@claude-flow/cli 3.42.2 → 3.42.3

package/node_modules/@claude-flow/codex/README.md

@@ -1,1044 +1,1044 @@
-# @claude-flow/codex
-
-<p align="center">
-  <strong>OpenAI Codex CLI Adapter for Claude Flow V3</strong><br/>
-  <em>Self-learning multi-agent orchestration following the <a href="https://agentics.org">Agentics Foundation</a> standard</em>
-</p>
-
-<p align="center">
-  <a href="https://www.npmjs.com/package/@claude-flow/codex"><img src="https://img.shields.io/npm/v/@claude-flow/codex?label=npm&color=blue" alt="npm version"></a>
-  <a href="https://www.npmjs.com/package/@claude-flow/codex"><img src="https://img.shields.io/npm/dm/@claude-flow/codex?label=downloads&color=cb3837" alt="npm downloads"></a>
-  <a href="https://github.com/ruvnet/ruflo"><img src="https://img.shields.io/badge/license-MIT-green" alt="license"></a>
-  <a href="https://agentics.org"><img src="https://img.shields.io/badge/standard-Agentics-purple" alt="Agentics Standard"></a>
-</p>
-
----
-
-## Why @claude-flow/codex?
-
-Transform OpenAI Codex CLI into a **self-improving AI development system**. While Codex executes code, claude-flow orchestrates, coordinates, and **learns from every interaction**.
-
-| Traditional Codex | With Claude-Flow |
-|-------------------|------------------|
-| Stateless execution | Persistent vector memory |
-| Single-agent | Multi-agent swarms (up to 15) |
-| Manual coordination | Automatic orchestration |
-| No learning | Self-learning patterns (HNSW) |
-| One platform | Dual-mode (Claude Code + Codex) |
-
-## Key Concept: Execution Model
-
-```
-┌─────────────────────────────────────────────────────────────────┐
-│  CLAUDE-FLOW = ORCHESTRATOR (tracks state, stores memory)       │
-│  CODEX = EXECUTOR (writes code, runs commands, implements)      │
-└─────────────────────────────────────────────────────────────────┘
-```
-
-**Codex does the work. Claude-flow coordinates and learns.**
-
-### The Self-Learning Loop
-
-```
-    ┌──────────────┐
-    │   SEARCH     │ ──→ Find relevant patterns from past successes
-    │   memory     │
-    └──────┬───────┘
-           │
-    ┌──────▼───────┐
-    │  COORDINATE  │ ──→ Initialize swarm, spawn specialized agents
-    │   swarm      │
-    └──────┬───────┘
-           │
-    ┌──────▼───────┐
-    │   EXECUTE    │ ──→ Codex writes code, runs commands
-    │   codex      │
-    └──────┬───────┘
-           │
-    ┌──────▼───────┐
-    │    STORE     │ ──→ Save successful patterns for future use
-    │   memory     │
-    └──────────────┘
-```
-
-## Quick Start
-
-```bash
-# Initialize for Codex (recommended)
-npx ruflo@latest init --codex
-
-# Full setup with all 137+ skills
-npx ruflo@latest init --codex --full
-
-# Dual mode (both Claude Code and Codex)
-npx ruflo@latest init --dual
-```
-
-**That's it!** The MCP server is auto-registered, skills are installed, and your project is ready for self-learning development.
-
----
-
-<details>
-<summary><b>Features</b></summary>
-
-| Feature | Description |
-|---------|-------------|
-| **AGENTS.md Generation** | Creates project instructions for Codex |
-| **MCP Integration** | Self-learning via memory and vector search |
-| **137+ Skills** | Invoke with `$skill-name` syntax |
-| **Vector Memory** | Semantic pattern search (384-dim embeddings) |
-| **Dual Platform** | Supports both Claude Code and Codex |
-| **Auto-Registration** | MCP server registered during init |
-| **HNSW Search** | 150x-12,500x faster pattern matching |
-| **Self-Learning** | Learn from successes, remember patterns |
-| **GPT-5.3 Support** | Optimized for latest OpenAI models |
-| **Neural Training** | Train patterns with SONA architecture |
-
-</details>
-
----
-
-<details>
-<summary><b>MCP Integration (Self-Learning)</b></summary>
-
-### Automatic Registration
-
-When you run `init --codex`, the MCP server is **automatically registered** with Codex:
-
-```bash
-# Verify MCP is registered
-codex mcp list
-
-# Expected output:
-# Name         Command  Args                   Status
-# claude-flow  npx      claude-flow mcp start  enabled
-```
-
-### Manual Registration
-
-If MCP is not present, add manually:
-
-```bash
-codex mcp add claude-flow -- npx claude-flow mcp start
-```
-
-### MCP Tools Reference
-
-| Tool | Purpose | When to Use |
-|------|---------|-------------|
-| `memory_search` | Semantic vector search | **BEFORE** starting any task |
-| `memory_store` | Save patterns with embeddings | **AFTER** completing successfully |
-| `swarm_init` | Initialize coordination | Start of complex tasks |
-| `agent_spawn` | Register agent roles | Multi-agent workflows |
-| `neural_train` | Train on patterns | Periodic improvement |
-
-### Tool Parameters
-
-**memory_search**
-```json
-{
-  "query": "search terms",
-  "namespace": "patterns",
-  "limit": 5
-}
-```
-
-**memory_store**
-```json
-{
-  "key": "pattern-name",
-  "value": "what worked",
-  "namespace": "patterns",
-  "upsert": true
-}
-```
-
-**swarm_init**
-```json
-{
-  "topology": "hierarchical",
-  "maxAgents": 5,
-  "strategy": "specialized"
-}
-```
-
-</details>
-
----
-
-<details>
-<summary><b>Self-Learning Workflow</b></summary>
-
-### The 4-Step Pattern
-
-```
-1. LEARN:    memory_search(query="task keywords") → Find similar patterns
-2. COORD:    swarm_init(topology="hierarchical") → Set up coordination
-3. EXECUTE:  YOU write code, run commands        → Codex does real work
-4. REMEMBER: memory_store(key, value, upsert=true) → Save for future
-```
-
-### Complete Example Prompt
-
-```
-Build an email validator using a learning-enabled swarm.
-
-STEP 1 - LEARN (use MCP tool):
-Use tool: memory_search
-  query: "validation utility function patterns"
-  namespace: "patterns"
-If score > 0.7, use that pattern as reference.
-
-STEP 2 - COORDINATE (use MCP tools):
-Use tool: swarm_init with topology="hierarchical", maxAgents=3
-Use tool: agent_spawn with type="coder", name="validator"
-
-STEP 3 - EXECUTE (YOU do this - DON'T STOP HERE):
-Create /tmp/validator/email.js with validateEmail() function
-Create /tmp/validator/test.js with test cases
-Run the tests
-
-STEP 4 - REMEMBER (use MCP tool):
-Use tool: memory_store
-  key: "pattern-email-validator"
-  value: "Email validation: regex, returns boolean, test cases"
-  namespace: "patterns"
-  upsert: true
-
-YOU execute all code. MCP tools are for learning only.
-```
-
-### Similarity Score Guide
-
-| Score | Meaning | Action |
-|-------|---------|--------|
-| > 0.7 | Strong match | Use the pattern directly |
-| 0.5 - 0.7 | Partial match | Adapt and modify |
-| < 0.5 | Weak match | Create new approach |
-
-</details>
-
----
-
-<details>
-<summary><b>Directory Structure</b></summary>
-
-```
-project/
-├── AGENTS.md                    # Main project instructions (Codex format)
-├── .agents/
-│   ├── config.toml              # Project configuration
-│   ├── skills/                  # 137+ skills
-│   │   ├── swarm-orchestration/
-│   │   │   └── SKILL.md
-│   │   ├── memory-management/
-│   │   │   └── SKILL.md
-│   │   ├── sparc-methodology/
-│   │   │   └── SKILL.md
-│   │   └── ...
-│   └── README.md                # Directory documentation
-├── .codex/                      # Local overrides (gitignored)
-│   ├── config.toml              # Local development settings
-│   └── AGENTS.override.md       # Local instruction overrides
-└── .claude-flow/                # Runtime data
-    ├── config.yaml              # Runtime configuration
-    ├── data/                    # Memory and cache
-    │   └── memory.db            # SQLite with vector embeddings
-    └── logs/                    # Log files
-```
-
-### Key Files
-
-| File | Purpose |
-|------|---------|
-| `AGENTS.md` | Main instructions for Codex (required) |
-| `.agents/config.toml` | Project-wide configuration |
-| `.codex/config.toml` | Local overrides (gitignored) |
-| `.claude-flow/data/memory.db` | Vector memory database |
-
-</details>
-
----
-
-<details>
-<summary><b>Templates</b></summary>
-
-### Available Templates
-
-| Template | Skills | Learning | Best For |
-|----------|--------|----------|----------|
-| `minimal` | 2 | Basic | Quick prototypes |
-| `default` | 4 | Yes | Standard projects |
-| `full` | 137+ | Yes | Full-featured development |
-| `enterprise` | 137+ | Advanced | Team environments |
-
-### Usage
-
-```bash
-# Minimal (fastest init)
-npx ruflo@latest init --codex --minimal
-
-# Default
-npx ruflo@latest init --codex
-
-# Full (all skills)
-npx ruflo@latest init --codex --full
-```
-
-### Template Contents
-
-**Minimal:**
-- Core swarm orchestration
-- Basic memory management
-
-**Default:**
-- Swarm orchestration
-- Memory management
-- SPARC methodology
-- Basic coding patterns
-
-**Full:**
-- All 137+ skills
-- GitHub integration
-- Security scanning
-- Performance optimization
-- AgentDB vector search
-- Neural pattern training
-
-</details>
-
----
-
-<details>
-<summary><b>Platform Comparison (Claude Code vs Codex)</b></summary>
-
-| Feature | Claude Code | OpenAI Codex |
-|---------|-------------|--------------|
-| Config File | `CLAUDE.md` | `AGENTS.md` |
-| Skills Dir | `.claude/skills/` | `.agents/skills/` |
-| Skill Syntax | `/skill-name` | `$skill-name` |
-| Settings | `settings.json` | `config.toml` |
-| MCP | Native | Via `codex mcp add` |
-| Overrides | `.claude.local.md` | `.codex/config.toml` |
-
-### Dual Mode
-
-Run `init --dual` to set up both platforms:
-
-```bash
-npx ruflo@latest init --dual
-```
-
-This creates:
-- `CLAUDE.md` for Claude Code users
-- `AGENTS.md` for Codex users
-- Shared `.claude-flow/` runtime
-- Cross-compatible skills
-
-</details>
-
----
-
-<details>
-<summary><b>Skill Invocation</b></summary>
-
-### Syntax
-
-In OpenAI Codex CLI, invoke skills with `$` prefix:
-
-```
-$swarm-orchestration
-$memory-management
-$sparc-methodology
-$security-audit
-$agent-coder
-$agent-tester
-$github-workflow
-$performance-optimization
-```
-
-### Complete Skills Table (137+ Skills)
-
-#### V3 Core Skills
-
-| Skill | Syntax | Description |
-|-------|--------|-------------|
-| V3 Security Overhaul | `$v3-security-overhaul` | Complete security architecture with CVE remediation |
-| V3 Memory Unification | `$v3-memory-unification` | Unify 6+ memory systems into AgentDB with HNSW |
-| V3 Integration Deep | `$v3-integration-deep` | Deep agentic-flow integration (ADR-001) |
-| V3 Performance Optimization | `$v3-performance-optimization` | Achieve 2.49x-7.47x speedup targets |
-| V3 Swarm Coordination | `$v3-swarm-coordination` | 15-agent hierarchical mesh coordination |
-| V3 DDD Architecture | `$v3-ddd-architecture` | Domain-Driven Design architecture |
-| V3 Core Implementation | `$v3-core-implementation` | Core module implementation |
-| V3 MCP Optimization | `$v3-mcp-optimization` | MCP server optimization and transport |
-| V3 CLI Modernization | `$v3-cli-modernization` | CLI modernization and hooks enhancement |
-
-#### AgentDB & Memory Skills
-
-| Skill | Syntax | Description |
-|-------|--------|-------------|
-| AgentDB Advanced | `$agentdb-advanced` | Advanced QUIC sync, distributed coordination |
-| AgentDB Memory Patterns | `$agentdb-memory-patterns` | Persistent memory patterns for AI agents |
-| AgentDB Learning | `$agentdb-learning` | AI learning plugins with AgentDB |
-| AgentDB Optimization | `$agentdb-optimization` | Quantization (4-32bit), performance tuning |
-| AgentDB Vector Search | `$agentdb-vector-search` | Semantic vector search with HNSW |
-| ReasoningBank AgentDB | `$reasoningbank-agentdb` | ReasoningBank with AgentDB integration |
-| ReasoningBank Intelligence | `$reasoningbank-intelligence` | Adaptive learning with ReasoningBank |
-
-#### Swarm & Coordination Skills
-
-| Skill | Syntax | Description |
-|-------|--------|-------------|
-| Swarm Orchestration | `$swarm-orchestration` | Multi-agent swarms with agentic-flow |
-| Swarm Advanced | `$swarm-advanced` | Advanced swarm patterns for research/analysis |
-| Hive Mind Advanced | `$hive-mind-advanced` | Collective intelligence system |
-| Stream Chain | `$stream-chain` | Stream-JSON chaining for multi-agent pipelines |
-| Worker Integration | `$worker-integration` | Background worker integration |
-| Worker Benchmarks | `$worker-benchmarks` | Worker performance benchmarks |
-
-#### GitHub Integration Skills
-
-| Skill | Syntax | Description |
-|-------|--------|-------------|
-| GitHub Code Review | `$github-code-review` | AI-powered code review swarms |
-| GitHub Project Management | `$github-project-management` | Swarm-coordinated project management |
-| GitHub Multi-Repo | `$github-multi-repo` | Multi-repository coordination |
-| GitHub Release Management | `$github-release-management` | Release orchestration with AI swarms |
-| GitHub Workflow Automation | `$github-workflow-automation` | GitHub Actions automation |
-
-#### SPARC Methodology Skills (30+)
-
-| Skill | Syntax | Description |
-|-------|--------|-------------|
-| SPARC Methodology | `$sparc-methodology` | Full SPARC workflow orchestration |
-| SPARC Specification | `$sparc:spec-pseudocode` | Capture full project context |
-| SPARC Architecture | `$sparc:architect` | System architecture design |
-| SPARC Coder | `$sparc:coder` | Clean, efficient code generation |
-| SPARC Tester | `$sparc:tester` | Comprehensive testing |
-| SPARC Reviewer | `$sparc:reviewer` | Code review and quality |
-| SPARC Debugger | `$sparc:debugger` | Runtime bug troubleshooting |
-| SPARC Optimizer | `$sparc:optimizer` | Refactor and modularize |
-| SPARC Documenter | `$sparc:documenter` | Documentation generation |
-| SPARC DevOps | `$sparc:devops` | DevOps automation |
-| SPARC Security Review | `$sparc:security-review` | Static/dynamic security analysis |
-| SPARC Integration | `$sparc:integration` | System integration |
-| SPARC MCP | `$sparc:mcp` | MCP integration management |
-
-#### Flow Nexus Skills
-
-| Skill | Syntax | Description |
-|-------|--------|-------------|
-| Flow Nexus Neural | `$flow-nexus-neural` | Neural network training in E2B sandboxes |
-| Flow Nexus Platform | `$flow-nexus-platform` | Platform management and authentication |
-| Flow Nexus Swarm | `$flow-nexus-swarm` | Cloud-based AI swarm deployment |
-| Flow Nexus Payments | `$flow-nexus:payments` | Credit management and billing |
-| Flow Nexus Challenges | `$flow-nexus:challenges` | Coding challenges and achievements |
-| Flow Nexus Sandbox | `$flow-nexus:sandbox` | E2B sandbox management |
-| Flow Nexus App Store | `$flow-nexus:app-store` | App publishing and deployment |
-| Flow Nexus Workflow | `$flow-nexus:workflow` | Event-driven workflow automation |
-
-#### Development Skills
-
-| Skill | Syntax | Description |
-|-------|--------|-------------|
-| Pair Programming | `$pair-programming` | AI-assisted pair programming |
-| Skill Builder | `$skill-builder` | Create new Claude Code Skills |
-| Verification Quality | `$verification-quality` | Truth scoring and quality verification |
-| Performance Analysis | `$performance-analysis` | Bottleneck detection and optimization |
-| Agentic Jujutsu | `$agentic-jujutsu` | Quantum-resistant version control |
-| Hooks Automation | `$hooks-automation` | Automated coordination and learning |
-
-#### Memory Management Skills
-
-| Skill | Syntax | Description |
-|-------|--------|-------------|
-| Memory Neural | `$memory:neural` | Neural pattern training |
-| Memory Usage | `$memory:memory-usage` | Memory usage analysis |
-| Memory Search | `$memory:memory-search` | Semantic memory search |
-| Memory Persist | `$memory:memory-persist` | Memory persistence |
-
-#### Monitoring & Analysis Skills
-
-| Skill | Syntax | Description |
-|-------|--------|-------------|
-| Real-Time View | `$monitoring:real-time-view` | Real-time monitoring |
-| Agent Metrics | `$monitoring:agent-metrics` | Agent performance metrics |
-| Swarm Monitor | `$monitoring:swarm-monitor` | Swarm activity monitoring |
-| Token Usage | `$analysis:token-usage` | Token usage optimization |
-| Performance Report | `$analysis:performance-report` | Performance reporting |
-| Bottleneck Detect | `$analysis:bottleneck-detect` | Bottleneck detection |
-
-#### Training Skills
-
-| Skill | Syntax | Description |
-|-------|--------|-------------|
-| Specialization | `$training:specialization` | Agent specialization training |
-| Neural Patterns | `$training:neural-patterns` | Neural pattern training |
-| Pattern Learn | `$training:pattern-learn` | Pattern learning |
-| Model Update | `$training:model-update` | Model updates |
-
-#### Automation & Optimization Skills
-
-| Skill | Syntax | Description |
-|-------|--------|-------------|
-| Self-Healing | `$automation:self-healing` | Self-healing workflows |
-| Smart Agents | `$automation:smart-agents` | Smart agent auto-spawning |
-| Session Memory | `$automation:session-memory` | Cross-session memory |
-| Cache Manage | `$optimization:cache-manage` | Cache management |
-| Parallel Execute | `$optimization:parallel-execute` | Parallel task execution |
-| Topology Optimize | `$optimization:topology-optimize` | Automatic topology selection |
-
-#### Hooks Skills (17 Hooks + 12 Workers)
-
-| Skill | Syntax | Description |
-|-------|--------|-------------|
-| Pre-Edit | `$hooks:pre-edit` | Context before editing |
-| Post-Edit | `$hooks:post-edit` | Record editing outcome |
-| Pre-Task | `$hooks:pre-task` | Record task start |
-| Post-Task | `$hooks:post-task` | Record task completion |
-| Session End | `$hooks:session-end` | End session and persist |
-
-#### Dual-Mode Skills (NEW)
-
-| Skill | Syntax | Description |
-|-------|--------|-------------|
-| Dual Spawn | `$dual-spawn` | Spawn parallel Codex workers from Claude Code |
-| Dual Coordinate | `$dual-coordinate` | Coordinate Claude Code + Codex execution |
-| Dual Collect | `$dual-collect` | Collect results from parallel Codex instances |
-
-### Custom Skills
-
-Create custom skills in `.agents/skills/`:
-
-```
-.agents/skills/my-skill/
-└── SKILL.md
-```
-
-**SKILL.md format:**
-```markdown
-# My Custom Skill
-
-Instructions for what this skill does...
-
-## Usage
-Invoke with `$my-skill`
-```
-
-</details>
-
----
-
-<details>
-<summary><b>Dual-Mode Integration (Claude Code + Codex)</b></summary>
-
-### Hybrid Execution Model
-
-Run Claude Code for interactive development and spawn headless Codex workers for parallel background tasks:
-
-```
-┌─────────────────────────────────────────────────────────────────┐
-│  CLAUDE CODE (interactive)  ←→  CODEX WORKERS (headless)        │
-│  - Main conversation         - Parallel background execution    │
-│  - Complex reasoning         - Bulk code generation            │
-│  - Architecture decisions    - Test execution                   │
-│  - Final integration         - File processing                  │
-└─────────────────────────────────────────────────────────────────┘
-```
-
-### Setup
-
-```bash
-# Initialize dual-mode
-npx ruflo@latest init --dual
-
-# Creates both:
-# - CLAUDE.md (Claude Code configuration)
-# - AGENTS.md (Codex configuration)
-# - Shared .claude-flow/ runtime
-```
-
-### Spawning Parallel Codex Workers
-
-From Claude Code, spawn headless Codex instances:
-
-```bash
-# Spawn workers in parallel (each runs independently)
-claude -p "Analyze src/auth/ for security issues" --session-id "task-1" &
-claude -p "Write unit tests for src/api/" --session-id "task-2" &
-claude -p "Optimize database queries in src/db/" --session-id "task-3" &
-wait  # Wait for all to complete
-```
-
-### Dual-Mode Skills
-
-| Skill | Platform | Description |
-|-------|----------|-------------|
-| `$dual-spawn` | Codex | Spawn parallel workers from orchestrator |
-| `$dual-coordinate` | Both | Coordinate cross-platform execution |
-| `$dual-collect` | Claude Code | Collect results from Codex workers |
-
-### Dual-Mode Agents
-
-| Agent | Type | Execution |
-|-------|------|-----------|
-| `codex-worker` | Worker | Headless background execution |
-| `codex-coordinator` | Coordinator | Manage parallel worker pool |
-| `dual-orchestrator` | Orchestrator | Route tasks to appropriate platform |
-
-### Task Routing Rules
-
-| Task Complexity | Platform | Reason |
-|----------------|----------|--------|
-| Simple (1-2 files) | Codex Headless | Fast, parallel |
-| Medium (3-5 files) | Claude Code | Needs context |
-| Complex (architecture) | Claude Code | Reasoning required |
-| Bulk operations | Codex Workers | Parallelize |
-| Final review | Claude Code | Integration |
-
-### Example Workflow
-
-```
-1. Claude Code receives complex feature request
-2. Designs architecture and creates plan
-3. Spawns 4 Codex workers:
-   - Worker 1: Implement data models
-   - Worker 2: Create API endpoints
-   - Worker 3: Write unit tests
-   - Worker 4: Generate documentation
-4. Workers execute in parallel (headless)
-5. Claude Code collects and integrates results
-6. Final review and refinement in Claude Code
-```
-
-### Memory Sharing
-
-Both platforms share the same `.claude-flow/` runtime:
-
-```
-.claude-flow/
-├── data/
-│   └── memory.db      # Shared vector memory
-├── config.yaml        # Shared configuration
-└── sessions/          # Cross-platform sessions
-```
-
-### Benefits
-
-| Feature | Benefit |
-|---------|---------|
-| **Parallel Execution** | 4-8x faster for bulk tasks |
-| **Cost Optimization** | Route simple tasks to cheaper workers |
-| **Context Preservation** | Shared memory across platforms |
-| **Best of Both** | Interactive + batch processing |
-| **Unified Learning** | Patterns learned by both platforms |
-
-### CLI Commands (NEW in v3.0.0-alpha.8)
-
-The `@claude-flow/codex` package now includes built-in dual-mode orchestration:
-
-```bash
-# List available collaboration templates
-npx claude-flow-codex dual templates
-
-# Run a feature development swarm
-npx claude-flow-codex dual run --template feature --task "Add user authentication"
-
-# Run a security audit swarm
-npx claude-flow-codex dual run --template security --task "src/auth/"
-
-# Run a refactoring swarm
-npx claude-flow-codex dual run --template refactor --task "src/legacy/"
-
-# Check collaboration status
-npx claude-flow-codex dual status
-```
-
-### Codex Loop Runner
-
-Codex does not expose Claude Code's `ScheduleWakeup`, so `@claude-flow/codex` provides a process-based equivalent:
-
-```bash
-# Run Codex repeatedly until it creates .codex/loop/default.complete or reaches 10 iterations
-npx claude-flow-codex loop run "Fix failing tests and create the completion marker when done"
-
-# Use command mode for recurring Ruflo workers or custom scripts
-npx claude-flow-codex loop run --name testgaps --interval 270 --max-iterations 0 \
-  --command "npx claude-flow hooks worker dispatch --trigger testgaps"
-
-# Inspect or stop a loop from another terminal
-npx claude-flow-codex loop status --name testgaps
-npx claude-flow-codex loop stop --name testgaps
-```
-
-Loop state is stored in `.codex/loop/<name>.json`; `loop stop` writes `.codex/loop/<name>.stop`, which the runner observes between iterations.
-
-### Pre-Built Templates
-
-| Template | Pipeline | Platforms |
-|----------|----------|-----------|
-| **feature** | architect → coder → tester → reviewer | Claude (architect, reviewer) + Codex (coder, tester) |
-| **security** | scanner → analyzer → fixer | Codex (scanner, fixer) + Claude (analyzer) |
-| **refactor** | analyzer → planner → refactorer → validator | Claude (analyzer, planner) + Codex (refactorer, validator) |
-
-### Programmatic API
-
-```typescript
-import { DualModeOrchestrator, CollaborationTemplates } from '@claude-flow/codex';
-
-// Create orchestrator
-const orchestrator = new DualModeOrchestrator({
-  projectPath: process.cwd(),
-  maxConcurrent: 4,
-  sharedNamespace: 'collaboration',
-  timeout: 300000,
-});
-
-// Listen to events
-orchestrator.on('worker:started', ({ id, role }) => console.log(`Started: ${role}`));
-orchestrator.on('worker:completed', ({ id }) => console.log(`Completed: ${id}`));
-
-// Run collaboration with a template
-const workers = CollaborationTemplates.featureDevelopment('Add OAuth2 login');
-const result = await orchestrator.runCollaboration(workers, 'Feature: OAuth2');
-
-console.log(`Success: ${result.success}`);
-console.log(`Duration: ${result.totalDuration}ms`);
-console.log(`Workers: ${result.workers.length}`);
-```
-
-</details>
-
----
-
-<details>
-<summary><b>Configuration</b></summary>
-
-### .agents/config.toml
-
-```toml
-# Model configuration
-model = "gpt-5.3"
-
-# Approval policy: "always" | "on-request" | "never"
-approval_policy = "on-request"
-
-# Sandbox mode: "read-only" | "workspace-write" | "danger-full-access"
-sandbox_mode = "workspace-write"
-
-# Web search: "off" | "cached" | "live"
-web_search = "cached"
-
-# MCP Servers
-[mcp_servers.claude-flow]
-command = "npx"
-args = ["claude-flow", "mcp", "start"]
-enabled = true
-
-# Skills
-[[skills]]
-path = ".agents/skills/swarm-orchestration"
-enabled = true
-
-[[skills]]
-path = ".agents/skills/memory-management"
-enabled = true
-
-[[skills]]
-path = ".agents/skills/sparc-methodology"
-enabled = true
-```
-
-### .codex/config.toml (Local Overrides)
-
-```toml
-# Local development overrides (gitignored)
-# These settings override .agents/config.toml
-
-approval_policy = "never"
-sandbox_mode = "danger-full-access"
-web_search = "live"
-
-# Disable MCP in local if needed
-[mcp_servers.claude-flow]
-enabled = false
-```
-
-### Environment Variables
-
-```bash
-# Configuration paths
-CLAUDE_FLOW_CONFIG=./claude-flow.config.json
-CLAUDE_FLOW_MEMORY_PATH=./.claude-flow/data
-
-# Provider keys
-ANTHROPIC_API_KEY=sk-ant-...
-OPENAI_API_KEY=sk-...
-
-# MCP settings
-CLAUDE_FLOW_MCP_PORT=3000
-```
-
-</details>
-
----
-
-<details>
-<summary><b>Vector Search Details</b></summary>
-
-### Specifications
-
-| Property | Value |
-|----------|-------|
-| Embedding Dimensions | 384 |
-| Search Algorithm | HNSW |
-| Speed Improvement | 150x-12,500x faster |
-| Similarity Range | 0.0 - 1.0 |
-| Storage | SQLite with vector extension |
-| Model | all-MiniLM-L6-v2 |
-
-### Namespaces
-
-| Namespace | Purpose |
-|-----------|---------|
-| `patterns` | Successful code patterns |
-| `solutions` | Bug fixes and solutions |
-| `tasks` | Task completion records |
-| `coordination` | Swarm state |
-| `results` | Worker results |
-| `default` | General storage |
-
-### Example Searches
-
-```javascript
-// Find auth patterns
-memory_search({ query: "authentication JWT patterns", namespace: "patterns" })
-
-// Find bug solutions
-memory_search({ query: "null pointer fix", namespace: "solutions" })
-
-// Find past tasks
-memory_search({ query: "user profile API", namespace: "tasks" })
-```
-
-</details>
-
----
-
-<details>
-<summary><b>API Reference</b></summary>
-
-### CodexInitializer Class
-
-```typescript
-import { CodexInitializer } from '@claude-flow/codex';
-
-class CodexInitializer {
-  /**
-   * Initialize a Codex project
-   */
-  async initialize(options: CodexInitOptions): Promise<CodexInitResult>;
-
-  /**
-   * Preview what would be created without writing files
-   */
-  async dryRun(options: CodexInitOptions): Promise<string[]>;
-}
-```
-
-### initializeCodexProject Function
-
-```typescript
-import { initializeCodexProject } from '@claude-flow/codex';
-
-/**
- * Quick initialization helper
- */
-async function initializeCodexProject(
-  projectPath: string,
-  options?: Partial<CodexInitOptions>
-): Promise<CodexInitResult>;
-```
-
-### Types
-
-```typescript
-interface CodexInitOptions {
-  /** Project directory path */
-  projectPath: string;
-  /** Template to use */
-  template?: 'minimal' | 'default' | 'full' | 'enterprise';
-  /** Specific skills to include */
-  skills?: string[];
-  /** Overwrite existing files */
-  force?: boolean;
-  /** Enable dual mode (Claude Code + Codex) */
-  dual?: boolean;
-}
-
-interface CodexInitResult {
-  /** Whether initialization succeeded */
-  success: boolean;
-  /** List of files created */
-  filesCreated: string[];
-  /** List of skills generated */
-  skillsGenerated: string[];
-  /** Whether MCP was registered */
-  mcpRegistered?: boolean;
-  /** Non-fatal warnings */
-  warnings?: string[];
-  /** Fatal errors */
-  errors?: string[];
-}
-```
-
-### Programmatic Usage
-
-```typescript
-import { CodexInitializer, initializeCodexProject } from '@claude-flow/codex';
-
-// Quick initialization
-const result = await initializeCodexProject('/path/to/project', {
-  template: 'full',
-  force: true,
-  dual: false,
-});
-
-console.log(`Files created: ${result.filesCreated.length}`);
-console.log(`Skills: ${result.skillsGenerated.length}`);
-console.log(`MCP registered: ${result.mcpRegistered}`);
-
-// Or use the class directly
-const initializer = new CodexInitializer();
-const result = await initializer.initialize({
-  projectPath: '/path/to/project',
-  template: 'enterprise',
-  skills: ['swarm-orchestration', 'memory-management', 'security-audit'],
-  force: false,
-  dual: true,
-});
-
-if (result.warnings?.length) {
-  console.warn('Warnings:', result.warnings);
-}
-```
-
-</details>
-
----
-
-<details>
-<summary><b>Migration from Claude Code</b></summary>
-
-### Convert CLAUDE.md to AGENTS.md
-
-```typescript
-import { migrate } from '@claude-flow/codex';
-
-const result = await migrate({
-  sourcePath: './CLAUDE.md',
-  targetPath: './AGENTS.md',
-  preserveComments: true,
-  generateSkills: true,
-});
-
-console.log(`Migrated: ${result.success}`);
-console.log(`Skills generated: ${result.skillsGenerated.length}`);
-```
-
-### Manual Migration Checklist
-
-1. **Rename config file**: `CLAUDE.md` → `AGENTS.md`
-2. **Move skills**: `.claude/skills/` → `.agents/skills/`
-3. **Update syntax**: `/skill-name` → `$skill-name`
-4. **Convert settings**: `settings.json` → `config.toml`
-5. **Register MCP**: `codex mcp add claude-flow -- npx claude-flow mcp start`
-
-### Dual Mode Alternative
-
-Instead of migrating, use dual mode to support both:
-
-```bash
-npx ruflo@latest init --dual
-```
-
-This keeps both `CLAUDE.md` and `AGENTS.md` in sync.
-
-</details>
-
----
-
-<details>
-<summary><b>Troubleshooting</b></summary>
-
-### MCP Not Working
-
-```bash
-# Check if registered
-codex mcp list
-
-# Re-register
-codex mcp remove claude-flow
-codex mcp add claude-flow -- npx claude-flow mcp start
-
-# Test connection
-npx claude-flow mcp test
-```
-
-### Memory Search Returns Empty
-
-```bash
-# Initialize memory database
-npx claude-flow memory init --force
-
-# Check if entries exist
-npx claude-flow memory list
-
-# Manually add a test pattern
-npx claude-flow memory store --key "test" --value "test pattern" --namespace patterns
-```
-
-### Skills Not Loading
-
-```bash
-# Verify skill directory
-ls -la .agents/skills/
-
-# Check config.toml for skill registration
-cat .agents/config.toml | grep skills
-
-# Rebuild skills
-npx ruflo@latest init --codex --force
-```
-
-### Vector Search Slow
-
-```bash
-# Check HNSW index
-npx claude-flow memory stats
-
-# Rebuild index
-npx claude-flow memory optimize --rebuild-index
-```
-
-</details>
-
----
-
-## Related Packages
-
-| Package | Description |
-|---------|-------------|
-| [@claude-flow/cli](https://www.npmjs.com/package/@claude-flow/cli) | Main CLI (26 commands, 140+ subcommands) |
-| [claude-flow](https://www.npmjs.com/package/claude-flow) | Umbrella package |
-| [@claude-flow/memory](https://www.npmjs.com/package/@claude-flow/memory) | AgentDB with HNSW vector search |
-| [@claude-flow/security](https://www.npmjs.com/package/@claude-flow/security) | Security module |
-
-## License
-
-MIT
-
-## Support
-
-- Documentation: https://github.com/ruvnet/ruflo
-- Issues: https://github.com/ruvnet/ruflo/issues
+# @claude-flow/codex
+
+<p align="center">
+  <strong>OpenAI Codex CLI Adapter for Claude Flow V3</strong><br/>
+  <em>Self-learning multi-agent orchestration following the <a href="https://agentics.org">Agentics Foundation</a> standard</em>
+</p>
+
+<p align="center">
+  <a href="https://www.npmjs.com/package/@claude-flow/codex"><img src="https://img.shields.io/npm/v/@claude-flow/codex?label=npm&color=blue" alt="npm version"></a>
+  <a href="https://www.npmjs.com/package/@claude-flow/codex"><img src="https://img.shields.io/npm/dm/@claude-flow/codex?label=downloads&color=cb3837" alt="npm downloads"></a>
+  <a href="https://github.com/ruvnet/ruflo"><img src="https://img.shields.io/badge/license-MIT-green" alt="license"></a>
+  <a href="https://agentics.org"><img src="https://img.shields.io/badge/standard-Agentics-purple" alt="Agentics Standard"></a>
+</p>
+
+---
+
+## Why @claude-flow/codex?
+
+Transform OpenAI Codex CLI into a **self-improving AI development system**. While Codex executes code, claude-flow orchestrates, coordinates, and **learns from every interaction**.
+
+| Traditional Codex | With Claude-Flow |
+|-------------------|------------------|
+| Stateless execution | Persistent vector memory |
+| Single-agent | Multi-agent swarms (up to 15) |
+| Manual coordination | Automatic orchestration |
+| No learning | Self-learning patterns (HNSW) |
+| One platform | Dual-mode (Claude Code + Codex) |
+
+## Key Concept: Execution Model
+
+```
+┌─────────────────────────────────────────────────────────────────┐
+│  CLAUDE-FLOW = ORCHESTRATOR (tracks state, stores memory)       │
+│  CODEX = EXECUTOR (writes code, runs commands, implements)      │
+└─────────────────────────────────────────────────────────────────┘
+```
+
+**Codex does the work. Claude-flow coordinates and learns.**
+
+### The Self-Learning Loop
+
+```
+    ┌──────────────┐
+    │   SEARCH     │ ──→ Find relevant patterns from past successes
+    │   memory     │
+    └──────┬───────┘
+           │
+    ┌──────▼───────┐
+    │  COORDINATE  │ ──→ Initialize swarm, spawn specialized agents
+    │   swarm      │
+    └──────┬───────┘
+           │
+    ┌──────▼───────┐
+    │   EXECUTE    │ ──→ Codex writes code, runs commands
+    │   codex      │
+    └──────┬───────┘
+           │
+    ┌──────▼───────┐
+    │    STORE     │ ──→ Save successful patterns for future use
+    │   memory     │
+    └──────────────┘
+```
+
+## Quick Start
+
+```bash
+# Initialize for Codex (recommended)
+npx ruflo@latest init --codex
+
+# Full setup with all 137+ skills
+npx ruflo@latest init --codex --full
+
+# Dual mode (both Claude Code and Codex)
+npx ruflo@latest init --dual
+```
+
+**That's it!** The MCP server is auto-registered, skills are installed, and your project is ready for self-learning development.
+
+---
+
+<details>
+<summary><b>Features</b></summary>
+
+| Feature | Description |
+|---------|-------------|
+| **AGENTS.md Generation** | Creates project instructions for Codex |
+| **MCP Integration** | Self-learning via memory and vector search |
+| **137+ Skills** | Invoke with `$skill-name` syntax |
+| **Vector Memory** | Semantic pattern search (384-dim embeddings) |
+| **Dual Platform** | Supports both Claude Code and Codex |
+| **Auto-Registration** | MCP server registered during init |
+| **HNSW Search** | 150x-12,500x faster pattern matching |
+| **Self-Learning** | Learn from successes, remember patterns |
+| **GPT-5.3 Support** | Optimized for latest OpenAI models |
+| **Neural Training** | Train patterns with SONA architecture |
+
+</details>
+
+---
+
+<details>
+<summary><b>MCP Integration (Self-Learning)</b></summary>
+
+### Automatic Registration
+
+When you run `init --codex`, the MCP server is **automatically registered** with Codex:
+
+```bash
+# Verify MCP is registered
+codex mcp list
+
+# Expected output:
+# Name         Command  Args                   Status
+# claude-flow  npx      claude-flow mcp start  enabled
+```
+
+### Manual Registration
+
+If MCP is not present, add manually:
+
+```bash
+codex mcp add claude-flow -- npx claude-flow mcp start
+```
+
+### MCP Tools Reference
+
+| Tool | Purpose | When to Use |
+|------|---------|-------------|
+| `memory_search` | Semantic vector search | **BEFORE** starting any task |
+| `memory_store` | Save patterns with embeddings | **AFTER** completing successfully |
+| `swarm_init` | Initialize coordination | Start of complex tasks |
+| `agent_spawn` | Register agent roles | Multi-agent workflows |
+| `neural_train` | Train on patterns | Periodic improvement |
+
+### Tool Parameters
+
+**memory_search**
+```json
+{
+  "query": "search terms",
+  "namespace": "patterns",
+  "limit": 5
+}
+```
+
+**memory_store**
+```json
+{
+  "key": "pattern-name",
+  "value": "what worked",
+  "namespace": "patterns",
+  "upsert": true
+}
+```
+
+**swarm_init**
+```json
+{
+  "topology": "hierarchical",
+  "maxAgents": 5,
+  "strategy": "specialized"
+}
+```
+
+</details>
+
+---
+
+<details>
+<summary><b>Self-Learning Workflow</b></summary>
+
+### The 4-Step Pattern
+
+```
+1. LEARN:    memory_search(query="task keywords") → Find similar patterns
+2. COORD:    swarm_init(topology="hierarchical") → Set up coordination
+3. EXECUTE:  YOU write code, run commands        → Codex does real work
+4. REMEMBER: memory_store(key, value, upsert=true) → Save for future
+```
+
+### Complete Example Prompt
+
+```
+Build an email validator using a learning-enabled swarm.
+
+STEP 1 - LEARN (use MCP tool):
+Use tool: memory_search
+  query: "validation utility function patterns"
+  namespace: "patterns"
+If score > 0.7, use that pattern as reference.
+
+STEP 2 - COORDINATE (use MCP tools):
+Use tool: swarm_init with topology="hierarchical", maxAgents=3
+Use tool: agent_spawn with type="coder", name="validator"
+
+STEP 3 - EXECUTE (YOU do this - DON'T STOP HERE):
+Create /tmp/validator/email.js with validateEmail() function
+Create /tmp/validator/test.js with test cases
+Run the tests
+
+STEP 4 - REMEMBER (use MCP tool):
+Use tool: memory_store
+  key: "pattern-email-validator"
+  value: "Email validation: regex, returns boolean, test cases"
+  namespace: "patterns"
+  upsert: true
+
+YOU execute all code. MCP tools are for learning only.
+```
+
+### Similarity Score Guide
+
+| Score | Meaning | Action |
+|-------|---------|--------|
+| > 0.7 | Strong match | Use the pattern directly |
+| 0.5 - 0.7 | Partial match | Adapt and modify |
+| < 0.5 | Weak match | Create new approach |
+
+</details>
+
+---
+
+<details>
+<summary><b>Directory Structure</b></summary>
+
+```
+project/
+├── AGENTS.md                    # Main project instructions (Codex format)
+├── .agents/
+│   ├── config.toml              # Project configuration
+│   ├── skills/                  # 137+ skills
+│   │   ├── swarm-orchestration/
+│   │   │   └── SKILL.md
+│   │   ├── memory-management/
+│   │   │   └── SKILL.md
+│   │   ├── sparc-methodology/
+│   │   │   └── SKILL.md
+│   │   └── ...
+│   └── README.md                # Directory documentation
+├── .codex/                      # Local overrides (gitignored)
+│   ├── config.toml              # Local development settings
+│   └── AGENTS.override.md       # Local instruction overrides
+└── .claude-flow/                # Runtime data
+    ├── config.yaml              # Runtime configuration
+    ├── data/                    # Memory and cache
+    │   └── memory.db            # SQLite with vector embeddings
+    └── logs/                    # Log files
+```
+
+### Key Files
+
+| File | Purpose |
+|------|---------|
+| `AGENTS.md` | Main instructions for Codex (required) |
+| `.agents/config.toml` | Project-wide configuration |
+| `.codex/config.toml` | Local overrides (gitignored) |
+| `.claude-flow/data/memory.db` | Vector memory database |
+
+</details>
+
+---
+
+<details>
+<summary><b>Templates</b></summary>
+
+### Available Templates
+
+| Template | Skills | Learning | Best For |
+|----------|--------|----------|----------|
+| `minimal` | 2 | Basic | Quick prototypes |
+| `default` | 4 | Yes | Standard projects |
+| `full` | 137+ | Yes | Full-featured development |
+| `enterprise` | 137+ | Advanced | Team environments |
+
+### Usage
+
+```bash
+# Minimal (fastest init)
+npx ruflo@latest init --codex --minimal
+
+# Default
+npx ruflo@latest init --codex
+
+# Full (all skills)
+npx ruflo@latest init --codex --full
+```
+
+### Template Contents
+
+**Minimal:**
+- Core swarm orchestration
+- Basic memory management
+
+**Default:**
+- Swarm orchestration
+- Memory management
+- SPARC methodology
+- Basic coding patterns
+
+**Full:**
+- All 137+ skills
+- GitHub integration
+- Security scanning
+- Performance optimization
+- AgentDB vector search
+- Neural pattern training
+
+</details>
+
+---
+
+<details>
+<summary><b>Platform Comparison (Claude Code vs Codex)</b></summary>
+
+| Feature | Claude Code | OpenAI Codex |
+|---------|-------------|--------------|
+| Config File | `CLAUDE.md` | `AGENTS.md` |
+| Skills Dir | `.claude/skills/` | `.agents/skills/` |
+| Skill Syntax | `/skill-name` | `$skill-name` |
+| Settings | `settings.json` | `config.toml` |
+| MCP | Native | Via `codex mcp add` |
+| Overrides | `.claude.local.md` | `.codex/config.toml` |
+
+### Dual Mode
+
+Run `init --dual` to set up both platforms:
+
+```bash
+npx ruflo@latest init --dual
+```
+
+This creates:
+- `CLAUDE.md` for Claude Code users
+- `AGENTS.md` for Codex users
+- Shared `.claude-flow/` runtime
+- Cross-compatible skills
+
+</details>
+
+---
+
+<details>
+<summary><b>Skill Invocation</b></summary>
+
+### Syntax
+
+In OpenAI Codex CLI, invoke skills with `$` prefix:
+
+```
+$swarm-orchestration
+$memory-management
+$sparc-methodology
+$security-audit
+$agent-coder
+$agent-tester
+$github-workflow
+$performance-optimization
+```
+
+### Complete Skills Table (137+ Skills)
+
+#### V3 Core Skills
+
+| Skill | Syntax | Description |
+|-------|--------|-------------|
+| V3 Security Overhaul | `$v3-security-overhaul` | Complete security architecture with CVE remediation |
+| V3 Memory Unification | `$v3-memory-unification` | Unify 6+ memory systems into AgentDB with HNSW |
+| V3 Integration Deep | `$v3-integration-deep` | Deep agentic-flow integration (ADR-001) |
+| V3 Performance Optimization | `$v3-performance-optimization` | Achieve 2.49x-7.47x speedup targets |
+| V3 Swarm Coordination | `$v3-swarm-coordination` | 15-agent hierarchical mesh coordination |
+| V3 DDD Architecture | `$v3-ddd-architecture` | Domain-Driven Design architecture |
+| V3 Core Implementation | `$v3-core-implementation` | Core module implementation |
+| V3 MCP Optimization | `$v3-mcp-optimization` | MCP server optimization and transport |
+| V3 CLI Modernization | `$v3-cli-modernization` | CLI modernization and hooks enhancement |
+
+#### AgentDB & Memory Skills
+
+| Skill | Syntax | Description |
+|-------|--------|-------------|
+| AgentDB Advanced | `$agentdb-advanced` | Advanced QUIC sync, distributed coordination |
+| AgentDB Memory Patterns | `$agentdb-memory-patterns` | Persistent memory patterns for AI agents |
+| AgentDB Learning | `$agentdb-learning` | AI learning plugins with AgentDB |
+| AgentDB Optimization | `$agentdb-optimization` | Quantization (4-32bit), performance tuning |
+| AgentDB Vector Search | `$agentdb-vector-search` | Semantic vector search with HNSW |
+| ReasoningBank AgentDB | `$reasoningbank-agentdb` | ReasoningBank with AgentDB integration |
+| ReasoningBank Intelligence | `$reasoningbank-intelligence` | Adaptive learning with ReasoningBank |
+
+#### Swarm & Coordination Skills
+
+| Skill | Syntax | Description |
+|-------|--------|-------------|
+| Swarm Orchestration | `$swarm-orchestration` | Multi-agent swarms with agentic-flow |
+| Swarm Advanced | `$swarm-advanced` | Advanced swarm patterns for research/analysis |
+| Hive Mind Advanced | `$hive-mind-advanced` | Collective intelligence system |
+| Stream Chain | `$stream-chain` | Stream-JSON chaining for multi-agent pipelines |
+| Worker Integration | `$worker-integration` | Background worker integration |
+| Worker Benchmarks | `$worker-benchmarks` | Worker performance benchmarks |
+
+#### GitHub Integration Skills
+
+| Skill | Syntax | Description |
+|-------|--------|-------------|
+| GitHub Code Review | `$github-code-review` | AI-powered code review swarms |
+| GitHub Project Management | `$github-project-management` | Swarm-coordinated project management |
+| GitHub Multi-Repo | `$github-multi-repo` | Multi-repository coordination |
+| GitHub Release Management | `$github-release-management` | Release orchestration with AI swarms |
+| GitHub Workflow Automation | `$github-workflow-automation` | GitHub Actions automation |
+
+#### SPARC Methodology Skills (30+)
+
+| Skill | Syntax | Description |
+|-------|--------|-------------|
+| SPARC Methodology | `$sparc-methodology` | Full SPARC workflow orchestration |
+| SPARC Specification | `$sparc:spec-pseudocode` | Capture full project context |
+| SPARC Architecture | `$sparc:architect` | System architecture design |
+| SPARC Coder | `$sparc:coder` | Clean, efficient code generation |
+| SPARC Tester | `$sparc:tester` | Comprehensive testing |
+| SPARC Reviewer | `$sparc:reviewer` | Code review and quality |
+| SPARC Debugger | `$sparc:debugger` | Runtime bug troubleshooting |
+| SPARC Optimizer | `$sparc:optimizer` | Refactor and modularize |
+| SPARC Documenter | `$sparc:documenter` | Documentation generation |
+| SPARC DevOps | `$sparc:devops` | DevOps automation |
+| SPARC Security Review | `$sparc:security-review` | Static/dynamic security analysis |
+| SPARC Integration | `$sparc:integration` | System integration |
+| SPARC MCP | `$sparc:mcp` | MCP integration management |
+
+#### Flow Nexus Skills
+
+| Skill | Syntax | Description |
+|-------|--------|-------------|
+| Flow Nexus Neural | `$flow-nexus-neural` | Neural network training in E2B sandboxes |
+| Flow Nexus Platform | `$flow-nexus-platform` | Platform management and authentication |
+| Flow Nexus Swarm | `$flow-nexus-swarm` | Cloud-based AI swarm deployment |
+| Flow Nexus Payments | `$flow-nexus:payments` | Credit management and billing |
+| Flow Nexus Challenges | `$flow-nexus:challenges` | Coding challenges and achievements |
+| Flow Nexus Sandbox | `$flow-nexus:sandbox` | E2B sandbox management |
+| Flow Nexus App Store | `$flow-nexus:app-store` | App publishing and deployment |
+| Flow Nexus Workflow | `$flow-nexus:workflow` | Event-driven workflow automation |
+
+#### Development Skills
+
+| Skill | Syntax | Description |
+|-------|--------|-------------|
+| Pair Programming | `$pair-programming` | AI-assisted pair programming |
+| Skill Builder | `$skill-builder` | Create new Claude Code Skills |
+| Verification Quality | `$verification-quality` | Truth scoring and quality verification |
+| Performance Analysis | `$performance-analysis` | Bottleneck detection and optimization |
+| Agentic Jujutsu | `$agentic-jujutsu` | Quantum-resistant version control |
+| Hooks Automation | `$hooks-automation` | Automated coordination and learning |
+
+#### Memory Management Skills
+
+| Skill | Syntax | Description |
+|-------|--------|-------------|
+| Memory Neural | `$memory:neural` | Neural pattern training |
+| Memory Usage | `$memory:memory-usage` | Memory usage analysis |
+| Memory Search | `$memory:memory-search` | Semantic memory search |
+| Memory Persist | `$memory:memory-persist` | Memory persistence |
+
+#### Monitoring & Analysis Skills
+
+| Skill | Syntax | Description |
+|-------|--------|-------------|
+| Real-Time View | `$monitoring:real-time-view` | Real-time monitoring |
+| Agent Metrics | `$monitoring:agent-metrics` | Agent performance metrics |
+| Swarm Monitor | `$monitoring:swarm-monitor` | Swarm activity monitoring |
+| Token Usage | `$analysis:token-usage` | Token usage optimization |
+| Performance Report | `$analysis:performance-report` | Performance reporting |
+| Bottleneck Detect | `$analysis:bottleneck-detect` | Bottleneck detection |
+
+#### Training Skills
+
+| Skill | Syntax | Description |
+|-------|--------|-------------|
+| Specialization | `$training:specialization` | Agent specialization training |
+| Neural Patterns | `$training:neural-patterns` | Neural pattern training |
+| Pattern Learn | `$training:pattern-learn` | Pattern learning |
+| Model Update | `$training:model-update` | Model updates |
+
+#### Automation & Optimization Skills
+
+| Skill | Syntax | Description |
+|-------|--------|-------------|
+| Self-Healing | `$automation:self-healing` | Self-healing workflows |
+| Smart Agents | `$automation:smart-agents` | Smart agent auto-spawning |
+| Session Memory | `$automation:session-memory` | Cross-session memory |
+| Cache Manage | `$optimization:cache-manage` | Cache management |
+| Parallel Execute | `$optimization:parallel-execute` | Parallel task execution |
+| Topology Optimize | `$optimization:topology-optimize` | Automatic topology selection |
+
+#### Hooks Skills (17 Hooks + 12 Workers)
+
+| Skill | Syntax | Description |
+|-------|--------|-------------|
+| Pre-Edit | `$hooks:pre-edit` | Context before editing |
+| Post-Edit | `$hooks:post-edit` | Record editing outcome |
+| Pre-Task | `$hooks:pre-task` | Record task start |
+| Post-Task | `$hooks:post-task` | Record task completion |
+| Session End | `$hooks:session-end` | End session and persist |
+
+#### Dual-Mode Skills (NEW)
+
+| Skill | Syntax | Description |
+|-------|--------|-------------|
+| Dual Spawn | `$dual-spawn` | Spawn parallel Codex workers from Claude Code |
+| Dual Coordinate | `$dual-coordinate` | Coordinate Claude Code + Codex execution |
+| Dual Collect | `$dual-collect` | Collect results from parallel Codex instances |
+
+### Custom Skills
+
+Create custom skills in `.agents/skills/`:
+
+```
+.agents/skills/my-skill/
+└── SKILL.md
+```
+
+**SKILL.md format:**
+```markdown
+# My Custom Skill
+
+Instructions for what this skill does...
+
+## Usage
+Invoke with `$my-skill`
+```
+
+</details>
+
+---
+
+<details>
+<summary><b>Dual-Mode Integration (Claude Code + Codex)</b></summary>
+
+### Hybrid Execution Model
+
+Run Claude Code for interactive development and spawn headless Codex workers for parallel background tasks:
+
+```
+┌─────────────────────────────────────────────────────────────────┐
+│  CLAUDE CODE (interactive)  ←→  CODEX WORKERS (headless)        │
+│  - Main conversation         - Parallel background execution    │
+│  - Complex reasoning         - Bulk code generation            │
+│  - Architecture decisions    - Test execution                   │
+│  - Final integration         - File processing                  │
+└─────────────────────────────────────────────────────────────────┘
+```
+
+### Setup
+
+```bash
+# Initialize dual-mode
+npx ruflo@latest init --dual
+
+# Creates both:
+# - CLAUDE.md (Claude Code configuration)
+# - AGENTS.md (Codex configuration)
+# - Shared .claude-flow/ runtime
+```
+
+### Spawning Parallel Codex Workers
+
+From Claude Code, spawn headless Codex instances:
+
+```bash
+# Spawn workers in parallel (each runs independently)
+claude -p "Analyze src/auth/ for security issues" --session-id "task-1" &
+claude -p "Write unit tests for src/api/" --session-id "task-2" &
+claude -p "Optimize database queries in src/db/" --session-id "task-3" &
+wait  # Wait for all to complete
+```
+
+### Dual-Mode Skills
+
+| Skill | Platform | Description |
+|-------|----------|-------------|
+| `$dual-spawn` | Codex | Spawn parallel workers from orchestrator |
+| `$dual-coordinate` | Both | Coordinate cross-platform execution |
+| `$dual-collect` | Claude Code | Collect results from Codex workers |
+
+### Dual-Mode Agents
+
+| Agent | Type | Execution |
+|-------|------|-----------|
+| `codex-worker` | Worker | Headless background execution |
+| `codex-coordinator` | Coordinator | Manage parallel worker pool |
+| `dual-orchestrator` | Orchestrator | Route tasks to appropriate platform |
+
+### Task Routing Rules
+
+| Task Complexity | Platform | Reason |
+|----------------|----------|--------|
+| Simple (1-2 files) | Codex Headless | Fast, parallel |
+| Medium (3-5 files) | Claude Code | Needs context |
+| Complex (architecture) | Claude Code | Reasoning required |
+| Bulk operations | Codex Workers | Parallelize |
+| Final review | Claude Code | Integration |
+
+### Example Workflow
+
+```
+1. Claude Code receives complex feature request
+2. Designs architecture and creates plan
+3. Spawns 4 Codex workers:
+   - Worker 1: Implement data models
+   - Worker 2: Create API endpoints
+   - Worker 3: Write unit tests
+   - Worker 4: Generate documentation
+4. Workers execute in parallel (headless)
+5. Claude Code collects and integrates results
+6. Final review and refinement in Claude Code
+```
+
+### Memory Sharing
+
+Both platforms share the same `.claude-flow/` runtime:
+
+```
+.claude-flow/
+├── data/
+│   └── memory.db      # Shared vector memory
+├── config.yaml        # Shared configuration
+└── sessions/          # Cross-platform sessions
+```
+
+### Benefits
+
+| Feature | Benefit |
+|---------|---------|
+| **Parallel Execution** | 4-8x faster for bulk tasks |
+| **Cost Optimization** | Route simple tasks to cheaper workers |
+| **Context Preservation** | Shared memory across platforms |
+| **Best of Both** | Interactive + batch processing |
+| **Unified Learning** | Patterns learned by both platforms |
+
+### CLI Commands (NEW in v3.0.0-alpha.8)
+
+The `@claude-flow/codex` package now includes built-in dual-mode orchestration:
+
+```bash
+# List available collaboration templates
+npx claude-flow-codex dual templates
+
+# Run a feature development swarm
+npx claude-flow-codex dual run --template feature --task "Add user authentication"
+
+# Run a security audit swarm
+npx claude-flow-codex dual run --template security --task "src/auth/"
+
+# Run a refactoring swarm
+npx claude-flow-codex dual run --template refactor --task "src/legacy/"
+
+# Check collaboration status
+npx claude-flow-codex dual status
+```
+
+### Codex Loop Runner
+
+Codex does not expose Claude Code's `ScheduleWakeup`, so `@claude-flow/codex` provides a process-based equivalent:
+
+```bash
+# Run Codex repeatedly until it creates .codex/loop/default.complete or reaches 10 iterations
+npx claude-flow-codex loop run "Fix failing tests and create the completion marker when done"
+
+# Use command mode for recurring Ruflo workers or custom scripts
+npx claude-flow-codex loop run --name testgaps --interval 270 --max-iterations 0 \
+  --command "npx claude-flow hooks worker dispatch --trigger testgaps"
+
+# Inspect or stop a loop from another terminal
+npx claude-flow-codex loop status --name testgaps
+npx claude-flow-codex loop stop --name testgaps
+```
+
+Loop state is stored in `.codex/loop/<name>.json`; `loop stop` writes `.codex/loop/<name>.stop`, which the runner observes between iterations.
+
+### Pre-Built Templates
+
+| Template | Pipeline | Platforms |
+|----------|----------|-----------|
+| **feature** | architect → coder → tester → reviewer | Claude (architect, reviewer) + Codex (coder, tester) |
+| **security** | scanner → analyzer → fixer | Codex (scanner, fixer) + Claude (analyzer) |
+| **refactor** | analyzer → planner → refactorer → validator | Claude (analyzer, planner) + Codex (refactorer, validator) |
+
+### Programmatic API
+
+```typescript
+import { DualModeOrchestrator, CollaborationTemplates } from '@claude-flow/codex';
+
+// Create orchestrator
+const orchestrator = new DualModeOrchestrator({
+  projectPath: process.cwd(),
+  maxConcurrent: 4,
+  sharedNamespace: 'collaboration',
+  timeout: 300000,
+});
+
+// Listen to events
+orchestrator.on('worker:started', ({ id, role }) => console.log(`Started: ${role}`));
+orchestrator.on('worker:completed', ({ id }) => console.log(`Completed: ${id}`));
+
+// Run collaboration with a template
+const workers = CollaborationTemplates.featureDevelopment('Add OAuth2 login');
+const result = await orchestrator.runCollaboration(workers, 'Feature: OAuth2');
+
+console.log(`Success: ${result.success}`);
+console.log(`Duration: ${result.totalDuration}ms`);
+console.log(`Workers: ${result.workers.length}`);
+```
+
+</details>
+
+---
+
+<details>
+<summary><b>Configuration</b></summary>
+
+### .agents/config.toml
+
+```toml
+# Model configuration
+model = "gpt-5.3"
+
+# Approval policy: "always" | "on-request" | "never"
+approval_policy = "on-request"
+
+# Sandbox mode: "read-only" | "workspace-write" | "danger-full-access"
+sandbox_mode = "workspace-write"
+
+# Web search: "off" | "cached" | "live"
+web_search = "cached"
+
+# MCP Servers
+[mcp_servers.claude-flow]
+command = "npx"
+args = ["claude-flow", "mcp", "start"]
+enabled = true
+
+# Skills
+[[skills]]
+path = ".agents/skills/swarm-orchestration"
+enabled = true
+
+[[skills]]
+path = ".agents/skills/memory-management"
+enabled = true
+
+[[skills]]
+path = ".agents/skills/sparc-methodology"
+enabled = true
+```
+
+### .codex/config.toml (Local Overrides)
+
+```toml
+# Local development overrides (gitignored)
+# These settings override .agents/config.toml
+
+approval_policy = "never"
+sandbox_mode = "danger-full-access"
+web_search = "live"
+
+# Disable MCP in local if needed
+[mcp_servers.claude-flow]
+enabled = false
+```
+
+### Environment Variables
+
+```bash
+# Configuration paths
+CLAUDE_FLOW_CONFIG=./claude-flow.config.json
+CLAUDE_FLOW_MEMORY_PATH=./.claude-flow/data
+
+# Provider keys
+ANTHROPIC_API_KEY=sk-ant-...
+OPENAI_API_KEY=sk-...
+
+# MCP settings
+CLAUDE_FLOW_MCP_PORT=3000
+```
+
+</details>
+
+---
+
+<details>
+<summary><b>Vector Search Details</b></summary>
+
+### Specifications
+
+| Property | Value |
+|----------|-------|
+| Embedding Dimensions | 384 |
+| Search Algorithm | HNSW |
+| Speed Improvement | 150x-12,500x faster |
+| Similarity Range | 0.0 - 1.0 |
+| Storage | SQLite with vector extension |
+| Model | all-MiniLM-L6-v2 |
+
+### Namespaces
+
+| Namespace | Purpose |
+|-----------|---------|
+| `patterns` | Successful code patterns |
+| `solutions` | Bug fixes and solutions |
+| `tasks` | Task completion records |
+| `coordination` | Swarm state |
+| `results` | Worker results |
+| `default` | General storage |
+
+### Example Searches
+
+```javascript
+// Find auth patterns
+memory_search({ query: "authentication JWT patterns", namespace: "patterns" })
+
+// Find bug solutions
+memory_search({ query: "null pointer fix", namespace: "solutions" })
+
+// Find past tasks
+memory_search({ query: "user profile API", namespace: "tasks" })
+```
+
+</details>
+
+---
+
+<details>
+<summary><b>API Reference</b></summary>
+
+### CodexInitializer Class
+
+```typescript
+import { CodexInitializer } from '@claude-flow/codex';
+
+class CodexInitializer {
+  /**
+   * Initialize a Codex project
+   */
+  async initialize(options: CodexInitOptions): Promise<CodexInitResult>;
+
+  /**
+   * Preview what would be created without writing files
+   */
+  async dryRun(options: CodexInitOptions): Promise<string[]>;
+}
+```
+
+### initializeCodexProject Function
+
+```typescript
+import { initializeCodexProject } from '@claude-flow/codex';
+
+/**
+ * Quick initialization helper
+ */
+async function initializeCodexProject(
+  projectPath: string,
+  options?: Partial<CodexInitOptions>
+): Promise<CodexInitResult>;
+```
+
+### Types
+
+```typescript
+interface CodexInitOptions {
+  /** Project directory path */
+  projectPath: string;
+  /** Template to use */
+  template?: 'minimal' | 'default' | 'full' | 'enterprise';
+  /** Specific skills to include */
+  skills?: string[];
+  /** Overwrite existing files */
+  force?: boolean;
+  /** Enable dual mode (Claude Code + Codex) */
+  dual?: boolean;
+}
+
+interface CodexInitResult {
+  /** Whether initialization succeeded */
+  success: boolean;
+  /** List of files created */
+  filesCreated: string[];
+  /** List of skills generated */
+  skillsGenerated: string[];
+  /** Whether MCP was registered */
+  mcpRegistered?: boolean;
+  /** Non-fatal warnings */
+  warnings?: string[];
+  /** Fatal errors */
+  errors?: string[];
+}
+```
+
+### Programmatic Usage
+
+```typescript
+import { CodexInitializer, initializeCodexProject } from '@claude-flow/codex';
+
+// Quick initialization
+const result = await initializeCodexProject('/path/to/project', {
+  template: 'full',
+  force: true,
+  dual: false,
+});
+
+console.log(`Files created: ${result.filesCreated.length}`);
+console.log(`Skills: ${result.skillsGenerated.length}`);
+console.log(`MCP registered: ${result.mcpRegistered}`);
+
+// Or use the class directly
+const initializer = new CodexInitializer();
+const result = await initializer.initialize({
+  projectPath: '/path/to/project',
+  template: 'enterprise',
+  skills: ['swarm-orchestration', 'memory-management', 'security-audit'],
+  force: false,
+  dual: true,
+});
+
+if (result.warnings?.length) {
+  console.warn('Warnings:', result.warnings);
+}
+```
+
+</details>
+
+---
+
+<details>
+<summary><b>Migration from Claude Code</b></summary>
+
+### Convert CLAUDE.md to AGENTS.md
+
+```typescript
+import { migrate } from '@claude-flow/codex';
+
+const result = await migrate({
+  sourcePath: './CLAUDE.md',
+  targetPath: './AGENTS.md',
+  preserveComments: true,
+  generateSkills: true,
+});
+
+console.log(`Migrated: ${result.success}`);
+console.log(`Skills generated: ${result.skillsGenerated.length}`);
+```
+
+### Manual Migration Checklist
+
+1. **Rename config file**: `CLAUDE.md` → `AGENTS.md`
+2. **Move skills**: `.claude/skills/` → `.agents/skills/`
+3. **Update syntax**: `/skill-name` → `$skill-name`
+4. **Convert settings**: `settings.json` → `config.toml`
+5. **Register MCP**: `codex mcp add claude-flow -- npx claude-flow mcp start`
+
+### Dual Mode Alternative
+
+Instead of migrating, use dual mode to support both:
+
+```bash
+npx ruflo@latest init --dual
+```
+
+This keeps both `CLAUDE.md` and `AGENTS.md` in sync.
+
+</details>
+
+---
+
+<details>
+<summary><b>Troubleshooting</b></summary>
+
+### MCP Not Working
+
+```bash
+# Check if registered
+codex mcp list
+
+# Re-register
+codex mcp remove claude-flow
+codex mcp add claude-flow -- npx claude-flow mcp start
+
+# Test connection
+npx claude-flow mcp test
+```
+
+### Memory Search Returns Empty
+
+```bash
+# Initialize memory database
+npx claude-flow memory init --force
+
+# Check if entries exist
+npx claude-flow memory list
+
+# Manually add a test pattern
+npx claude-flow memory store --key "test" --value "test pattern" --namespace patterns
+```
+
+### Skills Not Loading
+
+```bash
+# Verify skill directory
+ls -la .agents/skills/
+
+# Check config.toml for skill registration
+cat .agents/config.toml | grep skills
+
+# Rebuild skills
+npx ruflo@latest init --codex --force
+```
+
+### Vector Search Slow
+
+```bash
+# Check HNSW index
+npx claude-flow memory stats
+
+# Rebuild index
+npx claude-flow memory optimize --rebuild-index
+```
+
+</details>
+
+---
+
+## Related Packages
+
+| Package | Description |
+|---------|-------------|
+| [@claude-flow/cli](https://www.npmjs.com/package/@claude-flow/cli) | Main CLI (26 commands, 140+ subcommands) |
+| [claude-flow](https://www.npmjs.com/package/claude-flow) | Umbrella package |
+| [@claude-flow/memory](https://www.npmjs.com/package/@claude-flow/memory) | AgentDB with HNSW vector search |
+| [@claude-flow/security](https://www.npmjs.com/package/@claude-flow/security) | Security module |
+
+## License
+
+MIT
+
+## Support
+
+- Documentation: https://github.com/ruvnet/ruflo
+- Issues: https://github.com/ruvnet/ruflo/issues