@weavelogic/knowledge-graph-agent 0.4.0 → 0.6.0

package/README.md

@@ -5,15 +5,17 @@ A powerful NPM library for creating and managing knowledge graphs for Claude Cod
 [![npm version](https://img.shields.io/npm/v/@weavelogic/knowledge-graph-agent.svg)](https://www.npmjs.com/package/@weavelogic/knowledge-graph-agent)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
-## Features at a Glance
-
-| Phase | Feature Area | Description |
-|-------|--------------|-------------|
-| 1 | Cultivation System | Codebase analysis, seed generation, deep analysis |
-| 2 | Core Features | Agent system, rules engine, workflows, MCP server |
-| 3 | Advanced Integration | Service management, config migrations, health monitoring |
-| 4 | Enterprise Features | Chunking, backup/recovery, advanced caching, diagnostics |
-| 5 | External Integrations | Workflow DevKit, RuVector semantic search, Exochain audit trail |
+## Features
+
+| Category | Features |
+|----------|----------|
+| **Core** | Knowledge graph generation, Obsidian integration, CLAUDE.md management |
+| **Cultivation** | Codebase analysis, seed generation, deep analysis with claude-flow |
+| **Agents** | Multi-agent system, rules engine, workflows, MCP server with 30+ tools |
+| **Services** | Service management, config migrations, health monitoring |
+| **Enterprise** | Chunking, backup/recovery, advanced caching, diagnostics |
+| **Integrations** | Workflow DevKit, RuVector semantic search, Exochain audit trail |
+| **API & UI** | Plugin system, GraphQL API, Web dashboard, concurrent servers |
 
 ## Installation
 
@@ -39,13 +41,13 @@ kg init-primitives
 # Generate knowledge graph
 kg graph
 
-# Start MCP server for Claude integration
-kg mcp start
+# Start all servers (MCP, GraphQL, Dashboard)
+kg serve --all
 ```
 
 ---
 
-## Phase 1: Cultivation System
+## Cultivation System
 
 ### SeedGenerator
 
@@ -97,21 +99,9 @@ const changed = await cache.getChangedFiles('/project/docs');
 console.log(`${changed.length} files changed since last sync`);
 ```
 
-### CLI Commands (Phase 1)
-
-| Command | Description |
-|---------|-------------|
-| `kg init-primitives` | Bootstrap primitives from codebase analysis |
-| `kg init-primitives --dry-run` | Preview without writing files |
-| `kg analyze-codebase` | Analyze dependencies and services |
-| `kg cultivate` | Run cultivation pipeline |
-| `kg cultivate --deep` | Deep analysis with agents |
-
 ---
 
-## Phase 2: Core Features
-
-### Agent System
+## Agent System
 
 A comprehensive agent framework with specialized agents for different tasks.
 
@@ -149,18 +139,8 @@ const result = await agent.execute(task);
 console.log(result.data);
 ```
 
-**BaseAgent Features:**
-- Task execution with timeout and retry handling
-- Input validation
-- Output formatting
-- Error handling and logging
-- Claude-flow hooks integration
-- Message passing between agents
-
 ### RulesEngine for Automation
 
-Define and execute automation rules based on triggers and conditions.
-
 ```typescript
 import { RulesEngine, RuleType, TriggerType } from '@weavelogic/knowledge-graph-agent';
 
@@ -180,8 +160,6 @@ engine.start();
 
 ### Workflow Registry
 
-Multi-step workflow orchestration with dependencies.
-
 ```typescript
 import { WorkflowRegistry } from '@weavelogic/knowledge-graph-agent';
 
@@ -200,258 +178,276 @@ registry.register({
 await registry.execute('documentation-sync', { projectRoot: '/project' });
 ```
 
-### VaultMemorySync
+---
 
-Synchronize knowledge graph with claude-flow memory.
+## Plugin System
 
-```typescript
-import { VaultMemorySync } from '@weavelogic/knowledge-graph-agent';
+Extensible plugin architecture for custom analyzers with 13 lifecycle hooks.
 
-const sync = new VaultMemorySync({
-  vaultPath: '/project/docs',
-  namespace: 'knowledge-graph',
-});
-
-await sync.syncAll();
-```
+### Built-in Plugins
 
-### Git Integration
+| Plugin | Description |
+|--------|-------------|
+| `code-complexity` | Cyclomatic, cognitive, and Halstead complexity metrics |
+| `dependency-health` | Vulnerability scanning, outdated detection, health scores |
 
-Automatic commit message generation and staged changes analysis.
+### Plugin CLI
 
 ```bash
-# Show status with suggested commit message
-kg commit
+# List installed plugins
+kg plugin list
 
-# Auto-commit with generated message
-kg commit -a
+# Install a plugin
+kg plugin install <source>
 
-# Interactive commit mode
-kg commit -i
+# Run an analyzer
+kg plugin run code-complexity src/index.ts
 
-# Show recent commits
-kg commit log
+# Show plugin details
+kg plugin info dependency-health
+
+# Create a plugin from template
+kg plugin create my-analyzer
 ```
 
+### Custom Plugin Development
+
 ```typescript
-import { analyzeGitChanges, generateCommitMessage } from '@weavelogic/knowledge-graph-agent';
+import { AnalyzerPlugin, PluginContext } from '@weavelogic/knowledge-graph-agent';
+
+export class MyAnalyzerPlugin implements AnalyzerPlugin {
+  name = 'my-analyzer';
+  version = '1.0.0';
+  supportedContentTypes = ['text/typescript', 'text/javascript'];
+
+  async analyze(input: AnalysisInput): Promise<AnalysisResult> {
+    // Analysis logic
+    return {
+      success: true,
+      analysisType: 'my-analyzer',
+      entities: [...],
+      relationships: [...],
+      tags: [...],
+    };
+  }
 
-const changes = await analyzeGitChanges('/project');
-const message = generateCommitMessage(changes);
-console.log(message);
+  // Streaming support
+  async *analyzeStream(input: AnalysisInput): AsyncIterable<AnalysisStreamChunk> {
+    yield { type: 'progress', progress: 50 };
+    yield { type: 'entity', data: { id: '...', type: '...' } };
+    yield { type: 'complete', data: { message: 'Done' } };
+  }
+}
 ```
 
-### MCP Server with 30+ Tools
+---
 
-Model Context Protocol server for Claude integration.
+## GraphQL API
 
-```bash
-# Start MCP server
-kg mcp start
+Full-featured GraphQL API with real-time subscriptions.
 
-# Or via npx
-npx @weavelogic/knowledge-graph-agent mcp start
-```
+### Start GraphQL Server
 
-**Available MCP Tools:**
-
-| Category | Tools |
-|----------|-------|
-| Graph | `kg_query`, `kg_stats`, `kg_get_node`, `kg_list_tags` |
-| Cache | `kg_cache_stats` |
-| Agents | `kg_agent_spawn`, `kg_agent_list` |
-| System | `kg_health`, `kg_health_check` |
-| Search | `kg_search_nodes`, `kg_search_tags` |
-| Workflow | `kg_workflow_start`, `kg_workflow_status`, `kg_workflow_list` |
-| Vector | `kg_vector_search`, `kg_vector_upsert` |
-| Trajectory | `kg_trajectory_list` |
-| Audit | `kg_audit_query`, `kg_audit_checkpoint` |
-| Sync | `kg_sync_status` |
+```bash
+# Start GraphQL server on port 4000
+kg serve --graphql
 
----
+# Custom port
+kg serve --graphql --port-graphql 8080
+```
 
-## Phase 3: Advanced Integration
+### Query Examples
+
+```graphql
+# Get all nodes
+query {
+  nodes(filter: { type: CONCEPT }, pagination: { first: 10 }) {
+    edges {
+      node {
+        id
+        title
+        type
+        tags
+      }
+    }
+    pageInfo {
+      hasNextPage
+      endCursor
+    }
+  }
+}
 
-### ServiceManager
+# Search nodes
+query {
+  searchNodes(query: "authentication", options: { limit: 5 }) {
+    id
+    title
+    score
+    snippet
+  }
+}
 
-Centralized management for background services with health monitoring.
+# Get graph structure
+query {
+  graph {
+    nodes { id title type }
+    edges { source target type }
+    stats { nodeCount edgeCount }
+  }
+}
+```
 
-```typescript
-import { createServiceManager, ServiceHandler } from '@weavelogic/knowledge-graph-agent';
-
-const manager = createServiceManager();
-
-// Register a service
-await manager.register(
-  {
-    id: 'file-watcher',
-    name: 'File Watcher',
-    type: 'watcher',
-    autoStart: true,
-    healthCheckInterval: 60000,
-    restartOnFailure: true,
-    maxRestarts: 3,
-  },
-  myWatcherService
-);
+### Subscriptions
 
-// Listen for events
-manager.on('started', (state) => console.log(`${state.name} started`));
-manager.on('healthCheck', ({ id, healthy }) => console.log(`${id}: ${healthy}`));
+```graphql
+# Real-time node updates
+subscription {
+  nodeCreated {
+    id
+    title
+    createdAt
+  }
+}
 
-// Graceful shutdown
-process.on('SIGTERM', () => manager.shutdown());
+subscription {
+  analysisProgress(analysisId: "abc123") {
+    progress
+    phase
+    message
+  }
+}
 ```
 
-### ConfigManager with Migrations
+### Custom Scalars
 
-Configuration management with version migrations and validation.
+- `DateTime` - ISO 8601 timestamps
+- `JSON` - Arbitrary JSON data
+- `UUID` - RFC 4122 UUIDs
+- `FilePath` - Validated file paths
 
-```typescript
-import { createConfigManager } from '@weavelogic/knowledge-graph-agent';
+---
 
-const config = createConfigManager('/project');
+## Web Dashboard
 
-// Get configuration
-const dbConfig = config.get('database');
-console.log(dbConfig.path);
+Interactive visualization dashboard built with Next.js 14.
 
-// Update configuration
-config.update({
-  cache: { maxSize: 2000, evictionPolicy: 'lfu' },
-});
+### Start Dashboard
 
-// Register and run migrations
-config.registerMigration({
-  version: '1.1.0',
-  up: (cfg) => ({ ...cfg, newField: 'value' }),
-  down: (cfg) => { const { newField, ...rest } = cfg; return rest; },
-});
+```bash
+# Start dashboard on port 3000
+kg serve --dashboard
+
+# Development mode with hot reload
+kg dashboard start
 
-config.migrate('1.1.0');
+# Build for production
+kg dashboard build
 
-// Validate configuration
-const { valid, errors } = config.validate();
+# Serve production build
+kg dashboard serve
 ```
 
-### HealthMonitor
+### Features
 
-System health monitoring with alerts and history.
+- **Graph Visualization**: Interactive cytoscape.js graph with zoom, pan, and node selection
+- **Data Tables**: Sortable, filterable tables with TanStack Table
+- **Search**: Full-text and semantic search with filters
+- **Real-time Updates**: WebSocket subscriptions for live data
+- **Agent Monitoring**: View agent status and execution history
+- **Workflow Tracking**: Monitor workflow progress and results
 
-```typescript
-import { createHealthMonitor, createMemoryCheck, createDatabaseCheck } from '@weavelogic/knowledge-graph-agent';
+### Dashboard CLI
 
-const monitor = createHealthMonitor({ checkInterval: 30000 });
+```bash
+kg dashboard start               # Start dev server
+kg dashboard start --port 8080   # Custom port
+kg dashboard start --open        # Open in browser
+kg dashboard build               # Production build
+kg dashboard serve               # Serve production
+kg dashboard status              # Check status
+kg dashboard open                # Open in browser
+```
 
-// Register health checks
-monitor.registerCheck(createMemoryCheck(85)); // Alert at 85% heap usage
-monitor.registerCheck(createDatabaseCheck('/project/.kg/knowledge.db'));
+---
 
-// Listen for alerts
-monitor.on('alert', (alert) => {
-  console.error(`[${alert.severity}] ${alert.component}: ${alert.message}`);
-});
+## Concurrent Server Execution
 
-// Start monitoring
-monitor.start();
+Run multiple servers simultaneously with the `serve` command.
 
-// Get current health
-const health = await monitor.runAllChecks();
-console.log(`System status: ${health.status}`);
-console.log(`Uptime: ${health.uptime}ms`);
-```
+```bash
+# Start all servers
+kg serve --all
 
-### DecisionTracker for Explainability
+# Start specific servers
+kg serve --mcp --graphql
+kg serve --graphql --dashboard
 
-Track and explain AI reasoning and decisions.
+# Custom ports
+kg serve --all --port-graphql 4001 --port-dashboard 3001
 
-```typescript
-import { createDecisionTracker } from '@weavelogic/knowledge-graph-agent';
+# With custom database
+kg serve --all --db ./data/knowledge.db
+```
 
-const tracker = createDecisionTracker();
+### Server Options
 
-// Start a reasoning chain
-const chainId = tracker.startChain('Process user query');
+| Flag | Description | Default |
+|------|-------------|---------|
+| `--mcp` | Enable MCP server (stdio) | Enabled by default |
+| `--graphql` | Enable GraphQL server | Port 4000 |
+| `--dashboard` | Enable web dashboard | Port 3000 |
+| `--all` | Enable all servers | - |
+| `--port-graphql <port>` | GraphQL port | 4000 |
+| `--port-dashboard <port>` | Dashboard port | 3000 |
+| `--db <path>` | Database path | .kg/knowledge.db |
 
-// Record decisions
-const decision = tracker.recordDecision({
-  action: 'Extract entities from query',
-  reasoning: [
-    'Query contains multiple noun phrases',
-    'NLP analysis identified 3 potential entities',
-    'Confidence scores above threshold',
-  ],
-  confidence: 'high',
-  context: {
-    trigger: 'user_query',
-    inputs: { query: 'Tell me about React and TypeScript' },
-    constraints: ['max 10 entities'],
-    alternatives: [],
-  },
-});
+---
 
-// Record outcome
-tracker.recordOutcome(decision.id, {
-  success: true,
-  result: { entities: ['React', 'TypeScript'] },
-  duration: 150,
-  sideEffects: [],
-});
+## MCP Server
 
-// Get explanation
-console.log(tracker.explainDecision(decision.id));
+Model Context Protocol server for Claude integration with 30+ tools.
 
-// End chain
-tracker.endChain(chainId);
+```bash
+# Start MCP server
+kg serve --mcp
 
-// Get statistics
-const stats = tracker.getStats();
-console.log(`Success rate: ${stats.successRate * 100}%`);
+# Or via npx
+npx @weavelogic/knowledge-graph-agent mcp start
 ```
 
----
+**Available MCP Tools:**
 
-## Phase 4: Enterprise Features
+| Category | Tools |
+|----------|-------|
+| Graph | `kg_query`, `kg_stats`, `kg_get_node`, `kg_list_tags` |
+| Cache | `kg_cache_stats` |
+| Agents | `kg_agent_spawn`, `kg_agent_list` |
+| System | `kg_health`, `kg_health_check` |
+| Search | `kg_search_nodes`, `kg_search_tags` |
+| Workflow | `kg_workflow_start`, `kg_workflow_status`, `kg_workflow_list` |
+| Vector | `kg_vector_search`, `kg_vector_upsert` |
+| Trajectory | `kg_trajectory_list` |
+| Audit | `kg_audit_query`, `kg_audit_checkpoint` |
 
-### Chunker for Large Documents
+---
 
-Split large documents into manageable chunks with multiple strategies.
+## Enterprise Features
 
-**Strategies:**
-- `fixed` - Character-based chunking with overlap
-- `semantic` - Paragraph-based chunking
-- `markdown` - Respects markdown structure (headers, sections)
-- `code` - Preserves code blocks as atomic units
-- `adaptive` - Auto-selects best strategy based on content
+### Chunker for Large Documents
 
 ```typescript
 import { createChunker, chunkDocument } from '@weavelogic/knowledge-graph-agent';
 
-// Quick usage
 const result = chunkDocument(largeMarkdownContent, {
-  strategy: 'adaptive',
+  strategy: 'adaptive', // fixed, semantic, markdown, code, adaptive
   maxSize: 2000,
   overlap: 50,
 });
 
 console.log(`Split into ${result.chunks.length} chunks`);
-console.log(`Processing time: ${result.processingTime}ms`);
-
-// With configuration
-const chunker = createChunker({
-  defaultStrategy: 'markdown',
-  defaultMaxSize: 4000,
-});
-
-const chunks = chunker.chunk(content);
-for (const chunk of chunks) {
-  console.log(`Chunk ${chunk.id}: ${chunk.metadata.wordCount} words`);
-}
 ```
 
-### BackupManager with Compression
-
-Automatic backup with gzip compression and checksums.
+### BackupManager
 
 ```typescript
 import { createBackupManager } from '@weavelogic/knowledge-graph-agent';
@@ -461,323 +457,93 @@ const backup = createBackupManager('/project/.kg/knowledge.db', {
   interval: 86400000, // 24 hours
   maxBackups: 5,
   compress: true,
-  backupPath: '/project/.kg/backups',
 });
 
-// Create backup
-const info = await backup.createBackup();
-console.log(`Backup created: ${info.id}`);
-console.log(`Size: ${info.size} bytes`);
-console.log(`Checksum: ${info.checksum}`);
-
-// List backups
-const backups = backup.listBackups();
-for (const b of backups) {
-  console.log(`${b.id}: ${b.timestamp.toISOString()}`);
-}
-
-// Restore from backup
-await backup.restore(backups[0].id);
-
-// Start automatic backups
+await backup.createBackup();
 backup.startAutoBackup();
 ```
 
-### IntegrityChecker for Database Validation
-
-Comprehensive database integrity checking and repair.
-
-```typescript
-import { createIntegrityChecker, checkDatabaseIntegrity } from '@weavelogic/knowledge-graph-agent';
-
-// Quick check
-const result = checkDatabaseIntegrity('/project/.kg/knowledge.db');
-console.log(`Valid: ${result.valid}`);
-console.log(`Errors: ${result.errors.length}`);
-console.log(`Warnings: ${result.warnings.length}`);
-
-// Detailed check with repair
-const checker = createIntegrityChecker('/project/.kg/knowledge.db');
-const check = checker.check();
-
-for (const table of check.tables) {
-  console.log(`${table.name}: ${table.rowCount} rows, valid: ${table.valid}`);
-  if (!table.valid) {
-    console.log(`  Issues: ${table.issues.join(', ')}`);
-  }
-}
-
-// Repair database
-if (!check.valid) {
-  const repaired = checker.repair();
-  console.log(`Repair ${repaired ? 'successful' : 'failed'}`);
-}
-
-// Get database stats
-const stats = checker.getStats();
-console.log(`Pages: ${stats.pageCount}, Free: ${stats.freePages}`);
-console.log(`WAL mode: ${stats.walMode}`);
-```
-
-### AdvancedCache with Multiple Eviction Policies
-
-High-performance caching with LRU, LFU, FIFO, and TTL eviction.
+### AdvancedCache
 
 ```typescript
 import { createAdvancedCache } from '@weavelogic/knowledge-graph-agent';
 
 const cache = createAdvancedCache<User>({
-  maxSize: 50 * 1024 * 1024, // 50MB
+  maxSize: 50 * 1024 * 1024,
   maxEntries: 1000,
-  defaultTTL: 300000, // 5 minutes
-  evictionPolicy: 'lru', // 'lru' | 'lfu' | 'fifo' | 'ttl'
-  onEvict: (key, value) => console.log(`Evicted: ${key}`),
+  defaultTTL: 300000,
+  evictionPolicy: 'lru', // lru, lfu, fifo, ttl
 });
 
-// Basic operations
-cache.set('user:123', userData, { tags: ['user', 'active'] });
+cache.set('user:123', userData, { tags: ['user'] });
 const user = cache.get<User>('user:123');
-
-// Tag-based operations
-const activeUsers = cache.getByTag('active');
-cache.deleteByTag('user');
-
-// Get or set with factory
-const result = await cache.getOrSet('expensive:key', async () => {
-  return await expensiveComputation();
-}, { ttl: 60000 });
-
-// Statistics
-const stats = cache.getStats();
-console.log(`Hit rate: ${(stats.hitRate * 100).toFixed(1)}%`);
-console.log(`Evictions: ${stats.evictions}`);
-
-// Change policy at runtime
-cache.setEvictionPolicy('lfu');
-```
-
-### Diagnostics CLI
-
-Comprehensive troubleshooting tools.
-
-```bash
-# Run full diagnostics
-kg diag run
-
-# Attempt to fix issues
-kg diag run --fix
-
-# Check system health
-kg diag health
-
-# Repair database issues
-kg diag repair
-
-# Create database backup
-kg diag backup
-
-# List existing backups
-kg diag backup --list
-
-# Show system information
-kg diag info
 ```
 
----
-
-## Phase 5: External Integrations
-
-### Workflow DevKit Integration (useworkflow.dev)
-
-Integration with the Workflow DevKit for durable workflow orchestration with Postgres persistence.
-
-**Key Concepts:**
-- **Postgres World**: Durable state persistence with transactional guarantees
-- **"use workflow" / "use step" directives**: Declarative workflow definition
-- **DurableAgent**: Agents that survive restarts and can resume from any step
-- **GOAP Planning**: Goal-Oriented Action Planning for intelligent task decomposition
+### HealthMonitor
 
 ```typescript
-import { WorkflowManager } from '@weavelogic/knowledge-graph-agent';
+import { createHealthMonitor, createMemoryCheck } from '@weavelogic/knowledge-graph-agent';
 
-const workflow = new WorkflowManager({
-  postgres: process.env.DATABASE_URL,
-  durableAgents: true,
-});
-
-// Start a durable workflow
-const execution = await workflow.start('document-analysis', {
-  input: { path: '/docs' },
-  resumable: true,
-});
-
-// Check workflow status
-const status = await workflow.getStatus(execution.id);
-console.log(`Step ${status.currentStep}/${status.totalSteps}: ${status.state}`);
-
-// List active workflows
-const active = await workflow.list({ status: 'running' });
+const monitor = createHealthMonitor({ checkInterval: 30000 });
+monitor.registerCheck(createMemoryCheck(85));
+monitor.on('alert', (alert) => console.error(alert));
+monitor.start();
 ```
 
-**CLI Commands:**
-
-| Command | Description |
-|---------|-------------|
-| `kg workflow start <name>` | Start a named workflow |
-| `kg workflow status <id>` | Get workflow execution status |
-| `kg workflow list` | List active workflow executions |
-| `kg workflow resume <id>` | Resume a paused workflow |
-| `kg workflow cancel <id>` | Cancel a running workflow |
-| `kg workflow history <name>` | Show workflow execution history |
-| `kg workflow steps <name>` | List steps in a workflow definition |
-
-**MCP Tools:**
-- `kg_workflow_start` - Start a workflow execution
-- `kg_workflow_status` - Get execution status and progress
-- `kg_workflow_list` - List workflows with filtering
-
 ---
 
-### RuVector Integration
+## External Integrations
 
-High-performance semantic vector search with HNSW indexing and trajectory tracking for self-learning agents.
-
-**Key Features:**
-- **HNSW Approximate Nearest Neighbor**: Sub-millisecond search on millions of vectors
-- **Hybrid Search**: Combines vector similarity with keyword matching
-- **Trajectory Tracking**: Records decision paths for experience replay
-- **Self-Learning**: Agents improve through trajectory analysis
+### RuVector Semantic Search
 
 ```typescript
 import { VectorStore, TrajectoryTracker } from '@weavelogic/knowledge-graph-agent';
 
-// Initialize vector store
 const vectors = new VectorStore({
   dimensions: 1536,
   metric: 'cosine',
-  hnswConfig: { m: 16, efConstruction: 200 },
 });
 
-// Upsert vectors with metadata
 await vectors.upsert([
-  { id: 'doc-1', values: embedding, metadata: { type: 'concept', tags: ['api'] } },
+  { id: 'doc-1', values: embedding, metadata: { type: 'concept' } },
 ]);
 
-// Semantic search
-const results = await vectors.search(queryEmbedding, {
-  topK: 10,
-  filter: { type: 'concept' },
-  includeMetadata: true,
-});
-
-// Hybrid search (vector + keyword)
-const hybridResults = await vectors.hybridSearch({
-  vector: queryEmbedding,
-  keywords: ['authentication', 'oauth'],
-  alpha: 0.7, // Weight: 70% vector, 30% keyword
-});
-
-// Trajectory tracking for self-learning
-const tracker = new TrajectoryTracker();
-tracker.recordStep({
-  state: { context: 'user-query' },
-  action: 'search-knowledge-graph',
-  reward: 0.8,
-  nextState: { context: 'results-found' },
-});
-
-const trajectories = tracker.list({ minReward: 0.7 });
+const results = await vectors.search(queryEmbedding, { topK: 10 });
 ```
 
-**CLI Commands:**
-
-| Command | Description |
-|---------|-------------|
-| `kg vector search <query>` | Semantic search across knowledge graph |
-| `kg vector upsert <file>` | Add/update vectors from file |
-| `kg vector delete <ids>` | Delete vectors by ID |
-| `kg vector stats` | Show vector index statistics |
-| `kg trajectory list` | List recorded trajectories |
-| `kg trajectory analyze` | Analyze trajectory patterns |
-| `kg trajectory export` | Export trajectories for training |
-| `kg trajectory prune` | Remove low-value trajectories |
-
-**MCP Tools:**
-- `kg_vector_search` - Semantic search with filters
-- `kg_vector_upsert` - Add or update vectors
-- `kg_trajectory_list` - List agent trajectories
-
----
-
-### Exochain Integration
-
-Cryptographically verifiable audit trail with DAG-BFT consensus for distributed knowledge graph operations.
-
-**Key Features:**
-- **DAG-BFT Consensus**: Byzantine Fault Tolerant ordering without leader
-- **Hybrid Logical Clocks (HLC)**: Causally consistent timestamps
-- **BLAKE3 Hashing**: Fast cryptographic content addressing
-- **Ed25519 Signatures**: Agent-signed operations
-- **Syndication**: Replicate audit logs across nodes
+### Exochain Audit Trail
 
 ```typescript
-import { AuditTrail, SyncManager } from '@weavelogic/knowledge-graph-agent';
+import { AuditTrail } from '@weavelogic/knowledge-graph-agent';
 
-// Initialize audit trail
 const audit = new AuditTrail({
   signingKey: process.env.AGENT_PRIVATE_KEY,
   hlcEnabled: true,
-  dagBftQuorum: 3,
 });
 
-// Record an audited operation
 const checkpoint = await audit.checkpoint({
   operation: 'node_created',
   nodeId: 'concept-123',
   agent: 'coder-agent',
-  data: { title: 'Authentication Flow' },
 });
+```
 
-console.log(`Checkpoint: ${checkpoint.hash}`);
-console.log(`HLC: ${checkpoint.hlc}`);
-console.log(`Signature: ${checkpoint.signature}`);
+### Workflow DevKit
 
-// Query audit trail
-const history = await audit.query({
-  nodeId: 'concept-123',
-  since: '2024-01-01',
-  operations: ['node_created', 'node_updated'],
-});
+```typescript
+import { WorkflowManager } from '@weavelogic/knowledge-graph-agent';
 
-// Sync with remote nodes
-const sync = new SyncManager({
-  peers: ['node1.example.com', 'node2.example.com'],
-  syndication: true,
+const workflow = new WorkflowManager({
+  postgres: process.env.DATABASE_URL,
+  durableAgents: true,
 });
 
-const status = await sync.getStatus();
-console.log(`Synced: ${status.lastSyncedHash}`);
-console.log(`Peers: ${status.connectedPeers}/${status.totalPeers}`);
+const execution = await workflow.start('document-analysis', {
+  input: { path: '/docs' },
+  resumable: true,
+});
 ```
 
-**CLI Commands:**
-
-| Command | Description |
-|---------|-------------|
-| `kg audit query` | Query audit trail with filters |
-| `kg audit checkpoint` | Create a manual checkpoint |
-| `kg audit verify <hash>` | Verify checkpoint integrity |
-| `kg audit export` | Export audit log |
-| `kg audit stats` | Show audit trail statistics |
-| `kg sync status` | Show synchronization status |
-| `kg sync peers` | List connected peers |
-| `kg sync force` | Force synchronization |
-
-**MCP Tools:**
-- `kg_audit_query` - Query audit trail
-- `kg_audit_checkpoint` - Create checkpoint
-- `kg_sync_status` - Get sync status
-
 ---
 
 ## CLI Commands Reference
@@ -788,7 +554,6 @@ console.log(`Peers: ${status.connectedPeers}/${status.totalPeers}`);
 |---------|-------------|
 | `kg init` | Initialize knowledge graph in project |
 | `kg init-primitives` | Bootstrap primitives from codebase |
-| `kg init-primitives --dry-run` | Preview without writing files |
 | `kg analyze-codebase` | Analyze dependencies and services |
 
 ### Knowledge Graph
@@ -796,58 +561,44 @@ console.log(`Peers: ${status.connectedPeers}/${status.totalPeers}`);
 | Command | Description |
 |---------|-------------|
 | `kg graph` | Generate/update knowledge graph |
-| `kg graph --update` | Incremental update |
 | `kg stats` | Display graph statistics |
 | `kg search <query>` | Search the knowledge graph |
 
-### Documentation
+### Servers
 
 | Command | Description |
 |---------|-------------|
-| `kg docs init` | Initialize docs directory |
-| `kg docs status` | Show documentation status |
-| `kg analyze` | Analyze & migrate to knowledge graph |
-| `kg analyze deep` | Deep analysis with claude-flow |
-| `kg analyze report` | Generate analysis report |
-| `kg convert docs` | Convert docs/ to docs-nn/ |
+| `kg serve` | Start MCP server (default) |
+| `kg serve --all` | Start all servers |
+| `kg serve --graphql` | Start GraphQL server |
+| `kg serve --dashboard` | Start web dashboard |
 
-### Frontmatter
+### Plugin Management
 
 | Command | Description |
 |---------|-------------|
-| `kg frontmatter add` | Add frontmatter to markdown files |
-| `kg frontmatter validate` | Validate frontmatter |
-| `kg frontmatter update` | Update/regenerate frontmatter |
+| `kg plugin list` | List installed plugins |
+| `kg plugin install <source>` | Install a plugin |
+| `kg plugin run <name> [file]` | Run an analyzer |
+| `kg plugin info <name>` | Show plugin details |
+| `kg plugin create <name>` | Create plugin from template |
 
-### SOP Compliance
+### Dashboard
 
 | Command | Description |
 |---------|-------------|
-| `kg sop init` | Initialize SOP standards layer |
-| `kg sop check` | Check compliance against SOPs |
-| `kg sop gaps` | Analyze compliance gaps |
-| `kg sop report` | Generate compliance report |
-| `kg sop list` | List available SOPs |
-
-### Claude Integration
+| `kg dashboard start` | Start dashboard dev server |
+| `kg dashboard build` | Build for production |
+| `kg dashboard serve` | Serve production build |
+| `kg dashboard status` | Check dashboard status |
 
-| Command | Description |
-|---------|-------------|
-| `kg claude update` | Update CLAUDE.md |
-| `kg claude preview` | Preview CLAUDE.md content |
-| `kg sync` | Sync with claude-flow memory |
-
-### Git Integration
+### Documentation
 
 | Command | Description |
 |---------|-------------|
-| `kg commit` | Show status with suggested message |
-| `kg commit -a` | Auto-commit with generated message |
-| `kg commit -i` | Interactive commit mode |
-| `kg commit -m "msg"` | Commit with custom message |
-| `kg commit status` | Show git status with analysis |
-| `kg commit log` | Show recent commits |
-| `kg commit diff` | Show diff of changes |
+| `kg docs init` | Initialize docs directory |
+| `kg analyze` | Analyze & migrate to knowledge graph |
+| `kg convert docs` | Convert docs/ to docs-nn/ |
 
 ### Configuration
 
@@ -855,67 +606,25 @@ console.log(`Peers: ${status.connectedPeers}/${status.totalPeers}`);
 |---------|-------------|
 | `kg config show` | Show current configuration |
 | `kg config set <key> <value>` | Set configuration value |
-| `kg config reset` | Reset to defaults |
 
 ### Diagnostics
 
 | Command | Description |
 |---------|-------------|
 | `kg diag run` | Run full diagnostics |
-| `kg diag run --fix` | Attempt to fix issues |
 | `kg diag health` | Check system health |
 | `kg diag repair` | Repair database issues |
 | `kg diag backup` | Create database backup |
-| `kg diag backup --list` | List existing backups |
-| `kg diag info` | Show system information |
-
-### Workflow (Phase 5)
-
-| Command | Description |
-|---------|-------------|
-| `kg workflow start <name>` | Start a named workflow |
-| `kg workflow status <id>` | Get workflow execution status |
-| `kg workflow list` | List active workflow executions |
-| `kg workflow resume <id>` | Resume a paused workflow |
-| `kg workflow cancel <id>` | Cancel a running workflow |
-| `kg workflow history <name>` | Show workflow execution history |
-| `kg workflow steps <name>` | List steps in a workflow definition |
-
-### Vector Search (Phase 5)
 
-| Command | Description |
-|---------|-------------|
-| `kg vector search <query>` | Semantic search across knowledge graph |
-| `kg vector upsert <file>` | Add/update vectors from file |
-| `kg vector delete <ids>` | Delete vectors by ID |
-| `kg vector stats` | Show vector index statistics |
-
-### Trajectory (Phase 5)
-
-| Command | Description |
-|---------|-------------|
-| `kg trajectory list` | List recorded trajectories |
-| `kg trajectory analyze` | Analyze trajectory patterns |
-| `kg trajectory export` | Export trajectories for training |
-| `kg trajectory prune` | Remove low-value trajectories |
-
-### Audit Trail (Phase 5)
+### Workflows & Vectors
 
 | Command | Description |
 |---------|-------------|
-| `kg audit query` | Query audit trail with filters |
-| `kg audit checkpoint` | Create a manual checkpoint |
-| `kg audit verify <hash>` | Verify checkpoint integrity |
-| `kg audit export` | Export audit log |
-| `kg audit stats` | Show audit trail statistics |
-
-### Synchronization (Phase 5)
-
-| Command | Description |
-|---------|-------------|
-| `kg sync status` | Show synchronization status |
-| `kg sync peers` | List connected peers |
-| `kg sync force` | Force synchronization |
+| `kg workflow start <name>` | Start a workflow |
+| `kg workflow status <id>` | Get workflow status |
+| `kg vector search <query>` | Semantic search |
+| `kg trajectory list` | List trajectories |
+| `kg audit query` | Query audit trail |
 
 ---
 
@@ -946,25 +655,17 @@ Create `.kg/config.json` to customize behavior:
     "retryAttempts": 3,
     "claudeFlowEnabled": true
   },
-  "services": {
-    "watcherEnabled": true,
-    "schedulerEnabled": true,
-    "syncEnabled": true,
-    "healthCheckInterval": 60000
-  },
-  "logging": {
-    "level": "info",
-    "format": "text"
+  "graphql": {
+    "port": 4000,
+    "cors": true,
+    "playground": true
   },
-  "analyzer": {
-    "targetDir": "docs-nn",
-    "createMOC": true,
-    "linkOriginal": true
+  "dashboard": {
+    "port": 3000
   },
-  "claudeFlow": {
-    "enabled": true,
-    "namespace": "knowledge-graph",
-    "syncOnChange": true
+  "plugins": {
+    "autoLoad": true,
+    "searchPaths": ["./plugins", "./node_modules"]
   }
 }
 ```
@@ -978,24 +679,17 @@ import {
   // Core
   createKnowledgeGraph,
   createDatabase,
-
-  // Initialization
   quickInit,
-  initDocs,
-  generateClaudeMd,
 
   // Analysis
-  analyzeDocs,
-  convertDocs,
-  addFrontmatter,
   analyzeSeed,
   initPrimitives,
+  analyzeDocs,
 
   // Agents
   BaseAgent,
   getRegistry,
   AgentType,
-  createTask,
 
   // Services
   createServiceManager,
@@ -1005,33 +699,24 @@ import {
   // Enterprise
   createChunker,
   createBackupManager,
-  createIntegrityChecker,
   createAdvancedCache,
 
-  // Reasoning
-  createDecisionTracker,
+  // Plugins
+  createPluginManager,
+  CodeComplexityPlugin,
+  DependencyHealthPlugin,
 
-  // Phase 5 - Workflow DevKit
-  WorkflowManager,
-  DurableAgent,
-  GOAPPlanner,
+  // GraphQL
+  createGraphQLServer,
 
-  // Phase 5 - RuVector
-  VectorStore,
-  TrajectoryTracker,
+  // Server
+  createServerManager,
+  ServiceContainer,
 
-  // Phase 5 - Exochain
+  // Integrations
+  VectorStore,
   AuditTrail,
-  SyncManager,
-
-  // Types
-  type KGConfiguration,
-  type AgentConfig,
-  type ChunkOptions,
-  type WorkflowExecution,
-  type VectorSearchResult,
-  type Trajectory,
-  type AuditCheckpoint,
+  WorkflowManager,
 } from '@weavelogic/knowledge-graph-agent';
 ```
 
@@ -1039,83 +724,58 @@ import {
 
 ## Changelog
 
-### v0.5.0 (Phase 5 - External Integrations)
-
-- **NEW**: Workflow DevKit integration with MCP tools and CLI commands
-  - `WorkflowManager` with Postgres World persistence
-  - DurableAgent support for resumable workflows
-  - GOAP planning for intelligent task decomposition
-- **NEW**: RuVector semantic search with trajectory tracking
-  - `VectorStore` with HNSW approximate nearest neighbor search
-  - Hybrid search combining vector similarity and keyword matching
-  - `TrajectoryTracker` for self-learning agents
-- **NEW**: Exochain audit trail with DAG-BFT consensus
-  - `AuditTrail` with Hybrid Logical Clocks (HLC)
-  - BLAKE3 hashing and Ed25519 signatures
-  - `SyncManager` for peer syndication
-- **NEW**: 9 new MCP tools (`kg_workflow_start`, `kg_workflow_status`, `kg_workflow_list`, `kg_vector_search`, `kg_vector_upsert`, `kg_trajectory_list`, `kg_audit_query`, `kg_audit_checkpoint`, `kg_sync_status`)
-- **NEW**: 22 new CLI subcommands across `workflow`, `vector`, `trajectory`, `audit`, and `sync` command groups
-- **NEW**: 249 new integration tests for external integrations
-
-### v0.4.0 (Phase 4 - Enterprise Features)
-
-- **NEW**: `Chunker` with 5 chunking strategies (fixed, semantic, markdown, code, adaptive)
-- **NEW**: `BackupManager` with gzip compression and SHA-256 checksums
-- **NEW**: `IntegrityChecker` for database validation and repair
-- **NEW**: `AdvancedCache` with LRU/LFU/FIFO/TTL eviction policies
-- **NEW**: `kg diag` CLI commands for diagnostics and troubleshooting
-- **NEW**: Tag-based cache operations
-- **NEW**: Automatic backup scheduling
-
-### v0.3.0 (Phase 3 - Advanced Integration)
-
-- **NEW**: `ServiceManager` for background process management
-- **NEW**: `ConfigManager` with migration support and validation
-- **NEW**: `HealthMonitor` with component health checks and alerts
-- **NEW**: `DecisionTracker` for AI reasoning explainability
-- **NEW**: `kg config` CLI commands
-- **IMPROVED**: Health check history and performance metrics
-
-### v0.2.0 (Phase 2 - Core Features)
-
-- **NEW**: Agent system with BaseAgent and specialized agents
-- **NEW**: `RulesEngine` for automation
-- **NEW**: `WorkflowRegistry` for multi-step workflows
-- **NEW**: `VaultMemorySync` for memory synchronization
-- **NEW**: Git integration with auto-commit
-- **NEW**: MCP Server with 20+ tools
-- **NEW**: `kg commit` CLI commands
-
-### v0.1.0 (Phase 1 - Cultivation System)
-
-- **NEW**: `SeedGenerator` for codebase analysis
-- **NEW**: `DeepAnalyzer` with claude-flow integration
-- **NEW**: `init-primitives` and `cultivate` CLI commands
-- **NEW**: Shadow Cache for file change tracking
+### v0.6.0
+
+- Plugin system with custom analyzers (13 lifecycle hooks, async streaming)
+- Code Complexity Analyzer plugin (cyclomatic, cognitive, Halstead metrics)
+- Dependency Health Analyzer plugin (vulnerability scanning, health scores)
+- GraphQL API with graphql-yoga server and WebSocket subscriptions
+- Custom GraphQL scalars (DateTime, JSON, UUID, FilePath)
+- Web dashboard with Next.js 14, cytoscape.js visualization
+- Dashboard CLI commands (start, build, serve, status)
+- Concurrent server execution (`kg serve --all`)
+- ServiceContainer singleton for dependency injection
+- TypedEventBus for cross-service communication
+- Plugin CLI commands (list, install, run, info, create)
+
+### v0.5.0
+
+- Workflow DevKit integration with MCP tools
+- RuVector semantic search with trajectory tracking
+- Exochain audit trail with DAG-BFT consensus
+- 9 MCP tools for workflows, vectors, and audit
+- 22 CLI subcommands for external integrations
+
+### v0.4.0
+
+- Chunker with 5 chunking strategies
+- BackupManager with gzip compression
+- IntegrityChecker for database validation
+- AdvancedCache with LRU/LFU/FIFO/TTL eviction
+- Diagnostics CLI commands
+
+### v0.3.0
+
+- ServiceManager for background processes
+- ConfigManager with migrations
+- HealthMonitor with alerts
+- DecisionTracker for AI explainability
+
+### v0.2.0
+
+- Agent system with specialized agents
+- RulesEngine for automation
+- WorkflowRegistry for multi-step workflows
+- VaultMemorySync for memory synchronization
+- Git integration with auto-commit
+- MCP Server with 20+ tools
+
+### v0.1.0
+
+- SeedGenerator for codebase analysis
+- DeepAnalyzer with claude-flow
+- Shadow Cache for file tracking
 - Initial knowledge graph generation
-- Docs initialization
-- CLAUDE.md management
-- Full-text search
-
----
-
-## Roadmap
-
-### Completed Features
-
-- [x] Real-time collaboration support (implemented via webhook handlers in v0.5.0)
-- [x] Webhook integrations (implemented in v0.5.0)
-
-### Planned Features
-
-- [ ] Plugin system for custom analyzers
-- [ ] GraphQL API for queries
-- [ ] Web dashboard for visualization
-- [ ] Distributed caching with Redis
-
-### Deprecated Features
-
-- None currently
 
 ---