@claude-flow/cli 3.7.0-alpha.1 → 3.7.0-alpha.10

package/dist/src/init/executor.js

@@ -686,6 +686,51 @@ async function writeSettings(targetDir, options, result) {
     fs.writeFileSync(settingsPath, JSON.stringify(generated, null, 2), 'utf-8');
     result.created.files.push('.claude/settings.json');
 }
+/**
+ * #1779 — Walk parents of `targetDir` plus the user-global Claude Code
+ * config locations, looking for any `.mcp.json` (or `~/.claude.json`)
+ * that already declares a `ruflo`-keyed MCP server. We use this to skip
+ * writing our own `claude-flow`-keyed entry when the user has already
+ * registered the same binary under the new name — that's exactly the
+ * "same MCP server twice under two different prefixes" duplication the
+ * issue describes.
+ *
+ * Returns the path of the file that already declares `ruflo` (so we can
+ * surface it in the skipped-message), or null if none found.
+ */
+function detectExistingRufloMCP(targetDir) {
+    const home = (process.env.HOME ?? process.env.USERPROFILE) ?? '';
+    const candidates = new Set();
+    // User-global Claude Code config locations
+    if (home) {
+        candidates.add(path.join(home, '.claude.json'));
+        candidates.add(path.join(home, '.claude', 'mcp.json'));
+    }
+    // Walk parents of targetDir up to root, checking for .mcp.json at each
+    let dir = path.resolve(targetDir);
+    while (true) {
+        candidates.add(path.join(dir, '.mcp.json'));
+        const parent = path.dirname(dir);
+        if (parent === dir)
+            break;
+        dir = parent;
+    }
+    // Skip the targetDir itself — that's the one we're about to write
+    candidates.delete(path.join(path.resolve(targetDir), '.mcp.json'));
+    for (const candidate of candidates) {
+        if (!fs.existsSync(candidate))
+            continue;
+        try {
+            const parsed = JSON.parse(fs.readFileSync(candidate, 'utf-8'));
+            if (parsed && typeof parsed === 'object' && parsed.mcpServers && typeof parsed.mcpServers === 'object') {
+                if ('ruflo' in parsed.mcpServers)
+                    return candidate;
+            }
+        }
+        catch { /* malformed JSON — ignore */ }
+    }
+    return null;
+}
 /**
  * Write .mcp.json
  */
@@ -695,6 +740,19 @@ async function writeMCPConfig(targetDir, options, result) {
         result.skipped.push('.mcp.json');
         return;
     }
+    // #1779 — Skip writing if the user already has a `ruflo`-keyed MCP
+    // server registered elsewhere (parent .mcp.json, ~/.claude.json, etc).
+    // Writing our `claude-flow`-keyed entry on top of that produces the
+    // duplicate-registration the issue describes (~250 duplicate tools).
+    // Force-mode (`--force`) bypasses this guard for users who actually
+    // want both registrations.
+    if (!options.force) {
+        const existingRufloPath = detectExistingRufloMCP(targetDir);
+        if (existingRufloPath) {
+            result.skipped.push(`.mcp.json (existing 'ruflo' MCP registration found at ${existingRufloPath} — would create duplicate; pass --force to write anyway)`);
+            return;
+        }
+    }
     const content = generateMCPJson(options);
     fs.writeFileSync(mcpPath, content, 'utf-8');
     result.created.files.push('.mcp.json');
@@ -1060,61 +1118,61 @@ async function writeRuntimeConfig(targetDir, options, result) {
         result.skipped.push('.claude-flow/config.yaml');
         return;
     }
-    const config = `# RuFlo V3 Runtime Configuration
-# Generated: ${new Date().toISOString()}
-
-version: "3.0.0"
-
-swarm:
-  topology: ${options.runtime.topology}
-  maxAgents: ${options.runtime.maxAgents}
-  autoScale: true
-  coordinationStrategy: consensus
-
-memory:
-  backend: ${options.runtime.memoryBackend}
-  enableHNSW: ${options.runtime.enableHNSW}
-  persistPath: .claude-flow/data
-  cacheSize: 100
-  # ADR-049: Self-Learning Memory
-  learningBridge:
-    enabled: ${options.runtime.enableLearningBridge ?? options.runtime.enableNeural}
-    sonaMode: balanced
-    confidenceDecayRate: 0.005
-    accessBoostAmount: 0.03
-    consolidationThreshold: 10
-  memoryGraph:
-    enabled: ${options.runtime.enableMemoryGraph ?? true}
-    pageRankDamping: 0.85
-    maxNodes: 5000
-    similarityThreshold: 0.8
-  agentScopes:
-    enabled: ${options.runtime.enableAgentScopes ?? true}
-    defaultScope: project
-
-neural:
-  enabled: ${options.runtime.enableNeural}
-  modelPath: .claude-flow/neural
-
-hooks:
-  enabled: true
-  autoExecute: true
-
-mcp:
-  autoStart: ${options.mcp.autoStart}
-  port: ${options.mcp.port}
+    const config = `# RuFlo V3 Runtime Configuration
+# Generated: ${new Date().toISOString()}
+
+version: "3.0.0"
+
+swarm:
+  topology: ${options.runtime.topology}
+  maxAgents: ${options.runtime.maxAgents}
+  autoScale: true
+  coordinationStrategy: consensus
+
+memory:
+  backend: ${options.runtime.memoryBackend}
+  enableHNSW: ${options.runtime.enableHNSW}
+  persistPath: .claude-flow/data
+  cacheSize: 100
+  # ADR-049: Self-Learning Memory
+  learningBridge:
+    enabled: ${options.runtime.enableLearningBridge ?? options.runtime.enableNeural}
+    sonaMode: balanced
+    confidenceDecayRate: 0.005
+    accessBoostAmount: 0.03
+    consolidationThreshold: 10
+  memoryGraph:
+    enabled: ${options.runtime.enableMemoryGraph ?? true}
+    pageRankDamping: 0.85
+    maxNodes: 5000
+    similarityThreshold: 0.8
+  agentScopes:
+    enabled: ${options.runtime.enableAgentScopes ?? true}
+    defaultScope: project
+
+neural:
+  enabled: ${options.runtime.enableNeural}
+  modelPath: .claude-flow/neural
+
+hooks:
+  enabled: true
+  autoExecute: true
+
+mcp:
+  autoStart: ${options.mcp.autoStart}
+  port: ${options.mcp.port}
 `;
     fs.writeFileSync(configPath, config, 'utf-8');
     result.created.files.push('.claude-flow/config.yaml');
     // Write .gitignore
     const gitignorePath = path.join(targetDir, '.claude-flow', '.gitignore');
-    const gitignore = `# Claude Flow runtime files
-data/
-logs/
-sessions/
-neural/
-*.log
-*.tmp
+    const gitignore = `# Claude Flow runtime files
+data/
+logs/
+sessions/
+neural/
+*.log
+*.tmp
 `;
     if (!fs.existsSync(gitignorePath) || options.force) {
         fs.writeFileSync(gitignorePath, gitignore, 'utf-8');
@@ -1240,409 +1298,409 @@ async function writeCapabilitiesDoc(targetDir, options, result) {
         result.skipped.push('.claude-flow/CAPABILITIES.md');
         return;
     }
-    const capabilities = `# RuFlo V3 - Complete Capabilities Reference
-> Generated: ${new Date().toISOString()}
-> Full documentation: https://github.com/ruvnet/claude-flow
-
-## 📋 Table of Contents
-
-1. [Overview](#overview)
-2. [Swarm Orchestration](#swarm-orchestration)
-3. [Available Agents (60+)](#available-agents)
-4. [CLI Commands (26 Commands, 140+ Subcommands)](#cli-commands)
-5. [Hooks System (27 Hooks + 12 Workers)](#hooks-system)
-6. [Memory & Intelligence (RuVector)](#memory--intelligence)
-7. [Hive-Mind Consensus](#hive-mind-consensus)
-8. [Performance Targets](#performance-targets)
-9. [Integration Ecosystem](#integration-ecosystem)
-
----
-
-## Overview
-
-RuFlo V3 is a domain-driven design architecture for multi-agent AI coordination with:
-
-- **15-Agent Swarm Coordination** with hierarchical and mesh topologies
-- **HNSW Vector Search** - 150x-12,500x faster pattern retrieval
-- **SONA Neural Learning** - Self-optimizing with <0.05ms adaptation
-- **Byzantine Fault Tolerance** - Queen-led consensus mechanisms
-- **MCP Server Integration** - Model Context Protocol support
-
-### Current Configuration
-| Setting | Value |
-|---------|-------|
-| Topology | ${options.runtime.topology} |
-| Max Agents | ${options.runtime.maxAgents} |
-| Memory Backend | ${options.runtime.memoryBackend} |
-| HNSW Indexing | ${options.runtime.enableHNSW ? 'Enabled' : 'Disabled'} |
-| Neural Learning | ${options.runtime.enableNeural ? 'Enabled' : 'Disabled'} |
-| LearningBridge | ${options.runtime.enableLearningBridge ? 'Enabled (SONA + ReasoningBank)' : 'Disabled'} |
-| Knowledge Graph | ${options.runtime.enableMemoryGraph ? 'Enabled (PageRank + Communities)' : 'Disabled'} |
-| Agent Scopes | ${options.runtime.enableAgentScopes ? 'Enabled (project/local/user)' : 'Disabled'} |
-
----
-
-## Swarm Orchestration
-
-### Topologies
-| Topology | Description | Best For |
-|----------|-------------|----------|
-| \`hierarchical\` | Queen controls workers directly | Anti-drift, tight control |
-| \`mesh\` | Fully connected peer network | Distributed tasks |
-| \`hierarchical-mesh\` | V3 hybrid (recommended) | 10+ agents |
-| \`ring\` | Circular communication | Sequential workflows |
-| \`star\` | Central coordinator | Simple coordination |
-| \`adaptive\` | Dynamic based on load | Variable workloads |
-
-### Strategies
-- \`balanced\` - Even distribution across agents
-- \`specialized\` - Clear roles, no overlap (anti-drift)
-- \`adaptive\` - Dynamic task routing
-
-### Quick Commands
-\`\`\`bash
-# Initialize swarm
-npx @claude-flow/cli@latest swarm init --topology hierarchical --max-agents 8 --strategy specialized
-
-# Check status
-npx @claude-flow/cli@latest swarm status
-
-# Monitor activity
-npx @claude-flow/cli@latest swarm monitor
-\`\`\`
-
----
-
-## Available Agents
-
-### Core Development (5)
-\`coder\`, \`reviewer\`, \`tester\`, \`planner\`, \`researcher\`
-
-### V3 Specialized (4)
-\`security-architect\`, \`security-auditor\`, \`memory-specialist\`, \`performance-engineer\`
-
-### Swarm Coordination (5)
-\`hierarchical-coordinator\`, \`mesh-coordinator\`, \`adaptive-coordinator\`, \`collective-intelligence-coordinator\`, \`swarm-memory-manager\`
-
-### Consensus & Distributed (7)
-\`byzantine-coordinator\`, \`raft-manager\`, \`gossip-coordinator\`, \`consensus-builder\`, \`crdt-synchronizer\`, \`quorum-manager\`, \`security-manager\`
-
-### Performance & Optimization (5)
-\`perf-analyzer\`, \`performance-benchmarker\`, \`task-orchestrator\`, \`memory-coordinator\`, \`smart-agent\`
-
-### GitHub & Repository (9)
-\`github-modes\`, \`pr-manager\`, \`code-review-swarm\`, \`issue-tracker\`, \`release-manager\`, \`workflow-automation\`, \`project-board-sync\`, \`repo-architect\`, \`multi-repo-swarm\`
-
-### SPARC Methodology (6)
-\`sparc-coord\`, \`sparc-coder\`, \`specification\`, \`pseudocode\`, \`architecture\`, \`refinement\`
-
-### Specialized Development (8)
-\`backend-dev\`, \`mobile-dev\`, \`ml-developer\`, \`cicd-engineer\`, \`api-docs\`, \`system-architect\`, \`code-analyzer\`, \`base-template-generator\`
-
-### Testing & Validation (2)
-\`tdd-london-swarm\`, \`production-validator\`
-
-### Agent Routing by Task
-| Task Type | Recommended Agents | Topology |
-|-----------|-------------------|----------|
-| Bug Fix | researcher, coder, tester | mesh |
-| New Feature | coordinator, architect, coder, tester, reviewer | hierarchical |
-| Refactoring | architect, coder, reviewer | mesh |
-| Performance | researcher, perf-engineer, coder | hierarchical |
-| Security | security-architect, auditor, reviewer | hierarchical |
-| Docs | researcher, api-docs | mesh |
-
----
-
-## CLI Commands
-
-### Core Commands (12)
-| Command | Subcommands | Description |
-|---------|-------------|-------------|
-| \`init\` | 4 | Project initialization |
-| \`agent\` | 8 | Agent lifecycle management |
-| \`swarm\` | 6 | Multi-agent coordination |
-| \`memory\` | 11 | AgentDB with HNSW search |
-| \`mcp\` | 9 | MCP server management |
-| \`task\` | 6 | Task assignment |
-| \`session\` | 7 | Session persistence |
-| \`config\` | 7 | Configuration |
-| \`status\` | 3 | System monitoring |
-| \`workflow\` | 6 | Workflow templates |
-| \`hooks\` | 17 | Self-learning hooks |
-| \`hive-mind\` | 6 | Consensus coordination |
-
-### Advanced Commands (14)
-| Command | Subcommands | Description |
-|---------|-------------|-------------|
-| \`daemon\` | 5 | Background workers |
-| \`neural\` | 5 | Pattern training |
-| \`security\` | 6 | Security scanning |
-| \`performance\` | 5 | Profiling & benchmarks |
-| \`providers\` | 5 | AI provider config |
-| \`plugins\` | 5 | Plugin management |
-| \`deployment\` | 5 | Deploy management |
-| \`embeddings\` | 4 | Vector embeddings |
-| \`claims\` | 4 | Authorization |
-| \`migrate\` | 5 | V2→V3 migration |
-| \`process\` | 4 | Process management |
-| \`doctor\` | 1 | Health diagnostics |
-| \`completions\` | 4 | Shell completions |
-
-### Example Commands
-\`\`\`bash
-# Initialize
-npx @claude-flow/cli@latest init --wizard
-
-# Spawn agent
-npx @claude-flow/cli@latest agent spawn -t coder --name my-coder
-
-# Memory operations
-npx @claude-flow/cli@latest memory store --key "pattern" --value "data" --namespace patterns
-npx @claude-flow/cli@latest memory search --query "authentication"
-
-# Diagnostics
-npx @claude-flow/cli@latest doctor --fix
-\`\`\`
-
----
-
-## Hooks System
-
-### 27 Available Hooks
-
-#### Core Hooks (6)
-| Hook | Description |
-|------|-------------|
-| \`pre-edit\` | Context before file edits |
-| \`post-edit\` | Record edit outcomes |
-| \`pre-command\` | Risk assessment |
-| \`post-command\` | Command metrics |
-| \`pre-task\` | Task start + agent suggestions |
-| \`post-task\` | Task completion learning |
-
-#### Session Hooks (4)
-| Hook | Description |
-|------|-------------|
-| \`session-start\` | Start/restore session |
-| \`session-end\` | Persist state |
-| \`session-restore\` | Restore previous |
-| \`notify\` | Cross-agent notifications |
-
-#### Intelligence Hooks (5)
-| Hook | Description |
-|------|-------------|
-| \`route\` | Optimal agent routing |
-| \`explain\` | Routing decisions |
-| \`pretrain\` | Bootstrap intelligence |
-| \`build-agents\` | Generate configs |
-| \`transfer\` | Pattern transfer |
-
-#### Coverage Hooks (3)
-| Hook | Description |
-|------|-------------|
-| \`coverage-route\` | Coverage-based routing |
-| \`coverage-suggest\` | Improvement suggestions |
-| \`coverage-gaps\` | Gap analysis |
-
-### 12 Background Workers
-| Worker | Priority | Purpose |
-|--------|----------|---------|
-| \`ultralearn\` | normal | Deep knowledge |
-| \`optimize\` | high | Performance |
-| \`consolidate\` | low | Memory consolidation |
-| \`predict\` | normal | Predictive preload |
-| \`audit\` | critical | Security |
-| \`map\` | normal | Codebase mapping |
-| \`preload\` | low | Resource preload |
-| \`deepdive\` | normal | Deep analysis |
-| \`document\` | normal | Auto-docs |
-| \`refactor\` | normal | Suggestions |
-| \`benchmark\` | normal | Benchmarking |
-| \`testgaps\` | normal | Coverage gaps |
-
----
-
-## Memory & Intelligence
-
-### RuVector Intelligence System
-- **SONA**: Self-Optimizing Neural Architecture (<0.05ms)
-- **MoE**: Mixture of Experts routing
-- **HNSW**: 150x-12,500x faster search
-- **EWC++**: Prevents catastrophic forgetting
-- **Flash Attention**: 2.49x-7.47x speedup
-- **Int8 Quantization**: 3.92x memory reduction
-
-### 4-Step Intelligence Pipeline
-1. **RETRIEVE** - HNSW pattern search
-2. **JUDGE** - Success/failure verdicts
-3. **DISTILL** - LoRA learning extraction
-4. **CONSOLIDATE** - EWC++ preservation
-
-### Self-Learning Memory (ADR-049)
-
-| Component | Status | Description |
-|-----------|--------|-------------|
-| **LearningBridge** | ${options.runtime.enableLearningBridge ? '✅ Enabled' : '⏸ Disabled'} | Connects insights to SONA/ReasoningBank neural pipeline |
-| **MemoryGraph** | ${options.runtime.enableMemoryGraph ? '✅ Enabled' : '⏸ Disabled'} | PageRank knowledge graph + community detection |
-| **AgentMemoryScope** | ${options.runtime.enableAgentScopes ? '✅ Enabled' : '⏸ Disabled'} | 3-scope agent memory (project/local/user) |
-
-**LearningBridge** - Insights trigger learning trajectories. Confidence evolves: +0.03 on access, -0.005/hour decay. Consolidation runs the JUDGE/DISTILL/CONSOLIDATE pipeline.
-
-**MemoryGraph** - Builds a knowledge graph from entry references. PageRank identifies influential insights. Communities group related knowledge. Graph-aware ranking blends vector + structural scores.
-
-**AgentMemoryScope** - Maps Claude Code 3-scope directories:
-- \`project\`: \`<gitRoot>/.claude/agent-memory/<agent>/\`
-- \`local\`: \`<gitRoot>/.claude/agent-memory-local/<agent>/\`
-- \`user\`: \`~/.claude/agent-memory/<agent>/\`
-
-High-confidence insights (>0.8) can transfer between agents.
-
-### Memory Commands
-\`\`\`bash
-# Store pattern
-npx @claude-flow/cli@latest memory store --key "name" --value "data" --namespace patterns
-
-# Semantic search
-npx @claude-flow/cli@latest memory search --query "authentication"
-
-# List entries
-npx @claude-flow/cli@latest memory list --namespace patterns
-
-# Initialize database
-npx @claude-flow/cli@latest memory init --force
-\`\`\`
-
----
-
-## Hive-Mind Consensus
-
-### Queen Types
-| Type | Role |
-|------|------|
-| Strategic Queen | Long-term planning |
-| Tactical Queen | Execution coordination |
-| Adaptive Queen | Dynamic optimization |
-
-### Worker Types (8)
-\`researcher\`, \`coder\`, \`analyst\`, \`tester\`, \`architect\`, \`reviewer\`, \`optimizer\`, \`documenter\`
-
-### Consensus Mechanisms
-| Mechanism | Fault Tolerance | Use Case |
-|-----------|-----------------|----------|
-| \`byzantine\` | f < n/3 faulty | Adversarial |
-| \`raft\` | f < n/2 failed | Leader-based |
-| \`gossip\` | Eventually consistent | Large scale |
-| \`crdt\` | Conflict-free | Distributed |
-| \`quorum\` | Configurable | Flexible |
-
-### Hive-Mind Commands
-\`\`\`bash
-# Initialize
-npx @claude-flow/cli@latest hive-mind init --queen-type strategic
-
-# Status
-npx @claude-flow/cli@latest hive-mind status
-
-# Spawn workers
-npx @claude-flow/cli@latest hive-mind spawn --count 5 --type worker
-
-# Consensus
-npx @claude-flow/cli@latest hive-mind consensus --propose "task"
-\`\`\`
-
----
-
-## Performance Targets
-
-| Metric | Target | Status |
-|--------|--------|--------|
-| HNSW Search | 150x-12,500x faster | ✅ Implemented |
-| Memory Reduction | 50-75% | ✅ Implemented (3.92x) |
-| SONA Integration | Pattern learning | ✅ Implemented |
-| Flash Attention | 2.49x-7.47x | 🔄 In Progress |
-| MCP Response | <100ms | ✅ Achieved |
-| CLI Startup | <500ms | ✅ Achieved |
-| SONA Adaptation | <0.05ms | 🔄 In Progress |
-| Graph Build (1k) | <200ms | ✅ 2.78ms (71.9x headroom) |
-| PageRank (1k) | <100ms | ✅ 12.21ms (8.2x headroom) |
-| Insight Recording | <5ms/each | ✅ 0.12ms (41x headroom) |
-| Consolidation | <500ms | ✅ 0.26ms (1,955x headroom) |
-| Knowledge Transfer | <100ms | ✅ 1.25ms (80x headroom) |
-
----
-
-## Integration Ecosystem
-
-### Integrated Packages
-| Package | Version | Purpose |
-|---------|---------|---------|
-| agentic-flow | 3.0.0-alpha.1 | Core coordination + ReasoningBank + Router |
-| agentdb | 3.0.0-alpha.10 | Vector database + 8 controllers |
-| @ruvector/attention | 0.1.3 | Flash attention |
-| @ruvector/sona | 0.1.5 | Neural learning |
-
-### Optional Integrations
-| Package | Command |
-|---------|---------|
-| ruv-swarm | \`npx ruv-swarm mcp start\` |
-| flow-nexus | \`npx flow-nexus@latest mcp start\` |
-| agentic-jujutsu | \`npx agentic-jujutsu@latest\` |
-
-### MCP Server Setup
-\`\`\`bash
-# Add Ruflo MCP
-claude mcp add ruflo -- npx -y ruflo@latest
-
-# Optional servers
-claude mcp add ruv-swarm -- npx -y ruv-swarm mcp start
-claude mcp add flow-nexus -- npx -y flow-nexus@latest mcp start
-\`\`\`
-
----
-
-## Quick Reference
-
-### Essential Commands
-\`\`\`bash
-# Setup
-npx ruflo@latest init --wizard
-npx ruflo@latest daemon start
-npx ruflo@latest doctor --fix
-
-# Swarm
-npx ruflo@latest swarm init --topology hierarchical --max-agents 8
-npx ruflo@latest swarm status
-
-# Agents
-npx ruflo@latest agent spawn -t coder
-npx ruflo@latest agent list
-
-# Memory
-npx ruflo@latest memory search --query "patterns"
-
-# Hooks
-npx ruflo@latest hooks pre-task --description "task"
-npx ruflo@latest hooks worker dispatch --trigger optimize
-\`\`\`
-
-### File Structure
-\`\`\`
-.claude-flow/
-├── config.yaml      # Runtime configuration
-├── CAPABILITIES.md  # This file
-├── data/            # Memory storage
-├── logs/            # Operation logs
-├── sessions/        # Session state
-├── hooks/           # Custom hooks
-├── agents/          # Agent configs
-└── workflows/       # Workflow templates
-\`\`\`
-
----
-
-**Full Documentation**: https://github.com/ruvnet/claude-flow
-**Issues**: https://github.com/ruvnet/claude-flow/issues
+    const capabilities = `# RuFlo V3 - Complete Capabilities Reference
+> Generated: ${new Date().toISOString()}
+> Full documentation: https://github.com/ruvnet/claude-flow
+
+## 📋 Table of Contents
+
+1. [Overview](#overview)
+2. [Swarm Orchestration](#swarm-orchestration)
+3. [Available Agents (60+)](#available-agents)
+4. [CLI Commands (26 Commands, 140+ Subcommands)](#cli-commands)
+5. [Hooks System (27 Hooks + 12 Workers)](#hooks-system)
+6. [Memory & Intelligence (RuVector)](#memory--intelligence)
+7. [Hive-Mind Consensus](#hive-mind-consensus)
+8. [Performance Targets](#performance-targets)
+9. [Integration Ecosystem](#integration-ecosystem)
+
+---
+
+## Overview
+
+RuFlo V3 is a domain-driven design architecture for multi-agent AI coordination with:
+
+- **15-Agent Swarm Coordination** with hierarchical and mesh topologies
+- **HNSW Vector Search** - 150x-12,500x faster pattern retrieval
+- **SONA Neural Learning** - Self-optimizing with <0.05ms adaptation
+- **Byzantine Fault Tolerance** - Queen-led consensus mechanisms
+- **MCP Server Integration** - Model Context Protocol support
+
+### Current Configuration
+| Setting | Value |
+|---------|-------|
+| Topology | ${options.runtime.topology} |
+| Max Agents | ${options.runtime.maxAgents} |
+| Memory Backend | ${options.runtime.memoryBackend} |
+| HNSW Indexing | ${options.runtime.enableHNSW ? 'Enabled' : 'Disabled'} |
+| Neural Learning | ${options.runtime.enableNeural ? 'Enabled' : 'Disabled'} |
+| LearningBridge | ${options.runtime.enableLearningBridge ? 'Enabled (SONA + ReasoningBank)' : 'Disabled'} |
+| Knowledge Graph | ${options.runtime.enableMemoryGraph ? 'Enabled (PageRank + Communities)' : 'Disabled'} |
+| Agent Scopes | ${options.runtime.enableAgentScopes ? 'Enabled (project/local/user)' : 'Disabled'} |
+
+---
+
+## Swarm Orchestration
+
+### Topologies
+| Topology | Description | Best For |
+|----------|-------------|----------|
+| \`hierarchical\` | Queen controls workers directly | Anti-drift, tight control |
+| \`mesh\` | Fully connected peer network | Distributed tasks |
+| \`hierarchical-mesh\` | V3 hybrid (recommended) | 10+ agents |
+| \`ring\` | Circular communication | Sequential workflows |
+| \`star\` | Central coordinator | Simple coordination |
+| \`adaptive\` | Dynamic based on load | Variable workloads |
+
+### Strategies
+- \`balanced\` - Even distribution across agents
+- \`specialized\` - Clear roles, no overlap (anti-drift)
+- \`adaptive\` - Dynamic task routing
+
+### Quick Commands
+\`\`\`bash
+# Initialize swarm
+npx @claude-flow/cli@latest swarm init --topology hierarchical --max-agents 8 --strategy specialized
+
+# Check status
+npx @claude-flow/cli@latest swarm status
+
+# Monitor activity
+npx @claude-flow/cli@latest swarm monitor
+\`\`\`
+
+---
+
+## Available Agents
+
+### Core Development (5)
+\`coder\`, \`reviewer\`, \`tester\`, \`planner\`, \`researcher\`
+
+### V3 Specialized (4)
+\`security-architect\`, \`security-auditor\`, \`memory-specialist\`, \`performance-engineer\`
+
+### Swarm Coordination (5)
+\`hierarchical-coordinator\`, \`mesh-coordinator\`, \`adaptive-coordinator\`, \`collective-intelligence-coordinator\`, \`swarm-memory-manager\`
+
+### Consensus & Distributed (7)
+\`byzantine-coordinator\`, \`raft-manager\`, \`gossip-coordinator\`, \`consensus-builder\`, \`crdt-synchronizer\`, \`quorum-manager\`, \`security-manager\`
+
+### Performance & Optimization (5)
+\`perf-analyzer\`, \`performance-benchmarker\`, \`task-orchestrator\`, \`memory-coordinator\`, \`smart-agent\`
+
+### GitHub & Repository (9)
+\`github-modes\`, \`pr-manager\`, \`code-review-swarm\`, \`issue-tracker\`, \`release-manager\`, \`workflow-automation\`, \`project-board-sync\`, \`repo-architect\`, \`multi-repo-swarm\`
+
+### SPARC Methodology (6)
+\`sparc-coord\`, \`sparc-coder\`, \`specification\`, \`pseudocode\`, \`architecture\`, \`refinement\`
+
+### Specialized Development (8)
+\`backend-dev\`, \`mobile-dev\`, \`ml-developer\`, \`cicd-engineer\`, \`api-docs\`, \`system-architect\`, \`code-analyzer\`, \`base-template-generator\`
+
+### Testing & Validation (2)
+\`tdd-london-swarm\`, \`production-validator\`
+
+### Agent Routing by Task
+| Task Type | Recommended Agents | Topology |
+|-----------|-------------------|----------|
+| Bug Fix | researcher, coder, tester | mesh |
+| New Feature | coordinator, architect, coder, tester, reviewer | hierarchical |
+| Refactoring | architect, coder, reviewer | mesh |
+| Performance | researcher, perf-engineer, coder | hierarchical |
+| Security | security-architect, auditor, reviewer | hierarchical |
+| Docs | researcher, api-docs | mesh |
+
+---
+
+## CLI Commands
+
+### Core Commands (12)
+| Command | Subcommands | Description |
+|---------|-------------|-------------|
+| \`init\` | 4 | Project initialization |
+| \`agent\` | 8 | Agent lifecycle management |
+| \`swarm\` | 6 | Multi-agent coordination |
+| \`memory\` | 11 | AgentDB with HNSW search |
+| \`mcp\` | 9 | MCP server management |
+| \`task\` | 6 | Task assignment |
+| \`session\` | 7 | Session persistence |
+| \`config\` | 7 | Configuration |
+| \`status\` | 3 | System monitoring |
+| \`workflow\` | 6 | Workflow templates |
+| \`hooks\` | 17 | Self-learning hooks |
+| \`hive-mind\` | 6 | Consensus coordination |
+
+### Advanced Commands (14)
+| Command | Subcommands | Description |
+|---------|-------------|-------------|
+| \`daemon\` | 5 | Background workers |
+| \`neural\` | 5 | Pattern training |
+| \`security\` | 6 | Security scanning |
+| \`performance\` | 5 | Profiling & benchmarks |
+| \`providers\` | 5 | AI provider config |
+| \`plugins\` | 5 | Plugin management |
+| \`deployment\` | 5 | Deploy management |
+| \`embeddings\` | 4 | Vector embeddings |
+| \`claims\` | 4 | Authorization |
+| \`migrate\` | 5 | V2→V3 migration |
+| \`process\` | 4 | Process management |
+| \`doctor\` | 1 | Health diagnostics |
+| \`completions\` | 4 | Shell completions |
+
+### Example Commands
+\`\`\`bash
+# Initialize
+npx @claude-flow/cli@latest init --wizard
+
+# Spawn agent
+npx @claude-flow/cli@latest agent spawn -t coder --name my-coder
+
+# Memory operations
+npx @claude-flow/cli@latest memory store --key "pattern" --value "data" --namespace patterns
+npx @claude-flow/cli@latest memory search --query "authentication"
+
+# Diagnostics
+npx @claude-flow/cli@latest doctor --fix
+\`\`\`
+
+---
+
+## Hooks System
+
+### 27 Available Hooks
+
+#### Core Hooks (6)
+| Hook | Description |
+|------|-------------|
+| \`pre-edit\` | Context before file edits |
+| \`post-edit\` | Record edit outcomes |
+| \`pre-command\` | Risk assessment |
+| \`post-command\` | Command metrics |
+| \`pre-task\` | Task start + agent suggestions |
+| \`post-task\` | Task completion learning |
+
+#### Session Hooks (4)
+| Hook | Description |
+|------|-------------|
+| \`session-start\` | Start/restore session |
+| \`session-end\` | Persist state |
+| \`session-restore\` | Restore previous |
+| \`notify\` | Cross-agent notifications |
+
+#### Intelligence Hooks (5)
+| Hook | Description |
+|------|-------------|
+| \`route\` | Optimal agent routing |
+| \`explain\` | Routing decisions |
+| \`pretrain\` | Bootstrap intelligence |
+| \`build-agents\` | Generate configs |
+| \`transfer\` | Pattern transfer |
+
+#### Coverage Hooks (3)
+| Hook | Description |
+|------|-------------|
+| \`coverage-route\` | Coverage-based routing |
+| \`coverage-suggest\` | Improvement suggestions |
+| \`coverage-gaps\` | Gap analysis |
+
+### 12 Background Workers
+| Worker | Priority | Purpose |
+|--------|----------|---------|
+| \`ultralearn\` | normal | Deep knowledge |
+| \`optimize\` | high | Performance |
+| \`consolidate\` | low | Memory consolidation |
+| \`predict\` | normal | Predictive preload |
+| \`audit\` | critical | Security |
+| \`map\` | normal | Codebase mapping |
+| \`preload\` | low | Resource preload |
+| \`deepdive\` | normal | Deep analysis |
+| \`document\` | normal | Auto-docs |
+| \`refactor\` | normal | Suggestions |
+| \`benchmark\` | normal | Benchmarking |
+| \`testgaps\` | normal | Coverage gaps |
+
+---
+
+## Memory & Intelligence
+
+### RuVector Intelligence System
+- **SONA**: Self-Optimizing Neural Architecture (<0.05ms)
+- **MoE**: Mixture of Experts routing
+- **HNSW**: 150x-12,500x faster search
+- **EWC++**: Prevents catastrophic forgetting
+- **Flash Attention**: 2.49x-7.47x speedup
+- **Int8 Quantization**: 3.92x memory reduction
+
+### 4-Step Intelligence Pipeline
+1. **RETRIEVE** - HNSW pattern search
+2. **JUDGE** - Success/failure verdicts
+3. **DISTILL** - LoRA learning extraction
+4. **CONSOLIDATE** - EWC++ preservation
+
+### Self-Learning Memory (ADR-049)
+
+| Component | Status | Description |
+|-----------|--------|-------------|
+| **LearningBridge** | ${options.runtime.enableLearningBridge ? '✅ Enabled' : '⏸ Disabled'} | Connects insights to SONA/ReasoningBank neural pipeline |
+| **MemoryGraph** | ${options.runtime.enableMemoryGraph ? '✅ Enabled' : '⏸ Disabled'} | PageRank knowledge graph + community detection |
+| **AgentMemoryScope** | ${options.runtime.enableAgentScopes ? '✅ Enabled' : '⏸ Disabled'} | 3-scope agent memory (project/local/user) |
+
+**LearningBridge** - Insights trigger learning trajectories. Confidence evolves: +0.03 on access, -0.005/hour decay. Consolidation runs the JUDGE/DISTILL/CONSOLIDATE pipeline.
+
+**MemoryGraph** - Builds a knowledge graph from entry references. PageRank identifies influential insights. Communities group related knowledge. Graph-aware ranking blends vector + structural scores.
+
+**AgentMemoryScope** - Maps Claude Code 3-scope directories:
+- \`project\`: \`<gitRoot>/.claude/agent-memory/<agent>/\`
+- \`local\`: \`<gitRoot>/.claude/agent-memory-local/<agent>/\`
+- \`user\`: \`~/.claude/agent-memory/<agent>/\`
+
+High-confidence insights (>0.8) can transfer between agents.
+
+### Memory Commands
+\`\`\`bash
+# Store pattern
+npx @claude-flow/cli@latest memory store --key "name" --value "data" --namespace patterns
+
+# Semantic search
+npx @claude-flow/cli@latest memory search --query "authentication"
+
+# List entries
+npx @claude-flow/cli@latest memory list --namespace patterns
+
+# Initialize database
+npx @claude-flow/cli@latest memory init --force
+\`\`\`
+
+---
+
+## Hive-Mind Consensus
+
+### Queen Types
+| Type | Role |
+|------|------|
+| Strategic Queen | Long-term planning |
+| Tactical Queen | Execution coordination |
+| Adaptive Queen | Dynamic optimization |
+
+### Worker Types (8)
+\`researcher\`, \`coder\`, \`analyst\`, \`tester\`, \`architect\`, \`reviewer\`, \`optimizer\`, \`documenter\`
+
+### Consensus Mechanisms
+| Mechanism | Fault Tolerance | Use Case |
+|-----------|-----------------|----------|
+| \`byzantine\` | f < n/3 faulty | Adversarial |
+| \`raft\` | f < n/2 failed | Leader-based |
+| \`gossip\` | Eventually consistent | Large scale |
+| \`crdt\` | Conflict-free | Distributed |
+| \`quorum\` | Configurable | Flexible |
+
+### Hive-Mind Commands
+\`\`\`bash
+# Initialize
+npx @claude-flow/cli@latest hive-mind init --queen-type strategic
+
+# Status
+npx @claude-flow/cli@latest hive-mind status
+
+# Spawn workers
+npx @claude-flow/cli@latest hive-mind spawn --count 5 --type worker
+
+# Consensus
+npx @claude-flow/cli@latest hive-mind consensus --propose "task"
+\`\`\`
+
+---
+
+## Performance Targets
+
+| Metric | Target | Status |
+|--------|--------|--------|
+| HNSW Search | 150x-12,500x faster | ✅ Implemented |
+| Memory Reduction | 50-75% | ✅ Implemented (3.92x) |
+| SONA Integration | Pattern learning | ✅ Implemented |
+| Flash Attention | 2.49x-7.47x | 🔄 In Progress |
+| MCP Response | <100ms | ✅ Achieved |
+| CLI Startup | <500ms | ✅ Achieved |
+| SONA Adaptation | <0.05ms | 🔄 In Progress |
+| Graph Build (1k) | <200ms | ✅ 2.78ms (71.9x headroom) |
+| PageRank (1k) | <100ms | ✅ 12.21ms (8.2x headroom) |
+| Insight Recording | <5ms/each | ✅ 0.12ms (41x headroom) |
+| Consolidation | <500ms | ✅ 0.26ms (1,955x headroom) |
+| Knowledge Transfer | <100ms | ✅ 1.25ms (80x headroom) |
+
+---
+
+## Integration Ecosystem
+
+### Integrated Packages
+| Package | Version | Purpose |
+|---------|---------|---------|
+| agentic-flow | 3.0.0-alpha.1 | Core coordination + ReasoningBank + Router |
+| agentdb | 3.0.0-alpha.10 | Vector database + 8 controllers |
+| @ruvector/attention | 0.1.3 | Flash attention |
+| @ruvector/sona | 0.1.5 | Neural learning |
+
+### Optional Integrations
+| Package | Command |
+|---------|---------|
+| ruv-swarm | \`npx ruv-swarm mcp start\` |
+| flow-nexus | \`npx flow-nexus@latest mcp start\` |
+| agentic-jujutsu | \`npx agentic-jujutsu@latest\` |
+
+### MCP Server Setup
+\`\`\`bash
+# Add Ruflo MCP
+claude mcp add ruflo -- npx -y ruflo@latest
+
+# Optional servers
+claude mcp add ruv-swarm -- npx -y ruv-swarm mcp start
+claude mcp add flow-nexus -- npx -y flow-nexus@latest mcp start
+\`\`\`
+
+---
+
+## Quick Reference
+
+### Essential Commands
+\`\`\`bash
+# Setup
+npx ruflo@latest init --wizard
+npx ruflo@latest daemon start
+npx ruflo@latest doctor --fix
+
+# Swarm
+npx ruflo@latest swarm init --topology hierarchical --max-agents 8
+npx ruflo@latest swarm status
+
+# Agents
+npx ruflo@latest agent spawn -t coder
+npx ruflo@latest agent list
+
+# Memory
+npx ruflo@latest memory search --query "patterns"
+
+# Hooks
+npx ruflo@latest hooks pre-task --description "task"
+npx ruflo@latest hooks worker dispatch --trigger optimize
+\`\`\`
+
+### File Structure
+\`\`\`
+.claude-flow/
+├── config.yaml      # Runtime configuration
+├── CAPABILITIES.md  # This file
+├── data/            # Memory storage
+├── logs/            # Operation logs
+├── sessions/        # Session state
+├── hooks/           # Custom hooks
+├── agents/          # Agent configs
+└── workflows/       # Workflow templates
+\`\`\`
+
+---
+
+**Full Documentation**: https://github.com/ruvnet/claude-flow
+**Issues**: https://github.com/ruvnet/claude-flow/issues
 `;
     fs.writeFileSync(capabilitiesPath, capabilities, 'utf-8');
     result.created.files.push('.claude-flow/CAPABILITIES.md');