")
  Read("$workspaces$ruv-FANN$ruv-swarm$npm$package.json")
  
  // Search for architectural patterns using gh CLI
  ARCH_PATTERNS=$(Bash(`gh search repos "language:javascript template architecture" \
    --limit 10 \
    --json fullName,description,stargazersCount \
    --sort stars \
    --order desc`))
  
  // Create optimized structure files
  mcp__github__push_files {
    branch: "architecture$optimization",
    files: [
      {
        path: "claude-code-flow$claude-code-flow/.github/ISSUE_TEMPLATE$integration.yml",
        content: "[Integration issue template]"
      },
      {
        path: "claude-code-flow$claude-code-flow/.github/PULL_REQUEST_TEMPLATE.md",
        content: "[Standardized PR template]"
      },
      {
        path: "claude-code-flow$claude-code-flow$docs/ARCHITECTURE.md",
        content: "[Architecture documentation]"
      },
      {
        path: "ruv-swarm$npm/.github$workflows$cross-package-test.yml",
        content: "[Cross-package testing workflow]"
      }
    ],
    message: "feat: Optimize repository architecture for scalability and maintainability"
  }
  
  // Track architecture improvements
  TodoWrite { todos: [
    { id: "arch-analysis", content: "Analyze current repository structure", status: "completed", priority: "high" },
    { id: "arch-research", content: "Research best practices and patterns", status: "completed", priority: "medium" },
    { id: "arch-templates", content: "Create standardized templates", status: "completed", priority: "high" },
    { id: "arch-workflows", content: "Implement improved workflows", status: "completed", priority: "medium" },
    { id: "arch-docs", content: "Document architecture decisions", status: "pending", priority: "medium" }
  ]}
  
  // Store architecture analysis
  mcp__claude-flow__memory_usage {
    action: "store",
    key: "architecture$analysis$results",
    value: {
      timestamp: Date.now(),
      repositories_analyzed: ["claude-code-flow", "ruv-swarm"],
      optimization_areas: ["structure", "workflows", "templates", "documentation"],
      recommendations: ["standardize_structure", "improve_workflows", "enhance_templates"],
      implementation_status: "in_progress"
    }
  }

ruv-FANN/
├── packages/
│   ├── claude-code-flow/
│   │   ├── src/
│   │   ├── .claude/
│   │   └── package.json
│   ├── ruv-swarm/
│   │   ├── src/
│   │   ├── wasm/
│   │   └── package.json
│   └── shared/
│       ├── types/
│       ├── utils/
│       └── config/
├── tools/
│   ├── build/
│   ├── test/
│   └── deploy/
├── docs/
│   ├── architecture/
│   ├── integration/
│   └── examples/
└── .github/
    ├── workflows/
    ├── templates/
    └── actions/

.claude/
├── commands/
│   ├── github/
│   │   ├── github-modes.md
│   │   ├── pr-manager.md
│   │   ├── issue-tracker.md
│   │   └── sync-coordinator.md
│   ├── sparc/
│   │   ├── sparc-modes.md
│   │   ├── coder.md
│   │   └── tester.md
│   └── swarm/
│       ├── coordination.md
│       └── orchestration.md
├── templates/
│   ├── issue.md
│   ├── pr.md
│   └── project.md
└── config.json

const integrationPattern = {
  packages: {
    "claude-code-flow": {
      role: "orchestration_layer",
      dependencies: ["ruv-swarm"],
      provides: ["CLI", "workflows", "commands"]
    },
    "ruv-swarm": {
      role: "coordination_engine", 
      dependencies: [],
      provides: ["MCP_tools", "neural_networks", "memory"]
    }
  },
  communication: "MCP_protocol",
  coordination: "swarm_based",
  state_management: "persistent_memory"
}