# Initialize with GitHub authentication (recommended)
npx claude-flow@alpha github init

# Or use API key
export CLAUDE_FLOW_API_KEY="your-api-key"
npx claude-flow@alpha config set --api-key $CLAUDE_FLOW_API_KEY

// Add Claude-Flow as MCP server
claude mcp add claude-flow npx claude-flow@alpha mcp start

// Available MCP servers:
// - claude-flow: 87 native tools
// - ruv-swarm: 25 advanced coordination tools

# Generate session token
npx claude-flow@alpha auth login

# Use token in API calls
curl -H "Authorization: Bearer $(npx claude-flow@alpha auth token)" \
  https://api.claude-flow.ai/v2/agents

# ✅ CORRECT - Updated syntax
npx claude-flow@alpha [command] [options]

# ❌ OUTDATED - Do not use
npx claude-flow [command] [options]

# Swarm operations
npx claude-flow@alpha coordination swarm-init --topology hierarchical
npx claude-flow@alpha coordination agent-spawn --type coder
npx claude-flow@alpha coordination task-orchestrate --task "Build API"

# Memory operations
npx claude-flow@alpha memory usage --action store --key project/context
npx claude-flow@alpha memory search --pattern "authentication"

# Performance analysis
npx claude-flow@alpha performance report --timeframe 24h
npx claude-flow@alpha bottleneck analyze --component swarm

# GitHub integration
npx claude-flow@alpha github repo-analyze --repo owner/repo
npx claude-flow@alpha github pr-manage --action create

const ws = new WebSocket('wss://api.claude-flow.ai/v2/ws');

// Authentication
ws.on('open', () => {
  ws.send(JSON.stringify({
    type: 'auth',
    token: 'your-session-token'
  }));
});

// Subscribe to agent events
ws.send(JSON.stringify({
  type: 'subscribe',
  channels: ['agents', 'swarms', 'tasks', 'memory']
}));

// Agent spawned
{
  "type": "agent.spawned",
  "data": {
    "agentId": "agent_123",
    "type": "coder",
    "name": "Backend Developer",
    "status": "active"
  }
}

// Agent status change
{
  "type": "agent.status",
  "data": {
    "agentId": "agent_123",
    "status": "busy",
    "currentTask": "implement-auth",
    "progress": 0.65
  }
}

// Swarm coordination event
{
  "type": "swarm.coordination",
  "data": {
    "swarmId": "swarm_456",
    "topology": "hierarchical",
    "agentCount": 8,
    "efficiency": 0.94
  }
}

// Task orchestration
{
  "type": "swarm.task",
  "data": {
    "taskId": "task_789",
    "assignedAgents": ["agent_123", "agent_456"],
    "strategy": "parallel",
    "progress": 0.45
  }
}

// Memory synchronization
{
  "type": "memory.sync",
  "data": {
    "namespace": "project-alpha",
    "entriesSync": 1247,
    "compressionRatio": 0.65,
    "latency": "12ms"
  }
}

# 1. Initialize project with GitHub integration
npx claude-flow@alpha github init

# 2. Set up swarm for development
npx claude-flow@alpha coordination swarm-init \
  --topology hierarchical \
  --max-agents 8 \
  --strategy adaptive

# 3. Spawn development team (concurrent)
npx claude-flow@alpha coordination agent-spawn --type system-architect --name "Lead Architect"
npx claude-flow@alpha coordination agent-spawn --type backend-dev --name "API Developer"
npx claude-flow@alpha coordination agent-spawn --type coder --name "Frontend Dev"
npx claude-flow@alpha coordination agent-spawn --type tester --name "QA Engineer"
npx claude-flow@alpha coordination agent-spawn --type code-analyzer --name "Code Reviewer"

# 4. Store project context in memory
npx claude-flow@alpha memory usage \
  --action store \
  --key "project/architecture" \
  --value "Microservices with event sourcing and CQRS" \
  --namespace "development" \
  --ttl 86400

# 5. Orchestrate development task
npx claude-flow@alpha coordination task-orchestrate \
  --task "Build complete REST API with authentication and testing" \
  --strategy parallel \
  --priority high

# 6. Monitor swarm performance
npx claude-flow@alpha coordination swarm-status
npx claude-flow@alpha performance report --timeframe 24h --format detailed

# 7. Analyze GitHub repository
npx claude-flow@alpha github repo-analyze \
  --repo "myorg/my-project" \
  --analysis-type code_quality

# 8. Create workflow for automation
npx claude-flow@alpha workflow create \
  --name "full-stack-pipeline" \
  --steps '[
    {"type": "swarm_init", "topology": "hierarchical"},
    {"type": "agent_spawn", "agents": ["architect", "coder", "tester"]},
    {"type": "task_orchestrate", "strategy": "parallel"},
    {"type": "github_integration", "automate": true}
  ]'

# 1. Check neural system status
npx claude-flow@alpha neural status

# 2. Train coordination patterns
npx claude-flow@alpha neural train \
  --pattern-type coordination \
  --training-data "./data/coordination-patterns.json" \
  --epochs 100

# 3. Make AI predictions
npx claude-flow@alpha neural predict \
  --model-id coordination_model_v1.2 \
  --input "complex microservices architecture with event sourcing"

# 4. Analyze cognitive patterns
npx claude-flow@alpha neural patterns \
  --pattern convergent \
  --analysis detailed

# 1. Store complex project data
npx claude-flow@alpha memory usage \
  --action store \
  --key "decisions/architecture" \
  --value '{
    "pattern": "microservices",
    "database": "postgres",
    "auth": "jwt",
    "caching": "redis"
  }' \
  --namespace "project-alpha" \
  --ttl 604800

# 2. Search for related information
npx claude-flow@alpha memory search \
  --pattern "microservices|architecture" \
  --namespace "project-alpha" \
  --limit 10

# 3. Create memory backup
npx claude-flow@alpha memory backup \
  --namespace "project-alpha" \
  --format compressed

# 4. Analyze memory usage
npx claude-flow@alpha memory analytics \
  --timeframe 7d \
  --include-compression-stats

# 1. Run comprehensive performance report
npx claude-flow@alpha performance report \
  --timeframe 24h \
  --format detailed \
  --include-recommendations

# 2. Identify bottlenecks
npx claude-flow@alpha bottleneck analyze \
  --component swarm_coordination \
  --metrics "response_time,throughput,error_rate" \
  --severity all

# 3. Optimize swarm topology
npx claude-flow@alpha topology optimize \
  --swarm-id "swarm_123" \
  --target-efficiency 0.95

# 4. Health check all systems
npx claude-flow@alpha health-check \
  --components '["swarm", "neural", "memory", "mcp"]' \
  --detailed true

# Agent spawn failure
{
  "error": "AGENT_SPAWN_FAILED",
  "message": "Maximum agent limit reached",
  "details": {
    "currentAgents": 8,
    "maxAgents": 8,
    "swarmId": "swarm_123"
  }
}

# Memory operation failure
{
  "error": "MEMORY_STORAGE_FULL",
  "message": "Memory storage limit exceeded",
  "details": {
    "usedMemory": "512MB",
    "maxMemory": "512MB",
    "namespace": "project-alpha"
  }
}

# Neural training failure
{
  "error": "NEURAL_TRAINING_FAILED",
  "message": "Insufficient training data",
  "details": {
    "requiredSamples": 100,
    "providedSamples": 45,
    "patternType": "coordination"
  }
}

# Retry with backoff
npx claude-flow@alpha coordination agent-spawn \
  --type coder \
  --retry-attempts 3 \
  --retry-delay 1000

# Graceful degradation
npx claude-flow@alpha coordination swarm-init \
  --topology hierarchical \
  --fallback-topology mesh \
  --max-agents 8 \
  --min-agents 3

# Error notification
npx claude-flow@alpha hooks post-edit \
  --file "error.log" \
  --memory-key "errors/$(date +%s)" \
  --notify-on-failure true

# Always batch agent operations
# ✅ Good - Single message with multiple spawns
npx claude-flow@alpha coordination agent-spawn --type architect &
npx claude-flow@alpha coordination agent-spawn --type coder &
npx claude-flow@alpha coordination agent-spawn --type tester &
wait

# ❌ Bad - Sequential spawning
npx claude-flow@alpha coordination agent-spawn --type architect
npx claude-flow@alpha coordination agent-spawn --type coder
npx claude-flow@alpha coordination agent-spawn --type tester

# Use namespaces effectively
npx claude-flow@alpha memory usage \
  --action store \
  --key "config/database" \
  --namespace "project-$(date +%Y%m%d)" \
  --ttl 86400

# Regular cleanup
npx claude-flow@alpha memory compress \
  --namespace "temporary" \
  --threshold 0.8

# Monitor before scaling
npx claude-flow@alpha performance report --format summary
npx claude-flow@alpha coordination swarm-scale --target-size 12

# Use appropriate topologies
# Complex tasks -> hierarchical
# Collaborative work -> mesh
# Sequential processing -> ring
# Centralized control -> star

# Hook integration for automation
npx claude-flow@alpha hooks pre-task \
  --description "Auto-spawn agents based on task complexity"

npx claude-flow@alpha hooks post-edit \
  --file "src/**/*.js" \
  --memory-key "code-changes/$(date +%s)"

# Workflow templates for reusability
npx claude-flow@alpha workflow template \
  --name "api-development" \
  --export "./templates/api-dev-workflow.json"

# Secure authentication
npx claude-flow@alpha github init --secure-mode
npx claude-flow@alpha config set --api-key-encryption enabled

# Resource limits
npx claude-flow@alpha coordination swarm-init \
  --max-agents 10 \
  --memory-limit "1GB" \
  --cpu-limit "4 cores"

# Audit logging
npx claude-flow@alpha log-analysis \
  --include-security-events \
  --format audit

# Get help for any command
npx claude-flow@alpha --help
npx claude-flow@alpha coordination --help
npx claude-flow@alpha github --help

# Version information
npx claude-flow@alpha --version