claude-flow 3.0.0-alpha.7 → 3.0.0-alpha.9

package/README.md

@@ -1,1095 +1,1186 @@
-# Claude-Flow v3: Enterprise AI Orchestration Platform
+# @claude-flow/cli
 
-<div align="center">
+[![npm version](https://img.shields.io/npm/v/@claude-flow/cli.svg)](https://www.npmjs.com/package/@claude-flow/cli)
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+[![TypeScript](https://img.shields.io/badge/TypeScript-5.0+-blue.svg)](https://www.typescriptlang.org/)
+[![Node.js](https://img.shields.io/badge/Node.js-20+-green.svg)](https://nodejs.org/)
+[![Commands](https://img.shields.io/badge/Commands-14+-orange.svg)](https://github.com/ruvnet/claude-flow)
+[![Subcommands](https://img.shields.io/badge/Subcommands-92+-purple.svg)](https://github.com/ruvnet/claude-flow)
 
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+> Modern CLI module for Claude Flow V3 - comprehensive command-line interface with 14 commands, 92+ subcommands, interactive prompts, self-learning hooks, background workers, hive-mind coordination, and beautiful output formatting.
 
-**Production-ready multi-agent AI orchestration for Claude Code**
+## Features
 
-*Deploy 54+ specialized agents in coordinated swarms with self-learning capabilities, fault-tolerant consensus, and enterprise-grade security.*
+### Core Capabilities
+- **14 Main Commands** - Complete CLI coverage for all Claude Flow operations
+- **92+ Subcommands** - Fine-grained control over every aspect of the system
+- **Advanced Argument Parsing** - Full support for flags, options, subcommands, and positional arguments
+- **Interactive Prompts** - Rich interactive mode with confirmations, selections, and input validation
+- **Beautiful Output** - Colored output, tables, progress bars, spinners, and multiple formats (text, JSON, table)
 
-</div>
+### V3-Specific Features
+- **Self-Learning Hooks** - 17 hook subcommands + 12 background workers with pattern learning and neural integration
+- **Hive-Mind Coordination** - Queen-led Byzantine fault-tolerant multi-agent consensus
+- **15-Agent Swarm** - V3 hierarchical mesh coordination with domain specialization
+- **AgentDB Integration** - 150x-12,500x faster vector search with HNSW indexing
+- **SONA Learning** - Sub-0.05ms adaptation with Mixture of Experts routing
 
-## Overview
+### Developer Experience
+- **Type-Safe** - Full TypeScript support with comprehensive type definitions
+- **Global Options** - Built-in `--help`, `--version`, `--verbose`, `--quiet`, `--format`
+- **Auto-Completion** - Shell completion support for commands and options
+- **Migration Tools** - Built-in V2 to V3 migration with rollback support
 
-Claude-Flow is a comprehensive AI agent orchestration framework that transforms Claude Code into a powerful multi-agent development platform. It enables teams to deploy, coordinate, and optimize specialized AI agents working together on complex software engineering tasks.
+## Installation
 
-### Claude Code: With vs Without Claude-Flow
+```bash
+npm install @claude-flow/cli
+```
 
-| Capability | Claude Code Alone | Claude Code + Claude-Flow |
-|------------|-------------------|---------------------------|
-| **Agent Collaboration** | Agents work in isolation, no shared context | Agents collaborate via swarms with shared memory and consensus |
-| **Coordination** | Manual orchestration between tasks | Queen-led hierarchy with 5 consensus algorithms (Raft, Byzantine, Gossip) |
-| **Memory** | Session-only, no persistence | HNSW vector memory with 150x-12,500x faster retrieval |
-| **Learning** | Static behavior, no adaptation | SONA self-learning with <0.05ms adaptation, improves over time |
-| **Task Routing** | You decide which agent to use | Intelligent routing based on learned patterns (89% accuracy) |
-| **Complex Tasks** | Manual breakdown required | Automatic decomposition across 5 domains (Security, Core, Integration, Support) |
-| **Background Workers** | Nothing runs automatically | 12 context-triggered workers auto-dispatch on file changes, patterns, sessions |
-| **LLM Provider** | Anthropic only | 6 providers with automatic failover and cost-based routing (85% savings) |
-| **Security** | Standard protections | CVE-hardened with bcrypt, input validation, path traversal prevention |
-| **Performance** | Baseline | 2.8-4.4x faster tasks, 4-32x memory reduction via quantization |
+Or use globally:
 
-### Key Capabilities
+```bash
+npm install -g @claude-flow/cli
+claude-flow --version
+```
 
-- **54+ Specialized Agents** - Ready-to-use AI agents for coding, code review, testing, security audits, documentation, and DevOps tasks. Each agent is optimized for its specific role.
+## Quick Start
 
-- **Coordinated Agent Teams** - Run unlimited agents simultaneously in organized swarms. Agents can spawn sub-workers, communicate, share context, and divide work automatically using patterns like hierarchical (queen/workers) or mesh (peer-to-peer).
+```bash
+# Initialize a new project
+claude-flow init --wizard
 
-- **Learns From Your Workflow** - The system remembers what works. Successful patterns are stored and reused, routing similar tasks to the best-performing agents. Gets smarter over time.
+# Start MCP server
+claude-flow mcp start
 
-- **Works With Any LLM** - Switch between Claude, GPT-4, Gemini, Cohere, or local models like Llama. Automatic failover if one provider is unavailable. Smart routing picks the cheapest option that meets quality requirements.
+# Spawn an agent
+claude-flow agent spawn -t coder --name my-coder
 
-- **Plugs Into Claude Code** - Native integration via MCP (Model Context Protocol). Use claude-flow commands directly in your Claude Code sessions with full tool access.
+# Initialize a swarm
+claude-flow swarm init --v3-mode
 
-- **Production-Ready Security** - Built-in protection against common vulnerabilities: input validation, path traversal prevention, command injection blocking, and safe credential handling.
+# Search memory
+claude-flow memory search -q "authentication patterns"
+
+# Check system status
+claude-flow status --watch
+```
+
+## Complete Command Reference
+
+### Overview
+
+| Command | Subcommands | Description |
+|---------|-------------|-------------|
+| `init` | 4 | Project initialization with wizard, presets, and configuration |
+| `agent` | 8 | Agent lifecycle management (spawn, list, status, stop, metrics, pool, health, logs) |
+| `swarm` | 6 | Multi-agent swarm coordination and orchestration |
+| `memory` | 11 | AgentDB memory operations with vector search |
+| `mcp` | 9 | MCP server management and tool execution |
+| `task` | 6 | Task creation, assignment, and lifecycle management |
+| `session` | 7 | Session state management and persistence |
+| `config` | 7 | Configuration management and provider setup |
+| `status` | 3 | System status monitoring with watch mode |
+| `start` | 3 | Service startup and quick launch |
+| `workflow` | 6 | Workflow execution and template management |
+| `hooks` | 17 | Self-learning hooks with neural pattern recognition + 12 background workers |
+| `hive-mind` | 6 | Queen-led consensus-based multi-agent coordination |
+| `migrate` | 5 | V2 to V3 migration with rollback support |
 
 ---
 
-## Quick Start
+### `init` - Project Initialization
+
+Initialize Claude Flow V3 with interactive wizard or presets.
+
+```bash
+claude-flow init [subcommand] [options]
+```
+
+#### Subcommands
 
-### Prerequisites
+| Subcommand | Description |
+|------------|-------------|
+| `wizard` | Interactive setup wizard with step-by-step configuration |
+| `check` | Validate current configuration and environment |
+| `skills` | List and manage available skills |
+| `hooks` | Configure and validate hooks integration |
 
-- **Node.js 18+** or **Bun 1.0+** (Bun is faster)
-- **npm 9+** / **pnpm** / **bun** package manager
+#### Options
 
-**IMPORTANT**: Claude Code must be installed first:
+| Option | Short | Description | Default |
+|--------|-------|-------------|---------|
+| `--preset` | `-p` | Configuration preset (minimal, default, full, custom) | `default` |
+| `--force` | `-f` | Overwrite existing configuration | `false` |
+| `--skip-deps` | | Skip dependency installation | `false` |
+| `--topology` | `-t` | Swarm topology (hierarchical, mesh, hybrid) | `hierarchical` |
+| `--max-agents` | `-m` | Maximum concurrent agents | `15` |
+| `--memory-backend` | | Memory backend (agentdb, sqlite, hybrid) | `hybrid` |
+| `--enable-hnsw` | | Enable HNSW indexing (150x faster) | `true` |
+| `--enable-neural` | | Enable SONA neural learning | `true` |
+
+#### Examples
 
 ```bash
-# 1. Install Claude Code globally
-npm install -g @anthropic-ai/claude-code
+# Interactive wizard
+claude-flow init --wizard
+
+# Quick setup with defaults
+claude-flow init --preset default
+
+# Full V3 setup with all features
+claude-flow init --preset full --enable-hnsw --enable-neural
 
-# 2. (Optional) Skip permissions check for faster setup
-claude --dangerously-skip-permissions
+# Validate configuration
+claude-flow init check
 ```
 
-### Installation
+---
+
+### `agent` - Agent Management
+
+Spawn, manage, and monitor AI agents with various specializations.
 
 ```bash
-# With npm/npx (Node.js)
-npm install claude-flow@v3alpha
-npx claude-flow@v3alpha init
+claude-flow agent <subcommand> [options]
+```
+
+#### Subcommands
+
+| Subcommand | Aliases | Description |
+|------------|---------|-------------|
+| `spawn` | | Spawn a new agent with specified type and configuration |
+| `list` | `ls` | List all active agents with filtering options |
+| `status` | | Show detailed status and metrics for an agent |
+| `stop` | `kill` | Stop a running agent (graceful or forced) |
+| `metrics` | | Show agent performance metrics over time |
+| `pool` | | Manage agent pool for auto-scaling |
+| `health` | | Show agent health and resource metrics |
+| `logs` | | View agent activity logs with filtering |
+
+#### Agent Types
+
+| Type | Description | Capabilities |
+|------|-------------|--------------|
+| `coder` | Code development with neural patterns | code-generation, refactoring, debugging, testing |
+| `researcher` | Research with web access and data analysis | web-search, data-analysis, summarization, citation |
+| `tester` | Comprehensive testing with automation | unit-testing, integration-testing, coverage-analysis |
+| `reviewer` | Code review with security and quality checks | code-review, security-audit, quality-check |
+| `architect` | System design with enterprise patterns | system-design, pattern-analysis, scalability |
+| `coordinator` | Multi-agent orchestration and workflow | task-orchestration, agent-management, workflow-control |
+| `security-architect` | Security architecture and threat modeling | threat-modeling, security-patterns, compliance |
+| `security-auditor` | CVE remediation and security testing | vulnerability-scan, penetration-testing |
+| `memory-specialist` | AgentDB unification (150x-12,500x faster) | vector-search, agentdb, caching, optimization |
+| `performance-engineer` | 2.49x-7.47x optimization targets | benchmarking, profiling, optimization |
+
+#### Spawn Options
+
+| Option | Short | Description | Default |
+|--------|-------|-------------|---------|
+| `--type` | `-t` | Agent type to spawn | required |
+| `--name` | `-n` | Agent name/identifier | auto-generated |
+| `--provider` | `-p` | LLM provider (anthropic, openrouter, ollama) | `anthropic` |
+| `--model` | `-m` | Model to use | provider default |
+| `--task` | | Initial task for the agent | none |
+| `--timeout` | | Agent timeout in seconds | `300` |
+| `--auto-tools` | | Enable automatic tool usage | `true` |
+
+#### Examples
+
+```bash
+# Spawn a coder agent
+claude-flow agent spawn -t coder --name my-coder
+
+# Spawn researcher with initial task
+claude-flow agent spawn -t researcher --task "Research React 19 features"
+
+# List all active agents
+claude-flow agent list
+
+# List agents by type
+claude-flow agent list -t coder
 
-# With Bun (faster)
-bun add claude-flow@v3alpha
-bunx claude-flow@v3alpha init
+# Get detailed agent status
+claude-flow agent status agent-001
 
-# Start MCP server for Claude Code integration
-npx claude-flow@v3alpha mcp start
+# Show agent metrics for 24 hours
+claude-flow agent metrics -p 24h
 
-# Run a task with agents
-npx claude-flow@v3alpha --agent coder --task "Implement user authentication"
+# View agent logs
+claude-flow agent logs -i agent-001 -f
 
-# List available agents
-npx claude-flow@v3alpha --list
+# Configure agent pool
+claude-flow agent pool --size 5 --min 2 --max 15 --auto-scale
+
+# Health check with detailed metrics
+claude-flow agent health -d
+
+# Stop agent gracefully
+claude-flow agent stop agent-001
+
+# Force stop
+claude-flow agent stop agent-001 -f
 ```
 
 ---
 
-## Features
+### `swarm` - Swarm Coordination
 
-### Core Platform Capabilities
-
-| Capability | Description | Metrics |
-|------------|-------------|---------|
-| **54+ Specialized Agents** | Purpose-built AI agents for development, testing, security, and operations | 10 categories, unlimited concurrent |
-| **Multi-Topology Swarms** | Hierarchical, mesh, ring, star, and adaptive coordination patterns | 2.8-4.4x speed improvement |
-| **Self-Learning Hooks** | ReasoningBank pattern learning with HNSW vector search | 150x faster retrieval |
-| **MCP Integration** | Native Claude Code support via Model Context Protocol | 27+ tools available |
-| **Security-First Design** | Input validation, path traversal prevention, command sandboxing | CVE-1, CVE-2, CVE-3 addressed |
-| **Cross-Platform** | Full support for Windows, macOS, and Linux environments | Node.js 18+ |
-
-### Agent Ecosystem
-
-| Category | Agent Count | Key Agents | Purpose |
-|----------|-------------|------------|---------|
-| **Core Development** | 5 | coder, reviewer, tester, planner, researcher | Daily development tasks |
-| **V3 Specialized** | 10 | queen-coordinator, security-architect, memory-specialist | Enterprise orchestration |
-| **Swarm Coordination** | 5 | hierarchical-coordinator, mesh-coordinator, adaptive-coordinator | Multi-agent patterns |
-| **Consensus & Distributed** | 7 | byzantine-coordinator, raft-manager, gossip-coordinator | Fault-tolerant coordination |
-| **Performance** | 5 | perf-analyzer, performance-benchmarker, task-orchestrator | Optimization & monitoring |
-| **GitHub & Repository** | 9 | pr-manager, code-review-swarm, issue-tracker, release-manager | Repository automation |
-| **SPARC Methodology** | 6 | sparc-coord, specification, pseudocode, architecture | Structured development |
-| **Specialized Dev** | 8 | backend-dev, mobile-dev, ml-developer, cicd-engineer | Domain expertise |
-
-### Swarm Topologies
-
-| Topology | Recommended Agents | Best For | Execution Time | Memory/Agent |
-|----------|-------------------|----------|----------------|--------------|
-| **Hierarchical** | 6+ | Structured tasks, clear authority chains | 0.20s | 256 MB |
-| **Mesh** | 4+ | Collaborative work, high redundancy | 0.15s | 192 MB |
-| **Ring** | 3+ | Sequential processing pipelines | 0.12s | 128 MB |
-| **Star** | 5+ | Centralized control, spoke workers | 0.14s | 180 MB |
-| **Hybrid (Hierarchical-Mesh)** | 7+ | Complex multi-domain tasks | 0.18s | 320 MB |
-| **Adaptive** | 2+ | Dynamic workloads, auto-scaling | Variable | Dynamic |
-
-### Self-Learning & Intelligence
-
-| Feature | Technology | Performance | Description |
-|---------|------------|-------------|-------------|
-| **ReasoningBank** | HNSW Vector Search | 150x faster | Pattern storage with similarity-based retrieval |
-| **SONA Neural** | LoRA Fine-tuning | <0.05ms adaptation | Self-optimizing neural architecture |
-| **Pattern Learning** | EWC++ Memory | Zero forgetting | Continuous learning without catastrophic forgetting |
-| **Intent Routing** | MoE (Mixture of Experts) | 95%+ accuracy | Intelligent task-to-agent routing |
-| **Domain Detection** | Vector Clustering | Real-time | Automatic categorization (security, testing, performance) |
-| **Quality Tracking** | Success/Failure Metrics | Per-pattern | Historical performance tracking |
-
-### Memory & Storage
-
-| Backend | Technology | Performance | Use Case |
-|---------|------------|-------------|----------|
-| **AgentDB** | HNSW Indexing | 150x-12,500x faster | Primary vector storage |
-| **SQLite** | Relational DB | Standard | Metadata and structured data |
-| **Hybrid** | AgentDB + SQLite | Best of both | Recommended default |
-| **In-Memory** | RAM-based | Fastest | Temporary/session data |
-
-### MCP Tools & Integration
-
-| Category | Tools | Description |
-|----------|-------|-------------|
-| **Coordination** | `swarm_init`, `agent_spawn`, `task_orchestrate` | Swarm and agent lifecycle management |
-| **Monitoring** | `swarm_status`, `agent_list`, `agent_metrics`, `task_status` | Real-time status and metrics |
-| **Memory & Neural** | `memory_usage`, `neural_status`, `neural_train`, `neural_patterns` | Memory operations and learning |
-| **GitHub** | `github_swarm`, `repo_analyze`, `pr_enhance`, `issue_triage`, `code_review` | Repository integration |
-| **Workers** | `worker/run`, `worker/status`, `worker/alerts`, `worker/history` | Background task management |
-| **Hooks** | `hooks/pre-*`, `hooks/post-*`, `hooks/route`, `hooks/session-*`, `hooks/intelligence/*`, `hooks/worker/*` | 31 lifecycle hooks |
-
-### Security Features
-
-| Feature | Protection | Implementation |
-|---------|------------|----------------|
-| **Input Validation** | Injection attacks | Boundary validation on all inputs |
-| **Path Traversal Prevention** | Directory escape | Blocked patterns (`../`, `~/.`, `/etc/`) |
-| **Command Sandboxing** | Shell injection | Allowlisted commands, metacharacter blocking |
-| **Prototype Pollution** | Object manipulation | Safe JSON parsing with validation |
-| **TOCTOU Protection** | Race conditions | Symlink skipping and atomic operations |
-| **Information Disclosure** | Data leakage | Error message sanitization |
-| **CVE Monitoring** | Known vulnerabilities | Active scanning and patching |
-
-### Advanced Capabilities
-
-| Feature | Description | Benefit |
-|---------|-------------|---------|
-| **Automatic Topology Selection** | AI-driven topology choice based on task complexity | Optimal resource utilization |
-| **Parallel Execution** | Concurrent agent operation with load balancing | 2.8-4.4x speed improvement |
-| **Neural Training** | 27+ model support with continuous learning | Adaptive intelligence |
-| **Bottleneck Analysis** | Real-time performance monitoring and optimization | Proactive issue detection |
-| **Smart Auto-Spawning** | Dynamic agent creation based on workload | Elastic scaling |
-| **Self-Healing Workflows** | Automatic error recovery and task retry | High availability |
-| **Cross-Session Memory** | Persistent pattern storage across sessions | Continuous learning |
-| **Event Sourcing** | Complete audit trail with replay capability | Debugging and compliance |
-| **Background Workers** | 12 auto-triggered workers for analysis and optimization | Automated maintenance |
-| **GitHub Integration** | PR management, issue triage, code review automation | Repository workflow |
-
-### Plugin System (`@claude-flow/plugins`)
-
-| Component | Description | Key Features |
-|-----------|-------------|--------------|
-| **PluginBuilder** | Fluent builder for creating plugins | MCP tools, hooks, workers, providers |
-| **MCPToolBuilder** | Build MCP tools with typed parameters | String, number, boolean, enum params |
-| **HookBuilder** | Build hooks with conditions and transformers | Priorities, conditional execution, data transformation |
-| **WorkerPool** | Managed worker pool with auto-scaling | Min/max workers, task queuing, graceful shutdown |
-| **ProviderRegistry** | LLM provider management with fallback | Cost optimization, automatic failover |
-| **AgenticFlowBridge** | agentic-flow@alpha integration | Swarm coordination, agent spawning |
-| **AgentDBBridge** | Vector storage with HNSW indexing | 150x faster search, batch operations |
-| **Security Utilities** | Input validation and protection | Path traversal, injection, rate limiting |
-
-### Plugin Hook Events
-
-| Category | Events | Description |
-|----------|--------|-------------|
-| **Session** | `session:start`, `session:end` | Session lifecycle management |
-| **Agent** | `agent:pre-spawn`, `agent:post-spawn`, `agent:pre-terminate`, `agent:post-terminate` | Agent lifecycle hooks |
-| **Task** | `task:pre-execute`, `task:post-complete`, `task:error` | Task execution hooks |
-| **Tool** | `tool:pre-call`, `tool:post-call` | MCP tool invocation hooks |
-| **Memory** | `memory:pre-store`, `memory:post-store`, `memory:pre-retrieve`, `memory:post-retrieve` | Memory operation hooks |
-| **Swarm** | `swarm:initialized`, `swarm:shutdown`, `swarm:consensus-reached` | Swarm coordination hooks |
-| **File** | `file:pre-read`, `file:post-read`, `file:pre-write`, `file:post-write` | File operation hooks |
-| **Command** | `command:pre-execute`, `command:post-execute` | Shell command hooks |
-| **Learning** | `learning:pattern-learned`, `learning:pattern-applied` | Pattern learning hooks |
-
-### Plugin Worker Types
-
-| Worker Type | Purpose | Capabilities |
-|-------------|---------|--------------|
-| `coder` | Code implementation | Code generation, refactoring |
-| `reviewer` | Code review | Quality analysis, suggestions |
-| `tester` | Test generation/execution | Unit tests, integration tests |
-| `researcher` | Information gathering | Web search, documentation |
-| `planner` | Task planning | Decomposition, scheduling |
-| `coordinator` | Multi-agent coordination | Orchestration, consensus |
-| `security` | Security analysis | Vulnerability scanning, audit |
-| `performance` | Performance optimization | Profiling, benchmarking |
-| `specialized` | Custom capabilities | Domain-specific tasks |
-| `long-running` | Background tasks | Async processing, polling |
-
-### Plugin Performance
-
-| Metric | Target | Achieved |
-|--------|--------|----------|
-| Plugin load time | <50ms | ~20ms |
-| Hook execution | <1ms | ~0.5ms |
-| Worker spawn | <100ms | ~50ms |
-| Vector search (10K) | <10ms | ~5ms |
-
-### RuVector WASM Plugins
-
-| Plugin | Description | Performance |
-|--------|-------------|-------------|
-| **SemanticCodeSearchPlugin** | Semantic code search with vector embeddings | Real-time indexing |
-| **IntentRouterPlugin** | Routes user intents to optimal handlers | 95%+ accuracy |
-| **HookPatternLibraryPlugin** | Pre-built patterns for common tasks | Security, testing, performance |
-| **MCPToolOptimizerPlugin** | Optimizes MCP tool selection | Context-aware suggestions |
-| **ReasoningBankPlugin** | Vector-backed pattern storage with HNSW | 150x faster search |
-| **AgentConfigGeneratorPlugin** | Generates optimized agent configurations | From pretrain data |
-
-### Background Workers (12 Auto-Triggered)
-
-Workers run automatically in the background based on context, or can be dispatched manually via MCP tools.
-
-| Worker | Trigger | Purpose | Auto-Triggers On |
-|--------|---------|---------|------------------|
-| **UltraLearn** | `ultralearn` | Deep knowledge acquisition from codebase | New project, major refactors |
-| **Optimize** | `optimize` | Performance optimization suggestions | Slow operations detected |
-| **Consolidate** | `consolidate` | Memory pattern consolidation | Session end, memory threshold |
-| **Predict** | `predict` | Predictive resource preloading | Usage patterns detected |
-| **Audit** | `audit` | Security vulnerability analysis | Security-related file changes |
-| **Map** | `map` | Codebase structure mapping | New directories, large changes |
-| **Preload** | `preload` | Resource and dependency preloading | Project initialization |
-| **DeepDive** | `deepdive` | Deep code analysis and understanding | Complex file edits |
-| **Document** | `document` | Auto-documentation generation | New functions/classes created |
-| **Refactor** | `refactor` | Refactoring opportunity detection | Code smell patterns |
-| **Benchmark** | `benchmark` | Performance benchmarking | Performance-critical changes |
-| **TestGaps** | `testgaps` | Test coverage gap analysis | Code changes without tests |
-
-**Worker Commands:**
-```bash
-# Dispatch a worker manually
-npx claude-flow@v3alpha worker dispatch --trigger audit --context "./src"
+Multi-agent swarm initialization, coordination, and management.
 
-# Check worker status
-npx claude-flow@v3alpha worker status
-
-# View completed results
-npx claude-flow@v3alpha worker results --limit 10
+```bash
+claude-flow swarm <subcommand> [options]
 ```
 
-### LLM Providers (`@claude-flow/providers`)
+#### Subcommands
 
-| Provider | Models | Features | Cost |
-|----------|--------|----------|------|
-| **Anthropic** | Claude 3.5 Sonnet, Claude 3 Opus, Claude 3 Haiku | Native, streaming, tool calling | $3-15/1M tokens |
-| **OpenAI** | GPT-4o, GPT-4 Turbo, GPT-3.5, o1-preview, o3-mini | Function calling, vision | $0.50-60/1M tokens |
-| **Google** | Gemini 2.0 Flash, Gemini 1.5 Pro/Flash | Multimodal, long context | $0.075-7/1M tokens |
-| **Cohere** | Command R+, Command R, Command Light | RAG optimized | $0.50-15/1M tokens |
-| **Ollama** | Llama 3.2, Mistral, CodeLlama, DeepSeek | Local, free, offline | Free |
-| **RuVector** | Custom models via @ruvector/ruvllm | WASM optimized | Custom |
+| Subcommand | Description |
+|------------|-------------|
+| `init` | Initialize a new swarm with specified topology |
+| `start` | Start swarm execution with objective and strategy |
+| `status` | Show swarm status, progress, and metrics |
+| `stop` | Stop swarm execution (with state save option) |
+| `scale` | Scale swarm agent count up or down |
+| `coordinate` | Execute V3 15-agent hierarchical mesh coordination |
 
-### Provider Load Balancing
+#### Topologies
 
-| Strategy | Description | Best For |
+| Topology | Description | Best For |
 |----------|-------------|----------|
-| `round-robin` | Rotate through providers sequentially | Even distribution |
-| `least-loaded` | Use provider with lowest current load | High throughput |
-| `latency-based` | Use fastest responding provider | Low latency |
-| `cost-based` | Use cheapest provider that meets requirements | Cost optimization (85%+ savings) |
-
-### Embedding Providers (`@claude-flow/embeddings`)
+| `hierarchical` | Queen-led coordination with worker agents | Structured tasks, clear authority |
+| `mesh` | Fully connected peer-to-peer network | Collaborative work, redundancy |
+| `ring` | Circular communication pattern | Sequential processing |
+| `star` | Central coordinator with spoke agents | Centralized control |
+| `hybrid` | Hierarchical mesh for maximum flexibility | Complex multi-domain tasks |
 
-| Provider | Models | Dimensions | Latency | Cost |
-|----------|--------|------------|---------|------|
-| **OpenAI** | text-embedding-3-small/large, ada-002 | 1536-3072 | ~50-100ms | $0.02-0.13/1M tokens |
-| **Transformers.js** | all-MiniLM-L6-v2, all-mpnet-base-v2, bge-small | 384-768 | ~20-50ms | Free (local) |
-| **Mock** | Deterministic hash-based | Configurable | <1ms | Free |
+#### Strategies
 
-### Embedding Features
+| Strategy | Description | Agent Distribution |
+|----------|-------------|-------------------|
+| `research` | Distributed research and analysis | 1 coordinator, 4 researchers, 2 analysts |
+| `development` | Collaborative code development | 1 coordinator, 1 architect, 3 coders, 2 testers, 1 reviewer |
+| `testing` | Comprehensive test coverage | 1 test lead, 2 unit testers, 2 integration testers, 1 QA |
+| `optimization` | Performance optimization | 1 performance lead, 2 profilers, 2 optimizers |
+| `maintenance` | Codebase maintenance and refactoring | 1 coordinator, 2 refactorers, 1 documenter |
+| `analysis` | Code analysis and documentation | 1 analyst lead, 2 code analysts, 1 security analyst |
 
-| Feature | Description | Performance |
-|---------|-------------|-------------|
-| **LRU Caching** | Intelligent cache with hit rate tracking | <1ms cache hits |
-| **Batch Processing** | Efficient batch embedding with partial cache | 10 items <500ms |
-| **Similarity Functions** | Cosine, Euclidean, Dot product | Optimized math |
-| **Event System** | Observable operations with listeners | Real-time monitoring |
+#### Examples
 
-### Consensus Strategies (`@claude-flow/swarm`)
+```bash
+# Initialize V3 swarm (recommended)
+claude-flow swarm init --v3-mode
 
-| Strategy | Algorithm | Fault Tolerance | Latency | Best For |
-|----------|-----------|-----------------|---------|----------|
-| **Byzantine (PBFT)** | Practical Byzantine Fault Tolerance | f < n/3 faulty nodes | ~100ms | Adversarial environments |
-| **Raft** | Leader-based log replication | f < n/2 failures | ~50ms | Strong consistency |
-| **Gossip** | Epidemic protocol dissemination | High partition tolerance | ~200ms | Eventually consistent |
-| **CRDT** | Conflict-free Replicated Data Types | Strong eventual consistency | ~10ms | Concurrent updates |
-| **Quorum** | Configurable read/write quorums | Flexible | ~75ms | Tunable consistency |
+# Initialize with specific topology
+claude-flow swarm init -t mesh --max-agents 10
 
-### CLI Commands (`@claude-flow/cli`)
+# Start development swarm
+claude-flow swarm start -o "Build REST API with authentication" -s development
 
-| Command | Subcommands | Description |
-|---------|-------------|-------------|
-| `init` | 4 | Project initialization (wizard, check, skills, hooks) |
-| `agent` | 8 | Agent lifecycle (spawn, list, status, stop, metrics, pool, health, logs) |
-| `swarm` | 6 | Swarm coordination (init, start, status, stop, scale, coordinate) |
-| `memory` | 11 | Memory operations (store, retrieve, search, list, delete, stats, configure, cleanup, compress, export, import) |
-| `mcp` | 9 | MCP server (start, stop, status, health, restart, tools, toggle, exec, logs) |
-| `task` | 6 | Task management (create, list, status, cancel, assign, retry) |
-| `session` | 7 | Session management (list, save, restore, delete, export, import, current) |
-| `config` | 7 | Configuration (init, get, set, providers, reset, export, import) |
-| `status` | 3 | System status with watch mode (agents, tasks, memory) |
-| `workflow` | 6 | Workflow execution (run, validate, list, status, stop, template) |
-| `hooks` | 31 | Self-learning hooks (pre/post-edit, pre/post-command, route, explain, pretrain, session-*, intelligence/*, worker/*) |
-| `hive-mind` | 6 | Queen-led coordination (init, spawn, status, task, optimize-memory, shutdown) |
-| `migrate` | 5 | V2→V3 migration (status, run, verify, rollback, breaking) |
-
-### Testing Framework (`@claude-flow/testing`)
-
-| Component | Description | Features |
-|-----------|-------------|----------|
-| **London School TDD** | Behavior verification with mocks | Mock-first, interaction testing |
-| **Vitest Integration** | ADR-008 compliant test runner | 10x faster than Jest |
-| **Fixture Library** | Pre-defined test data | Agents, memory, swarm, MCP |
-| **Mock Factory** | Application and service mocks | Auto-reset, state tracking |
-| **Async Utilities** | waitFor, retry, withTimeout | Reliable async testing |
-| **Performance Assertions** | V3 target validation | Speedup, memory, latency checks |
-
-### Testing Fixtures
-
-| Fixture Type | Contents | Use Case |
-|--------------|----------|----------|
-| `agentConfigs` | 15 V3 agent configurations | Agent testing |
-| `memoryEntries` | Patterns, rules, embeddings | Memory testing |
-| `swarmConfigs` | V3 default, minimal, mesh, hierarchical | Swarm testing |
-| `mcpTools` | 27+ tool definitions | MCP testing |
-
-### Deployment & CI/CD (`@claude-flow/deployment`)
-
-| Feature | Description | Automation |
-|---------|-------------|------------|
-| **Version Bumping** | major, minor, patch, prerelease | Automatic semver |
-| **Changelog Generation** | Conventional commits parsing | Auto-generated |
-| **Git Integration** | Tagging, committing | Automatic |
-| **NPM Publishing** | alpha, beta, rc, latest tags | Tag-based |
-| **Validation** | Lint, test, build, dependency checks | Pre-release |
-| **Dry Run Mode** | Test releases without changes | Safe testing |
-
-### Release Channels
-
-| Channel | Version Format | Purpose |
-|---------|---------------|---------|
-| `alpha` | 1.0.0-alpha.1 | Early development |
-| `beta` | 1.0.0-beta.1 | Feature complete, testing |
-| `rc` | 1.0.0-rc.1 | Release candidate |
-| `latest` | 1.0.0 | Stable production |
-
-### Integration (`@claude-flow/integration`)
-
-| Component | Description | Performance |
-|-----------|-------------|-------------|
-| **AgenticFlowBridge** | agentic-flow@alpha integration | ADR-001 compliant |
-| **SONA Adapter** | Learning system integration | <0.05ms adaptation |
-| **Flash Attention** | Attention mechanism coordinator | 2.49x-7.47x speedup |
-| **SDK Bridge** | Version negotiation, API compatibility | Auto-detection |
-| **Feature Flags** | Dynamic feature management | 9 configurable flags |
-| **Runtime Detection** | NAPI, WASM, JS auto-selection | Optimal performance |
-
-### Integration Runtimes
-
-| Runtime | Performance | Requirements |
-|---------|-------------|--------------|
-| **NAPI** | Optimal | Native bindings, x64 |
-| **WASM** | Good | WebAssembly support |
-| **JS** | Fallback | Always available |
-
-### Performance Benchmarking (`@claude-flow/performance`)
-
-| Capability | Description | Output |
-|------------|-------------|--------|
-| **Statistical Analysis** | Mean, median, P95, P99, stddev | Comprehensive metrics |
-| **Memory Tracking** | Heap, RSS, external, array buffers | Resource monitoring |
-| **Auto-Calibration** | Automatic iteration adjustment | Statistical significance |
-| **Regression Detection** | Baseline comparison | Change detection |
-| **V3 Target Validation** | Built-in performance targets | Pass/fail checking |
-
-### V3 Benchmark Targets
-
-| Category | Benchmark | Target |
-|----------|-----------|--------|
-| **Startup** | CLI cold start | <500ms |
-| **Startup** | MCP server init | <400ms |
-| **Startup** | Agent spawn | <200ms |
-| **Memory** | Vector search | <1ms |
-| **Memory** | HNSW indexing | <10ms |
-| **Memory** | Memory write | <5ms |
-| **Swarm** | Agent coordination | <50ms |
-| **Swarm** | Consensus latency | <100ms |
-| **Neural** | SONA adaptation | <0.05ms |
-
-### Neural & SONA (`@claude-flow/neural`)
-
-| Feature | Description | Performance |
-|---------|-------------|-------------|
-| **SONA Learning** | Self-Optimizing Neural Architecture | <0.05ms adaptation |
-| **5 Learning Modes** | real-time, balanced, research, edge, batch | Mode-specific optimization |
-| **9 RL Algorithms** | PPO, A2C, DQN, Q-Learning, SARSA, Decision Transformer, etc. | Comprehensive RL |
-| **LoRA Integration** | Low-Rank Adaptation for efficient fine-tuning | Minimal memory overhead |
-| **MicroLoRA** | Ultra-lightweight LoRA for edge/real-time modes | <5MB memory footprint |
-| **EWC++ Memory** | Elastic Weight Consolidation prevents catastrophic forgetting | Zero knowledge loss |
-| **Trajectory Tracking** | Execution path recording for pattern extraction | Continuous learning |
+# Parallel analysis swarm
+claude-flow swarm start -o "Analyze codebase for performance issues" --parallel
 
-### Memory & Vector Optimization
+# Check swarm status
+claude-flow swarm status swarm-123
 
-| Feature | Description | Improvement |
-|---------|-------------|-------------|
-| **Scalar Quantization** | Reduce vector precision for memory savings | 4x memory reduction |
-| **Product Quantization** | Compress vectors into codebooks | 8-32x memory reduction |
-| **HNSW Indexing** | Hierarchical Navigable Small World graphs | 150x-12,500x faster search |
-| **LRU Caching** | Intelligent embedding cache with TTL | <1ms cache hits |
-| **Batch Processing** | Process multiple embeddings in single call | 10x throughput |
-| **Memory Compression** | Pattern distillation and pruning | 50-75% reduction |
+# Scale swarm
+claude-flow swarm scale swarm-123 --agents 20
 
-### Embedding System (`@claude-flow/embeddings`)
+# V3 15-agent coordination
+claude-flow swarm coordinate --agents 15
 
-| Feature | Description | Performance |
-|---------|-------------|-------------|
-| **Multi-Provider** | OpenAI, Transformers.js (local), Mock | Flexible deployment |
-| **Dimensions** | 384 to 3072 configurable | Quality vs speed tradeoff |
-| **Similarity Metrics** | Cosine, Euclidean, Dot product | Task-specific matching |
-| **Event System** | Observable operations with listeners | Real-time monitoring |
-| **Partial Cache Hits** | Batch requests use cached where available | Reduced API calls |
-
-### SONA Learning Modes
-
-| Mode | Adaptation | Quality | Memory | Use Case |
-|------|------------|---------|--------|----------|
-| `real-time` | <0.5ms | 70%+ | 25MB | Production, low-latency |
-| `balanced` | <18ms | 75%+ | 50MB | General purpose |
-| `research` | <100ms | 95%+ | 100MB | Deep exploration |
-| `edge` | <1ms | 80%+ | 5MB | Resource-constrained |
-| `batch` | <50ms | 85%+ | 75MB | High-throughput |
-
-### RL Algorithms
-
-| Algorithm | Type | Best For |
-|-----------|------|----------|
-| **PPO** | Policy Gradient | Stable continuous learning |
-| **A2C** | Actor-Critic | Balanced exploration/exploitation |
-| **DQN** | Value-based | Discrete action spaces |
-| **Q-Learning** | Tabular | Simple state spaces |
-| **SARSA** | On-policy | Online learning |
-| **Decision Transformer** | Sequence modeling | Long-horizon planning |
-
-### Hive-Mind Coordination
-
-| Feature | Description | Capability |
-|---------|-------------|------------|
-| **Queen-Led Topology** | Hierarchical command structure | Unlimited agents + sub-workers |
-| **Byzantine Consensus** | Fault-tolerant agreement | f < n/3 tolerance |
-| **Collective Memory** | Shared pattern storage | Distillation, compression |
-| **Specialist Spawning** | Domain-specific agents | Security, performance, etc. |
-| **Adaptive Topology** | Dynamic structure changes | Load-based optimization |
-
-### agentic-flow@alpha Integration
-
-| Feature | Description | Benefit |
-|---------|-------------|---------|
-| **ADR-001 Compliance** | Build on agentic-flow, don't duplicate | Eliminates 10,000+ duplicate lines |
-| **Core Foundation** | Use agentic-flow as the base layer | Unified architecture |
-| **SONA Integration** | Seamless learning system connection | <0.05ms adaptation |
-| **Flash Attention** | Optimized attention mechanisms | 2.49x-7.47x speedup |
-| **AgentDB Bridge** | Vector storage integration | 150x-12,500x faster search |
-| **Feature Flags** | Dynamic capability management | 9 configurable features |
-| **Runtime Detection** | NAPI/WASM/JS auto-selection | Optimal performance per platform |
-| **Graceful Fallback** | Works with or without agentic-flow | Always functional |
-
-### MCP Server (`@claude-flow/mcp`)
-
-| Feature | Description | Spec |
-|---------|-------------|------|
-| **MCP 2025-11-25** | Full specification compliance | Latest MCP standard |
-| **Multiple Transports** | stdio, HTTP, WebSocket, in-process | Flexible connectivity |
-| **Resources** | list, read, subscribe with caching | Dynamic content |
-| **Prompts** | Templates with arguments and embedding | Reusable prompts |
-| **Tasks** | Async operations with progress/cancel | Long-running ops |
-| **Tool Registry** | O(1) lookup, <10ms registration | Fast tool access |
-| **Connection Pooling** | Max 10 connections, configurable | Resource management |
-| **Session Management** | Timeout handling, authentication | Secure sessions |
-
-### MCP Methods
-
-| Method | Description |
-|--------|-------------|
-| `initialize` | Initialize connection |
-| `tools/list` | List available tools |
-| `tools/call` | Execute a tool |
-| `resources/list` | List resources with pagination |
-| `resources/read` | Read resource content |
-| `resources/subscribe` | Subscribe to updates |
-| `prompts/list` | List prompts with pagination |
-| `prompts/get` | Get prompt with arguments |
-| `tasks/status` | Get task status |
-| `tasks/cancel` | Cancel running task |
-| `completion/complete` | Auto-complete arguments |
-
-### Security Module (`@claude-flow/security`)
-
-| Feature | CVE/Issue | Description |
-|---------|-----------|-------------|
-| **Password Hashing** | CVE-2 | Secure bcrypt with 12+ rounds |
-| **Credential Generation** | CVE-3 | Cryptographically secure API keys |
-| **Safe Command Execution** | HIGH-1 | Allowlist-based command execution |
-| **Path Validation** | HIGH-2 | Path traversal and symlink protection |
-| **Input Validation** | General | Zod-based schema validation |
-| **Token Generation** | General | HMAC-signed secure tokens |
-| **HTML Sanitization** | XSS | Script and injection prevention |
-
-### Security Validation Schemas
-
-| Schema | Purpose |
-|--------|---------|
-| `SafeStringSchema` | Basic safe string with length limits |
-| `IdentifierSchema` | Alphanumeric identifiers |
-| `FilenameSchema` | Safe filenames |
-| `EmailSchema` | Email addresses |
-| `PasswordSchema` | Secure passwords (8-72 chars) |
-| `UUIDSchema` | UUID v4 format |
-| `HttpsUrlSchema` | HTTPS URLs only |
-| `SpawnAgentSchema` | Agent spawn requests |
-| `TaskInputSchema` | Task definitions |
-
-### Hooks System (`@claude-flow/hooks`)
-
-| Component | Description | Performance |
-|-----------|-------------|-------------|
-| **ReasoningBank** | Pattern storage with HNSW indexing | 150x faster retrieval |
-| **GuidanceProvider** | Context-aware development guidance | Real-time suggestions |
-| **PatternLearning** | Automatic strategy extraction | Continuous improvement |
-| **QualityTracking** | Success/failure rate per pattern | Performance metrics |
-| **DomainDetection** | Auto-categorization of patterns | Security, testing, etc. |
-| **AgentRouting** | Task-to-agent optimization | Historical performance |
-| **Consolidation** | Prune low-quality, promote high-quality | Memory optimization |
-
-### Hook Lifecycle Events
-
-| Phase | Hooks | Purpose |
-|-------|-------|---------|
-| **Pre-Edit** | `pre-edit` | Context gathering, security checks |
-| **Post-Edit** | `post-edit` | Outcome recording, pattern learning |
-| **Pre-Command** | `pre-command` | Risk assessment, validation |
-| **Post-Command** | `post-command` | Success/failure tracking |
-| **Pre-Task** | `pre-task` | Setup, resource allocation |
-| **Post-Task** | `post-task` | Cleanup, learning |
-| **Session** | `session-end`, `session-restore` | State management |
-
-### V3 Statusline (`@claude-flow/hooks`)
-
-Real-time development status display for Claude Code integration showing DDD progress, swarm activity, security status, and system metrics.
-
-**Output Format:**
+# Stop with state save
+claude-flow swarm stop swarm-123 --save-state
 ```
-▊ Claude Flow V3 ● ruvnet  │  ⎇ v3  │  Opus 4.5
-─────────────────────────────────────────────────────
-🏗️  DDD Domains    [●●●●●]  5/5    ⚡ 1.0x → 2.49x-7.47x
-🤖 Swarm  ◉ [58/15]  👥 0    🟢 CVE 3/3    💾 22282MB    📂  47%    🧠  10%
-🔧 Architecture    DDD ● 98%  │  Security ●CLEAN  │  Memory ●AgentDB  │  Integration ●
+
+---
+
+### `memory` - Memory Management
+
+AgentDB memory operations with vector search, caching, and optimization.
+
+```bash
+claude-flow memory <subcommand> [options]
 ```
 
-| Indicator | Description | Values |
-|-----------|-------------|--------|
-| `▊ Claude Flow V3` | Project header | Always shown |
-| `● ruvnet` | GitHub user (via `gh` CLI) | Dynamic |
-| `⎇ v3` | Current git branch | Dynamic |
-| `Opus 4.5` | Claude model name | From Claude Code |
-| `[●●●●●]` | DDD domain progress bar | 0-5 domains |
-| `⚡ 1.0x → 2.49x-7.47x` | Performance speedup target | Current → Target |
-| `◉/○` | Swarm coordination status | Active/Inactive |
-| `[58/15]` | Active agents / max agents | Process count |
-| `👥 0` | Sub-agents spawned | Task tool agents |
-| `🟢 CVE 3/3` | Security CVE remediation | Fixed/Total |
-| `💾 22282MB` | Memory usage (Node.js processes) | Real-time |
-| `📂 47%` | Context window usage | From Claude Code |
-| `🧠 10%` | Intelligence score (patterns learned) | 0-100% |
-| `DDD ● 98%` | Domain-Driven Design progress | Percentage |
-| `Security ●CLEAN` | Security audit status | CLEAN/PENDING/FAILED |
-| `Memory ●AgentDB` | Memory backend in use | AgentDB/SQLite/Hybrid |
-| `Integration ●` | agentic-flow integration status | Active/Inactive |
-
-**Usage:**
+#### Subcommands
+
+| Subcommand | Aliases | Description |
+|------------|---------|-------------|
+| `store` | | Store data in memory with optional vector embedding |
+| `retrieve` | `get` | Retrieve data from memory by key |
+| `search` | | Semantic/vector search with HNSW indexing |
+| `list` | `ls` | List memory entries with filtering |
+| `delete` | `rm` | Delete memory entry |
+| `stats` | | Show memory statistics and performance |
+| `configure` | `config` | Configure memory backend and HNSW parameters |
+| `cleanup` | | Clean up stale and expired entries |
+| `compress` | | Compress and optimize memory storage |
+| `export` | | Export memory to file (JSON, CSV, binary) |
+| `import` | | Import memory from file |
+
+#### Memory Backends
+
+| Backend | Description | Performance |
+|---------|-------------|-------------|
+| `agentdb` | Vector database with HNSW indexing | 150x-12,500x faster search |
+| `sqlite` | Lightweight local storage | Good for small datasets |
+| `hybrid` | SQLite + AgentDB (recommended) | Best of both worlds |
+| `memory` | In-memory (non-persistent) | Fastest, no persistence |
+
+#### Search Options
+
+| Option | Short | Description | Default |
+|--------|-------|-------------|---------|
+| `--query` | `-q` | Search query | required |
+| `--namespace` | `-n` | Memory namespace | all |
+| `--limit` | `-l` | Maximum results | `10` |
+| `--threshold` | | Similarity threshold (0-1) | `0.7` |
+| `--type` | `-t` | Search type (semantic, keyword, hybrid) | `semantic` |
+
+#### Examples
+
 ```bash
-# V3 statusline (Node.js)
-node v3/@claude-flow/hooks/bin/statusline.js
+# Store text data
+claude-flow memory store -k "api/auth" -v "JWT implementation with refresh tokens"
+
+# Store as vector embedding
+claude-flow memory store -k "pattern/singleton" -v "Singleton pattern description" --vector
+
+# Semantic search
+claude-flow memory search -q "authentication patterns"
 
-# JSON output for scripting
-node v3/@claude-flow/hooks/bin/statusline.js --json
+# Keyword search
+claude-flow memory search -q "JWT" -t keyword
 
-# Compact JSON (single line)
-node v3/@claude-flow/hooks/bin/statusline.js --compact
+# Hybrid search with threshold
+claude-flow memory search -q "security best practices" -t hybrid --threshold 0.8
 
-# Help
-node v3/@claude-flow/hooks/bin/statusline.js --help
+# List entries by namespace
+claude-flow memory list -n patterns
+
+# Show memory statistics
+claude-flow memory stats
+
+# Configure HNSW parameters
+claude-flow memory configure -b hybrid --hnsw-m 16 --hnsw-ef 200
+
+# Cleanup old entries
+claude-flow memory cleanup --older-than 30d
+
+# Cleanup expired TTL entries
+claude-flow memory cleanup --expired-only
+
+# Compress with quantization (32x memory reduction)
+claude-flow memory compress --quantize --bits 4
+
+# Export memory
+claude-flow memory export -o ./backup.json -f json
+
+# Import memory
+claude-flow memory import -i ./backup.json --merge
 ```
 
-**Claude Code Integration:**
+---
 
-Add to `.claude/settings.json`:
-```json
-{
-  "statusLine": {
-    "type": "command",
-    "command": "node v3/@claude-flow/hooks/bin/statusline.js"
-  }
-}
+### `mcp` - MCP Server Management
+
+Model Context Protocol server control and tool execution.
+
+```bash
+claude-flow mcp <subcommand> [options]
 ```
 
-**Data Sources:**
-- `.claude-flow/metrics/v3-progress.json` - DDD domain progress
-- `.claude-flow/metrics/swarm-activity.json` - Active agent counts
-- `.claude-flow/security/audit-status.json` - CVE remediation status
-- `.claude-flow/learning/patterns.db` - Intelligence score (pattern count)
-- Process detection via `ps aux` - Real-time memory and agent counts
-- Git branch via `git branch --show-current`
-- GitHub user via `gh api user`
+#### Subcommands
 
-### Background Daemons
+| Subcommand | Description |
+|------------|-------------|
+| `start` | Start MCP server with specified transport |
+| `stop` | Stop MCP server (graceful or forced) |
+| `status` | Show MCP server status and metrics |
+| `health` | Check MCP server health |
+| `restart` | Restart MCP server |
+| `tools` | List available MCP tools by category |
+| `toggle` | Enable or disable specific tools |
+| `exec` | Execute an MCP tool directly |
+| `logs` | Show MCP server logs |
 
-#### V3 Node.js Worker Daemon (Recommended)
+#### Transport Types
 
-Cross-platform TypeScript-based daemon service with auto-scheduling:
+| Transport | Description | Use Case |
+|-----------|-------------|----------|
+| `stdio` | Standard I/O (default) | Claude Code integration |
+| `http` | HTTP REST API | Web integrations, remote access |
+| `websocket` | WebSocket connection | Real-time bidirectional |
 
-| Worker | Interval | Priority | Description |
-|--------|----------|----------|-------------|
-| `map` | 5min | normal | Codebase structure mapping |
-| `audit` | 10min | critical | Security vulnerability scanning |
-| `optimize` | 15min | high | Performance optimization |
-| `consolidate` | 30min | low | Memory consolidation |
-| `testgaps` | 20min | normal | Test coverage analysis |
+#### Tool Categories
+
+| Category | Description | Tool Count |
+|----------|-------------|------------|
+| `agent` | Agent lifecycle management | 4 |
+| `swarm` | Swarm coordination | 3 |
+| `memory` | Memory operations | 3 |
+| `config` | Configuration | 3 |
+| `hooks` | Hook execution | 9 |
+| `system` | System operations | 3 |
+
+#### Examples
 
-**Commands:**
 ```bash
-# Start daemon (auto-runs on SessionStart hooks)
-npx claude-flow@v3alpha daemon start
+# Start with stdio (default)
+claude-flow mcp start
 
-# Check status with worker history
-npx claude-flow@v3alpha daemon status
+# Start HTTP server on port 8080
+claude-flow mcp start -t http -p 8080
 
-# Manually trigger a worker
-npx claude-flow@v3alpha daemon trigger map
+# Start as background daemon
+claude-flow mcp start -d
 
-# Enable/disable workers
-npx claude-flow@v3alpha daemon enable map audit optimize
+# Check server status
+claude-flow mcp status
 
-# Stop daemon
-npx claude-flow@v3alpha daemon stop
-```
+# Health check
+claude-flow mcp health
+
+# List all tools
+claude-flow mcp tools
+
+# List tools by category
+claude-flow mcp tools -c memory
+
+# Execute a tool
+claude-flow mcp exec -t swarm/init -p '{"topology":"mesh"}'
+
+# View logs
+claude-flow mcp logs -n 50 -f
 
-**Daemon Status Output:**
+# Restart server
+claude-flow mcp restart
+
+# Stop server
+claude-flow mcp stop
 ```
-+-- Worker Daemon ---+
-| Status: ● RUNNING  |
-| PID: 12345         |
-| Workers Enabled: 5 |
-| Max Concurrent: 3  |
-+--------------------+
-
-Worker Status
-+-------------+----+----------+------+---------+----------+----------+
-| Worker      | On | Status   | Runs | Success | Last Run | Next Run |
-+-------------+----+----------+------+---------+----------+----------+
-| map         | ✓  | idle     | 12   | 100%    | 2m ago   | in 3m    |
-| audit       | ✓  | idle     | 6    | 100%    | 5m ago   | in 5m    |
-| optimize    | ✓  | running  | 4    | 100%    | now      | -        |
-| consolidate | ✓  | idle     | 2    | 100%    | 15m ago  | in 15m   |
-| testgaps    | ✓  | idle     | 3    | 100%    | 8m ago   | in 12m   |
-+-------------+----+----------+------+---------+----------+----------+
+
+---
+
+### `task` - Task Management
+
+Create, assign, and manage tasks across agents.
+
+```bash
+claude-flow task <subcommand> [options]
 ```
 
-#### Legacy Shell Daemons (V2)
+#### Subcommands
 
-Shell-based daemons for monitoring (Linux/macOS only):
+| Subcommand | Description |
+|------------|-------------|
+| `create` | Create a new task with priority and dependencies |
+| `list` | List tasks with status filtering |
+| `status` | Show detailed task status |
+| `cancel` | Cancel a pending or running task |
+| `assign` | Assign task to specific agent |
+| `retry` | Retry a failed task |
 
-| Daemon | Interval | Purpose | Output |
-|--------|----------|---------|--------|
-| **Swarm Monitor** | 3s | Process detection, agent counting | `swarm-activity.json` |
-| **Metrics Daemon** | 30s | V3 progress sync, SQLite metrics | `metrics.db` |
+#### Examples
 
-**Commands:**
 ```bash
-# Start all daemons
-.claude/helpers/daemon-manager.sh start 3 5
+# Create a task
+claude-flow task create "Implement user authentication" -p high
 
-# Check daemon status
-.claude/helpers/daemon-manager.sh status
+# Create task with dependencies
+claude-flow task create "Write tests" --depends-on task-001
 
-# Stop all daemons
-.claude/helpers/daemon-manager.sh stop
-```
+# List all tasks
+claude-flow task list
 
-### Worker Manager (7 Scheduled Workers)
+# List pending tasks
+claude-flow task list -s pending
 
-| Worker | Interval | Purpose |
-|--------|----------|---------|
-| `perf` | 5 min | Performance benchmarks |
-| `health` | 5 min | Disk, memory, CPU monitoring |
-| `patterns` | 15 min | Pattern dedup & pruning |
-| `ddd` | 10 min | DDD progress tracking |
-| `adr` | 15 min | ADR compliance checking |
-| `security` | 30 min | Security vulnerability scans |
-| `learning` | 30 min | Learning pattern optimization |
+# Get task status
+claude-flow task status task-001
 
-**Commands:**
-```bash
-# Start worker manager
-.claude/helpers/worker-manager.sh start 60
+# Assign to agent
+claude-flow task assign task-001 --agent coder-001
 
-# Force run all workers immediately
-.claude/helpers/worker-manager.sh force
+# Cancel task
+claude-flow task cancel task-001
 
-# Check worker status
-.claude/helpers/worker-manager.sh status
+# Retry failed task
+claude-flow task retry task-001
 ```
 
 ---
 
-## Use Cases
+### `session` - Session Management
 
-| Use Case | Command |
-|----------|---------|
-| Code review | `npx claude-flow@v3alpha --agent reviewer --task "Review PR #123"` |
-| Test generation | `npx claude-flow@v3alpha --agent tester --task "Write tests for auth module"` |
-| Security audit | `npx claude-flow@v3alpha --agent security-architect --task "Audit for vulnerabilities"` |
-| Multi-agent swarm | `npx claude-flow@v3alpha swarm init --topology hierarchical` |
-| Route task | `npx claude-flow@v3alpha hooks route "Optimize database queries"` |
-| Performance analysis | `npx claude-flow@v3alpha --agent perf-analyzer --task "Profile API endpoints"` |
-| GitHub PR management | `npx claude-flow@v3alpha --agent pr-manager --task "Review open PRs"` |
+Manage session state, persistence, and restoration.
 
----
+```bash
+claude-flow session <subcommand> [options]
+```
+
+#### Subcommands
+
+| Subcommand | Description |
+|------------|-------------|
+| `list` | List all sessions |
+| `save` | Save current session state |
+| `restore` | Restore a previous session |
+| `delete` | Delete a session |
+| `export` | Export session to file |
+| `import` | Import session from file |
+| `current` | Show current session info |
 
-## Self-Learning Hooks Commands (26 Hooks)
+#### Examples
 
-### Core Tool Lifecycle Hooks
 ```bash
-# Before/after file editing
-npx claude-flow@v3alpha hooks pre-edit <filePath>
-npx claude-flow@v3alpha hooks post-edit <filePath> --success true --train-patterns
+# List all sessions
+claude-flow session list
 
-# Before/after commands
-npx claude-flow@v3alpha hooks pre-command "<command>"
-npx claude-flow@v3alpha hooks post-command "<command>" --success true
+# Save current session
+claude-flow session save --name "feature-auth"
 
-# Before/after tasks
-npx claude-flow@v3alpha hooks pre-task --description "<task>"
-npx claude-flow@v3alpha hooks post-task --task-id "<id>" --success true
-```
+# Restore session
+claude-flow session restore session-123
 
-### Intelligence & Routing Hooks
-```bash
-# Route task to optimal agent using learned patterns
-npx claude-flow@v3alpha hooks route "<task description>" --include-explanation
+# Export session
+claude-flow session export -o ./session-backup.json
 
-# Explain routing decision with transparency
-npx claude-flow@v3alpha hooks explain "<topic>" --depth comprehensive
+# Import session
+claude-flow session import -i ./session-backup.json
 
-# Bootstrap intelligence from repository
-npx claude-flow@v3alpha hooks pretrain --model-type moe --epochs 10
+# Show current session
+claude-flow session current
 
-# Generate optimized agent configs from pretrain data
-npx claude-flow@v3alpha hooks build-agents --agent-types coder,tester --config-format yaml
+# Delete old session
+claude-flow session delete session-123
+```
 
-# Transfer patterns from another project
-npx claude-flow@v3alpha hooks transfer <sourceProject>
+---
 
-# Initialize hooks system
-npx claude-flow@v3alpha hooks init
+### `config` - Configuration Management
 
-# View learning metrics dashboard
-npx claude-flow@v3alpha hooks metrics
+Manage configuration, providers, and settings.
 
-# List all registered hooks
-npx claude-flow@v3alpha hooks list
+```bash
+claude-flow config <subcommand> [options]
 ```
 
-### Session Management Hooks
+#### Subcommands
+
+| Subcommand | Description |
+|------------|-------------|
+| `init` | Initialize configuration file |
+| `get` | Get configuration value |
+| `set` | Set configuration value |
+| `providers` | Manage LLM provider configurations |
+| `reset` | Reset configuration to defaults |
+| `export` | Export configuration |
+| `import` | Import configuration |
+
+#### Examples
+
 ```bash
-# Start session with context loading
-npx claude-flow@v3alpha hooks session-start --session-id "<id>" --load-context
+# Initialize config
+claude-flow config init
+
+# Get a value
+claude-flow config get memory.backend
 
-# End session with persistence
-npx claude-flow@v3alpha hooks session-end --export-metrics true --persist-patterns
+# Set a value
+claude-flow config set swarm.topology mesh
 
-# Restore previous session context
-npx claude-flow@v3alpha hooks session-restore --session-id "<id>"
+# Configure providers
+claude-flow config providers --add anthropic --api-key $ANTHROPIC_API_KEY
 
-# Send notifications to swarm
-npx claude-flow@v3alpha hooks notify --message "<message>" --swarm-status
+# Reset to defaults
+claude-flow config reset --confirm
+
+# Export config
+claude-flow config export -o ./config-backup.json
+
+# Import config
+claude-flow config import -i ./config.json
 ```
 
-### RuVector Intelligence Hooks (Reinforcement Learning)
+---
+
+### `status` - System Status
+
+Monitor system status with real-time updates.
+
 ```bash
-# Trajectory-based learning (4-step pipeline: RETRIEVE, JUDGE, DISTILL, CONSOLIDATE)
-npx claude-flow@v3alpha hooks intelligence trajectory-start --session "<session>"
-npx claude-flow@v3alpha hooks intelligence trajectory-step --action "<action>" --reward 0.9
-npx claude-flow@v3alpha hooks intelligence trajectory-end --verdict success
+claude-flow status [subcommand] [options]
+```
 
-# Pattern storage with HNSW indexing (150x faster search)
-npx claude-flow@v3alpha hooks intelligence pattern-store --pattern "<pattern>" --embedding "[...]"
-npx claude-flow@v3alpha hooks intelligence pattern-search --query "<query>" --limit 10
+#### Subcommands
 
-# Learning stats and attention focus
-npx claude-flow@v3alpha hooks intelligence stats
-npx claude-flow@v3alpha hooks intelligence learn --experience '{"type":"success"}'
-npx claude-flow@v3alpha hooks intelligence attention --focus "<task>"
+| Subcommand | Description |
+|------------|-------------|
+| `agents` | Show status of all agents |
+| `tasks` | Show status of all tasks |
+| `memory` | Show memory system status |
 
-# Full intelligence system (SONA, MoE, HNSW, EWC++, Flash Attention)
-npx claude-flow@v3alpha hooks intelligence
-npx claude-flow@v3alpha hooks intelligence reset --confirm
+#### Options
 
-# ═══════════════════════════════════════════════════════════════
-# Background Worker Commands (12 workers for analysis/optimization)
-# ═══════════════════════════════════════════════════════════════
+| Option | Short | Description | Default |
+|--------|-------|-------------|---------|
+| `--watch` | `-w` | Watch mode with auto-refresh | `false` |
+| `--interval` | `-i` | Refresh interval in seconds | `5` |
 
-# List all available workers
-npx claude-flow@v3alpha hooks worker list
+#### Examples
 
-# Detect triggers from prompt text
-npx claude-flow@v3alpha hooks worker detect --prompt "optimize performance"
+```bash
+# Show all status
+claude-flow status
 
-# Auto-dispatch workers when triggers match (confidence ≥0.6)
-npx claude-flow@v3alpha hooks worker detect --prompt "deep dive into auth" --auto-dispatch --min-confidence 0.6
+# Watch mode with 2s refresh
+claude-flow status --watch -i 2
 
-# Manually dispatch a worker (ultralearn, optimize, audit, map, deepdive, document, refactor, benchmark, testgaps, etc.)
-npx claude-flow@v3alpha hooks worker dispatch --trigger refactor --context "auth module"
+# Agent status only
+claude-flow status agents
 
-# Check worker status
-npx claude-flow@v3alpha hooks worker status
+# Task status
+claude-flow status tasks
 
-# Cancel a running worker
-npx claude-flow@v3alpha hooks worker cancel --id worker_refactor_1_abc123
+# Memory status
+claude-flow status memory
 ```
 
 ---
 
-## Architecture
+### `workflow` - Workflow Management
 
-### V3 Module Structure
+Execute and manage automated workflows.
 
+```bash
+claude-flow workflow <subcommand> [options]
 ```
-v3/
-├── @claude-flow/hooks      # Event-driven lifecycle hooks + ReasoningBank
-├── @claude-flow/memory     # AgentDB unification module
-├── @claude-flow/security   # CVE remediation & patterns
-├── @claude-flow/swarm      # 15-agent coordination
-├── @claude-flow/plugins    # RuVector WASM plugins
-├── @claude-flow/cli        # CLI modernization
-├── @claude-flow/neural     # SONA learning integration
-├── @claude-flow/testing    # TDD London School framework
-├── @claude-flow/deployment # Release & CI/CD
-└── @claude-flow/shared     # Shared utilities & types
+
+#### Subcommands
+
+| Subcommand | Description |
+|------------|-------------|
+| `run` | Execute a workflow |
+| `validate` | Validate workflow definition |
+| `list` | List available workflows |
+| `status` | Show workflow execution status |
+| `stop` | Stop running workflow |
+| `template` | Manage workflow templates (list, show, create) |
+
+#### Examples
+
+```bash
+# Run a workflow
+claude-flow workflow run ./workflows/deploy.yaml
+
+# Validate workflow
+claude-flow workflow validate ./workflows/deploy.yaml
+
+# List workflows
+claude-flow workflow list
+
+# Check workflow status
+claude-flow workflow status workflow-123
+
+# Stop workflow
+claude-flow workflow stop workflow-123
+
+# List templates
+claude-flow workflow template list
+
+# Create from template
+claude-flow workflow template create --from deploy-standard
 ```
- 
-### Performance Metrics
-
-| Metric | Measured |
-|--------|----------|
-| Swarm task execution | 100% success rate (7/7 strategies) |
-| Average task duration | 0.15-0.30 seconds |
-| Memory usage per agent | 128-320 MB |
-| CPU utilization | 15-30% per agent |
-| Parallel agent capacity | Unlimited (resource-dependent) |
-
-### Topology Performance
-
-| Topology | Agents | Execution Time | Memory |
-|----------|--------|----------------|--------|
-| Centralized | 2-3 | 0.14-0.20s | 180-256 MB |
-| Distributed | 4-5 | 0.10-0.12s | 128-160 MB |
-| Hierarchical | 6 | 0.20s | 256 MB |
-| Mesh | 4 | 0.15s | 192 MB |
-| Hybrid | 7 | 0.18s | 320 MB |
 
 ---
 
-## Cross-Platform Support
+### `hooks` - Self-Learning Hooks
 
-### Windows (PowerShell)
+Advanced self-learning hooks with 17 subcommands for neural pattern recognition and background worker management.
 
-```powershell
-npx @claude-flow/security@latest audit --platform windows
-$env:CLAUDE_FLOW_MODE = "integration"
+```bash
+claude-flow hooks <subcommand> [options]
 ```
 
-### macOS (Bash/Zsh)
+#### Subcommands
+
+| Subcommand | Description |
+|------------|-------------|
+| `pre-edit` | Execute before file edit (get context, agent suggestions) |
+| `post-edit` | Execute after file edit (record outcome for learning) |
+| `pre-command` | Execute before command (risk assessment) |
+| `post-command` | Execute after command (record outcome) |
+| `pre-task` | Execute before task (setup, validation) |
+| `post-task` | Execute after task (cleanup, learning) |
+| `session-end` | Execute on session end (save state) |
+| `session-restore` | Execute on session restore (load state) |
+| `route` | Route task to optimal agent using learned patterns |
+| `explain` | Explain routing decision with transparency |
+| `pretrain` | Bootstrap intelligence from repository |
+| `build-agents` | Generate optimized agent configs from pretrain data |
+| `metrics` | View learning metrics dashboard |
+| `transfer` | Transfer patterns from another project |
+| `list` | List all registered hooks |
+| `intelligence` | RuVector intelligence (SONA, MoE, HNSW) |
+| `worker` | Background worker management (12 workers) |
+
+#### Learning Pipeline
+
+The hooks system implements a 4-step learning pipeline:
+
+1. **RETRIEVE** - Top-k memory injection with MMR diversity
+2. **JUDGE** - LLM-as-judge trajectory evaluation
+3. **DISTILL** - Extract strategy memories from trajectories
+4. **CONSOLIDATE** - Dedup, detect contradictions, prune old patterns
+
+#### Examples
 
 ```bash
-npx @claude-flow/security@latest audit --platform darwin
-export CLAUDE_FLOW_SECURITY_MODE="strict"
+# Pre-edit hook (get context and suggestions)
+claude-flow hooks pre-edit ./src/auth/login.ts
+
+# Post-edit hook (record success for learning)
+claude-flow hooks post-edit ./src/auth/login.ts --success true
+
+# Pre-command risk assessment
+claude-flow hooks pre-command "rm -rf ./node_modules"
+
+# Route task to optimal agent
+claude-flow hooks route "Implement OAuth2 authentication"
+
+# Explain routing decision
+claude-flow hooks explain "Implement OAuth2 authentication"
+
+# Bootstrap from repository
+claude-flow hooks pretrain
+
+# Build optimized agent configs
+claude-flow hooks build-agents --focus "security"
+
+# View learning metrics
+claude-flow hooks metrics
+
+# Transfer patterns from another project
+claude-flow hooks transfer ../other-project
+
+# View intelligence status (SONA, MoE, HNSW)
+claude-flow hooks intelligence
 ```
 
-### Linux (Bash)
+#### Worker Subcommands
+
+The `hooks worker` command manages 12 background workers for analysis and optimization tasks.
+
+| Worker | Priority | Est. Time | Description |
+|--------|----------|-----------|-------------|
+| `ultralearn` | normal | 60s | Deep knowledge acquisition and learning |
+| `optimize` | high | 30s | Performance optimization and tuning |
+| `consolidate` | low | 20s | Memory consolidation and cleanup |
+| `predict` | normal | 15s | Predictive preloading and anticipation |
+| `audit` | critical | 45s | Security analysis and vulnerability scanning |
+| `map` | normal | 30s | Codebase mapping and architecture analysis |
+| `preload` | low | 10s | Resource preloading and cache warming |
+| `deepdive` | normal | 60s | Deep code analysis and examination |
+| `document` | normal | 45s | Auto-documentation generation |
+| `refactor` | normal | 30s | Code refactoring suggestions |
+| `benchmark` | normal | 60s | Performance benchmarking |
+| `testgaps` | normal | 30s | Test coverage analysis |
+
+##### Worker Commands
 
 ```bash
-npx @claude-flow/security@latest audit --platform linux
-export CLAUDE_FLOW_MEMORY_PATH="./data"
+# List all available workers
+claude-flow hooks worker list
+
+# Detect triggers from prompt text
+claude-flow hooks worker detect --prompt "optimize performance"
+
+# Auto-dispatch workers when triggers match (min confidence 0.6)
+claude-flow hooks worker detect --prompt "deep dive into auth" --auto-dispatch --min-confidence 0.6
+
+# Manually dispatch a worker
+claude-flow hooks worker dispatch --trigger refactor --context "auth module"
+
+# Check worker status
+claude-flow hooks worker status
+
+# Cancel a running worker
+claude-flow hooks worker cancel --id worker_refactor_1_abc123
 ```
 
----
+##### Performance Targets
 
-## Environment Variables
+| Metric | Target |
+|--------|--------|
+| Trigger detection | <5ms |
+| Worker spawn | <50ms |
+| Max concurrent | 10 |
+
+##### UserPromptSubmit Integration
 
-| Variable | Description | Default |
-|----------|-------------|---------|
-| `CLAUDE_FLOW_MODE` | Operation mode (`development`, `production`, `integration`) | `development` |
-| `CLAUDE_FLOW_MEMORY_PATH` | Directory for persistent memory storage | `./data` |
-| `CLAUDE_FLOW_SECURITY_MODE` | Security level (`strict`, `standard`, `permissive`) | `standard` |
-| `CLAUDE_FLOW_LOG_LEVEL` | Logging verbosity (`debug`, `info`, `warn`, `error`) | `info` |
-| `CLAUDE_FLOW_MAX_AGENTS` | Default concurrent agent limit (increase for more parallelism) | `15` |
-| `CLAUDE_FLOW_TOPOLOGY` | Default swarm topology | `hierarchical` |
-| `CLAUDE_FLOW_HNSW_M` | HNSW index M parameter (connectivity) | `16` |
-| `CLAUDE_FLOW_HNSW_EF` | HNSW search ef parameter (accuracy) | `200` |
-| `CLAUDE_FLOW_EMBEDDING_DIM` | Vector embedding dimensions | `384` |
-| `ANTHROPIC_API_KEY` | Anthropic API key for Claude integration | - |
+Workers are automatically triggered via the `UserPromptSubmit` hook when prompt patterns match worker triggers with confidence ≥0.6.
 
 ---
 
-## Troubleshooting
+### `hive-mind` - Consensus Coordination
 
-### Common Issues
+Queen-led Byzantine fault-tolerant multi-agent coordination.
 
-**MCP server won't start**
 ```bash
-# Check if port is in use
-lsof -i :3000
-# Kill existing process
-kill -9 <PID>
-# Restart MCP server
-npx claude-flow@v3alpha mcp start
+claude-flow hive-mind <subcommand> [options]
 ```
 
-**Agent spawn failures**
-```bash
-# Check available memory
-free -m
-# Reduce max agents if memory constrained
-export CLAUDE_FLOW_MAX_AGENTS=5
-```
+#### Subcommands
+
+| Subcommand | Description |
+|------------|-------------|
+| `init` | Initialize hive-mind with topology and consensus strategy |
+| `spawn` | Spawn agents in the hive (queen, worker, specialist) |
+| `status` | Show hive-mind status with consensus health |
+| `task` | Submit task to hive-mind for collaborative execution |
+| `optimize-memory` | Optimize collective memory (distill, compress) |
+| `shutdown` | Gracefully shutdown hive-mind |
+
+#### Topologies
+
+| Topology | Description |
+|----------|-------------|
+| `hierarchical` | Queen controls workers directly |
+| `mesh` | Fully connected peer network |
+| `hierarchical-mesh` | Hybrid: Queen + mesh workers |
+| `adaptive` | Dynamic topology based on load |
+
+#### Consensus Strategies
+
+| Strategy | Description | Fault Tolerance |
+|----------|-------------|-----------------|
+| `byzantine` | Byzantine fault-tolerant (BFT) | Tolerates f < n/3 faulty nodes |
+| `raft` | Leader-based consensus | Tolerates f < n/2 failures |
+| `gossip` | Epidemic protocol for eventual consistency | High partition tolerance |
+| `crdt` | Conflict-free replicated data types | Strong eventual consistency |
+| `quorum` | Configurable quorum-based | Flexible fault tolerance |
+
+#### Examples
 
-**Pattern search returning no results**
 ```bash
-# Verify patterns are stored
-npx claude-flow@v3alpha hooks metrics
-# Re-run pretraining if empty
-npx claude-flow@v3alpha hooks pretrain
-```
+# Initialize with defaults
+claude-flow hive-mind init
+
+# Initialize with Byzantine consensus
+claude-flow hive-mind init -t hierarchical-mesh -c byzantine --agents 15
+
+# Spawn queen
+claude-flow hive-mind spawn --role queen --name hive-queen
+
+# Spawn workers
+claude-flow hive-mind spawn --role worker --count 5
+
+# Spawn specialist
+claude-flow hive-mind spawn --role specialist --specialty security
 
-**Windows path issues**
-```powershell
-# Use forward slashes or escape backslashes
-$env:CLAUDE_FLOW_MEMORY_PATH = "./data"
-# Or use absolute path
-$env:CLAUDE_FLOW_MEMORY_PATH = "C:/Users/name/claude-flow/data"
+# Submit task for collaborative execution
+claude-flow hive-mind task "Implement secure API endpoints" --consensus-required
+
+# Check hive status
+claude-flow hive-mind status --detailed
+
+# Optimize collective memory
+claude-flow hive-mind optimize-memory --distill --compress
+
+# Graceful shutdown
+claude-flow hive-mind shutdown --save-state
 ```
 
-**Permission denied errors**
+---
+
+### `migrate` - V2 to V3 Migration
+
+Migration tools for transitioning from V2 to V3.
+
 ```bash
-# Fix npm permissions (Linux/macOS)
-sudo chown -R $(whoami) ~/.npm
-# Or use nvm to manage Node.js
+claude-flow migrate <subcommand> [options]
 ```
 
-**High memory usage**
+#### Subcommands
+
+| Subcommand | Description |
+|------------|-------------|
+| `status` | Check migration status and pending items |
+| `run` | Execute migration (with dry-run option) |
+| `verify` | Verify migration integrity |
+| `rollback` | Rollback to previous version |
+| `breaking` | Show V3 breaking changes |
+
+#### Migration Targets
+
+| Target | Description |
+|--------|-------------|
+| `config` | Migrate configuration files |
+| `memory` | Migrate memory/database content |
+| `agents` | Migrate agent configurations |
+| `hooks` | Migrate hook definitions |
+| `workflows` | Migrate workflow definitions |
+| `all` | Full migration |
+
+#### Examples
+
 ```bash
-# Enable garbage collection
-node --expose-gc node_modules/.bin/claude-flow
-# Reduce HNSW parameters for lower memory
-export CLAUDE_FLOW_HNSW_M=8
-export CLAUDE_FLOW_HNSW_EF=100
+# Check migration status
+claude-flow migrate status
+
+# Preview migration (dry run)
+claude-flow migrate run --dry-run
+
+# Run full migration with backup
+claude-flow migrate run -t all --backup
+
+# Migrate specific component
+claude-flow migrate run -t memory
+
+# Verify migration
+claude-flow migrate verify
+
+# Auto-fix issues
+claude-flow migrate verify --fix
+
+# Show breaking changes
+claude-flow migrate breaking
+
+# Rollback
+claude-flow migrate rollback --backup-id backup-1704369600
 ```
 
 ---
 
-## Migration Guide (V2 → V3)
-
-### Breaking Changes
+## Global Options
+
+All commands support these global options:
+
+| Option | Short | Description | Default |
+|--------|-------|-------------|---------|
+| `--help` | `-h` | Show help information | |
+| `--version` | `-V` | Show version number | |
+| `--verbose` | `-v` | Enable verbose output | `false` |
+| `--quiet` | `-q` | Suppress non-essential output | `false` |
+| `--config` | `-c` | Path to configuration file | `./claude-flow.config.json` |
+| `--format` | `-f` | Output format (text, json, table) | `text` |
+| `--no-color` | | Disable colored output | `false` |
+| `--interactive` | `-i` | Enable interactive mode | `true` (if TTY) |
+
+## Programmatic API
+
+### CommandParser
+
+```typescript
+import { CommandParser, OutputFormatter } from '@claude-flow/cli';
+
+// Create a parser instance
+const parser = new CommandParser();
+
+// Register a command
+parser.registerCommand({
+  name: 'mycommand',
+  description: 'My custom command',
+  options: [
+    {
+      name: 'type',
+      short: 't',
+      description: 'Operation type',
+      type: 'string',
+      choices: ['a', 'b', 'c'],
+      default: 'a'
+    }
+  ],
+  subcommands: [
+    { name: 'sub1', description: 'First subcommand' },
+    { name: 'sub2', description: 'Second subcommand' }
+  ],
+  action: async (ctx) => {
+    // Command implementation
+    return { success: true };
+  }
+});
 
-1. **Module Structure**: V3 uses scoped packages (`@claude-flow/*`)
-2. **Memory Backend**: Default changed from JSON to AgentDB with HNSW
-3. **Hooks System**: New ReasoningBank replaces basic pattern storage
-4. **Security**: Stricter input validation enabled by default
+// Parse arguments
+const result = parser.parse(process.argv.slice(2));
 
-### Upgrade Steps
+// Validate flags
+const errors = parser.validateFlags(result.flags, result.command);
 
-```bash
-# 1. Backup existing data
-cp -r ./data ./data-backup-v2
+// Get all registered commands
+const commands = parser.getAllCommands();
+```
 
-# 2. Update to V3
-npm install claude-flow@latest
+### Output Formatting
+
+```typescript
+import { OutputFormatter, output, Progress, Spinner } from '@claude-flow/cli';
+
+// Use the singleton instance
+output.printSuccess('Operation completed');
+output.printError('Something went wrong');
+output.printWarning('Proceed with caution');
+output.printInfo('FYI: This is informational');
+
+// Or create a custom formatter
+const formatter = new OutputFormatter({ color: true });
+
+// Color methods
+formatter.success('Green text');
+formatter.error('Red text');
+formatter.warning('Yellow text');
+formatter.bold('Bold text');
+formatter.dim('Dimmed text');
+formatter.highlight('Highlighted text');
+
+// Structured output
+output.printTable({
+  columns: [
+    { key: 'name', header: 'Name', width: 20 },
+    { key: 'status', header: 'Status', width: 10, align: 'right' }
+  ],
+  data: [
+    { name: 'Agent 1', status: 'active' },
+    { name: 'Agent 2', status: 'idle' }
+  ]
+});
+
+output.printJson({ key: 'value' });
+output.printList(['Item 1', 'Item 2', 'Item 3']);
+output.printBox('Content here', 'Title');
+output.progressBar(50, 100, 40); // 50% of 100, width 40
+
+// Progress indication
+const spinner = new Spinner('Loading...');
+spinner.start();
+// ... do work
+spinner.succeed('Completed');
+
+const progress = new Progress({ total: 100 });
+progress.update(50); // 50%
+progress.finish();
+```
 
-# 3. Run migration
-npx claude-flow@v3alpha migrate --from v2
+### Interactive Prompts
+
+```typescript
+import { text, select, confirm, input, multiSelect } from '@claude-flow/cli';
+
+// Text input
+const name = await text('Enter your name:');
+
+// Selection
+const choice = await select({
+  message: 'Choose option:',
+  options: [
+    { label: 'Option A', value: 'A', hint: 'First option' },
+    { label: 'Option B', value: 'B', hint: 'Second option' },
+  ],
+  default: 'A'
+});
+
+// Confirmation
+const confirmed = await confirm({
+  message: 'Continue?',
+  default: false
+});
+
+// Input with validation
+const email = await input({
+  message: 'Enter email:',
+  validate: (v) => v.includes('@') || 'Invalid email'
+});
+
+// Multi-select
+const features = await multiSelect({
+  message: 'Select features:',
+  options: [
+    { label: 'Feature A', value: 'a' },
+    { label: 'Feature B', value: 'b' },
+    { label: 'Feature C', value: 'c' },
+  ]
+});
+```
 
-# 4. Verify installation
-npx claude-flow@v3alpha --version
-npx claude-flow@v3alpha hooks metrics
+## TypeScript Types
+
+```typescript
+import type {
+  // Command types
+  Command,
+  CommandOption,
+  CommandContext,
+  CommandResult,
+
+  // Parser types
+  ParseResult,
+  ParsedFlags,
+  ParserOptions,
+
+  // Config types
+  V3Config,
+  ProviderConfig,
+  SwarmConfig,
+  MemoryConfig,
+
+  // Output types
+  TableColumn,
+  TableOptions,
+  SpinnerOptions,
+  ProgressOptions,
+
+  // Prompt types
+  SelectOption,
+  InputOptions,
+  ConfirmOptions,
+} from '@claude-flow/cli';
 ```
 
-### Configuration Changes
+## Environment Variables
 
 ```bash
-# V2 (deprecated)
-npx claude-flow init --mode basic
-
-# V3 (new)
-npx claude-flow@v3alpha init
-npx claude-flow@v3alpha hooks pretrain  # Bootstrap learning
+# Configuration
+CLAUDE_FLOW_CONFIG=./claude-flow.config.json
+CLAUDE_FLOW_LOG_LEVEL=info
+
+# Provider API Keys
+ANTHROPIC_API_KEY=sk-ant-...
+OPENAI_API_KEY=sk-...
+GOOGLE_API_KEY=...
+
+# MCP Server
+CLAUDE_FLOW_MCP_PORT=3000
+CLAUDE_FLOW_MCP_HOST=localhost
+CLAUDE_FLOW_MCP_TRANSPORT=stdio
+
+# Memory
+CLAUDE_FLOW_MEMORY_BACKEND=hybrid
+CLAUDE_FLOW_MEMORY_PATH=./data/memory
 ```
 
-### API Changes
+## Performance Targets
 
-| V2 API | V3 API |
-|--------|--------|
-| `claude-flow start` | `claude-flow mcp start` |
-| `--pattern-store` | `--memory-backend agentdb` |
-| `hooks record` | `hooks post-edit --success` |
-| `swarm create` | `swarm init --topology` |
+The CLI is optimized for V3 performance targets:
 
----
+| Metric | Target | Description |
+|--------|--------|-------------|
+| Startup | <500ms | CLI initialization time |
+| Command parsing | <5ms | Argument parsing time |
+| MCP tool execution | <100ms | Tool call overhead |
+| Memory search | 150x-12,500x faster | With HNSW indexing |
+| SONA adaptation | <0.05ms | Neural learning overhead |
+
+## Related Packages
 
-## Documentation
-
-### V3 Module Documentation
-
-| Module | Description | Docs |
-|--------|-------------|------|
-| `@claude-flow/plugins` | Plugin SDK with workers, hooks, providers, security | [README](./v3/@claude-flow/plugins/README.md) |
-| `@claude-flow/hooks` | Event-driven lifecycle hooks + ReasoningBank | [Source](./v3/@claude-flow/hooks/) |
-| `@claude-flow/memory` | AgentDB unification with HNSW indexing | [Source](./v3/@claude-flow/memory/) |
-| `@claude-flow/security` | CVE remediation & security patterns | [Source](./v3/@claude-flow/security/) |
-| `@claude-flow/swarm` | 15-agent coordination engine | [Source](./v3/@claude-flow/swarm/) |
-| `@claude-flow/cli` | CLI modernization | [Source](./v3/@claude-flow/cli/) |
-| `@claude-flow/neural` | SONA learning integration | [Source](./v3/@claude-flow/neural/) |
-| `@claude-flow/testing` | TDD London School framework | [Source](./v3/@claude-flow/testing/) |
-| `@claude-flow/mcp` | MCP server & tools | [Source](./v3/@claude-flow/mcp/) |
-| `@claude-flow/embeddings` | Vector embedding providers | [Source](./v3/@claude-flow/embeddings/) |
-| `@claude-flow/providers` | LLM provider integrations | [Source](./v3/@claude-flow/providers/) |
-| `@claude-flow/integration` | agentic-flow@alpha integration | [Source](./v3/@claude-flow/integration/) |
-| `@claude-flow/performance` | Benchmarking & optimization | [Source](./v3/@claude-flow/performance/) |
-| `@claude-flow/deployment` | Release & CI/CD | [Source](./v3/@claude-flow/deployment/) |
-| `@claude-flow/shared` | Shared utilities & types | [Source](./v3/@claude-flow/shared/) |
-
-### Additional Resources
-
-- [V2 Documentation](./v2/README.md)
-- [Architecture Decisions (ADRs)](./v3/docs/adr/)
-- [API Reference](./v2/docs/technical/)
-- [Examples](./v2/examples/)
-
-## Support
-
-- Documentation: https://github.com/ruvnet/claude-flow
-- Issues: https://github.com/ruvnet/claude-flow/issues
-- Discord: [Agentics Foundation](https://discord.com/invite/dfxmpwkG2D)
+- [@claude-flow/shared](../shared) - Shared types and utilities
+- [@claude-flow/swarm](../swarm) - Swarm coordination module
+- [@claude-flow/memory](../memory) - AgentDB memory system
+- [@claude-flow/mcp](../mcp) - MCP server implementation
+- [@claude-flow/hooks](../hooks) - Self-learning hooks system
+- [@claude-flow/neural](../neural) - SONA neural learning
 
 ## License
 
-MIT - [RuvNet](https://github.com/ruvnet)
+MIT