musubix 3.4.7 → 3.5.0

package/docs/USER-GUIDE.md

@@ -1,3022 +0,0 @@
-# MUSUBIX User Guide
-
-> Neuro-Symbolic AI Coding with Ultimate Specification Driven Development
-
----
-
-## Table of Contents
-
-1. [Introduction](#introduction)
-2. [Installation](#installation)
-3. [CLI Usage](#cli-usage)
-4. [Quick Start](#quick-start)
-5. [SDD Workflow](#sdd-workflow)
-6. [Self-Learning System](#self-learning-system)
-7. [C4 Code Generation](#c4-code-generation)
-8. [Symbolic Reasoning](#symbolic-reasoning) *(v1.2.0)*
-9. [Consistency Validation](#consistency-validation) *(v1.4.1)*
-10. [Advanced Inference](#advanced-inference) *(v1.4.5)*
-11. [Interactive REPL Mode](#interactive-repl-mode) *(v1.5.0)*
-12. [YATA Local](#yata-local) *(v1.6.3)*
-13. [YATA Global](#yata-global) *(v1.6.3)*
-14. [KGPR - Knowledge Graph Pull Request](#kgpr---knowledge-graph-pull-request) *(v1.6.4)*
-15. [YATA Platform Enhancements](#yata-platform-enhancements) *(v1.7.0)*
-16. [Formal Verification](#formal-verification) *(v1.7.5)*
-17. [Security Analysis](#security-analysis) *(v1.8.0)*
-18. [DFG/CFG Extraction](#dfgcfg-extraction) *(v2.0.0)*
-19. [Lean 4 Integration](#lean-4-integration) *(v2.0.0)*
-20. [YATA Scale](#yata-scale) *(v2.0.0)*
-21. [Library Learning](#library-learning) *(v2.0.0)*
-22. [Neural Search](#neural-search) *(v2.0.0)*
-23. [Program Synthesis](#program-synthesis) *(v2.0.0)*
-24. [Advanced Learning Enhancement](#advanced-learning-enhancement) *(v2.2.0)*
-25. [Performance Optimization](#performance-optimization) *(v3.1.0 NEW!)*
-26. [MCP Server Integration](#mcp-server-integration)
-27. [YATA Integration](#yata-integration)
-28. [Best Practices](#best-practices)
-29. [Troubleshooting](#troubleshooting)
-
----
-
-## Introduction
-
-### What is MUSUBIX?
-
-**MUSUBIX** is an Ultimate Specification Driven Development (SDD) platform based on Neuro-Symbolic AI. By integrating MUSUBI (SDD Engine) with YATA (Knowledge Graph), it provides an AI-assisted development environment that maintains requirements, design, and implementation consistency.
-
-### 9 Constitutional Articles
-
-MUSUBIX development follows 9 Articles:
-
-| Article | Description |
-|---------|-------------|
-| Article 1 | EARS-format requirements |
-| Article 2 | C4 architecture design |
-| Article 3 | ADR-based technical decisions |
-| Article 4 | Test-first development (TDD) |
-| Article 5 | Full requirement traceability |
-| Article 6 | CI/CD automation |
-| Article 7 | Knowledge graph management |
-| Article 8 | AI-assisted code review |
-| Article 9 | Continuous quality improvement |
-
----
-
-## Installation
-
-### System Requirements
-
-- Node.js: >= 20.0.0
-- npm: >= 10.0.0
-- TypeScript: >= 5.3
-
-### Method 1: Global Installation (Recommended)
-
-```bash
-# Global installation
-npm install -g musubix
-
-# Verify installation
-musubix --version
-```
-
-### Method 2: Using npx
-
-```bash
-# Initialize project without installation
-npx musubix init my-project
-
-# Project templates
-npx musubix init my-app --template typescript
-npx musubix init my-api --template node
-npx musubix init my-web --template react
-```
-
-### Method 3: Project Dependency
-
-```bash
-# Add to existing project
-npm install musubix
-
-# Use with npx
-npx musubix --help
-```
-
-### Method 4: From Source
-
-```bash
-# Clone repository
-git clone https://github.com/nahisaho/MUSUBIX.git
-cd MUSUBIX
-
-# Install dependencies
-npm install
-
-# Build
-npm run build
-
-# Global link
-npm link
-```
-
-### YATA Installation (Optional)
-
-If you want to use knowledge graph features, install YATA separately:
-
-```bash
-# Install uv (if not installed)
-curl -LsSf https://astral.sh/uv/install.sh | sh
-
-# Clone YATA
-git clone https://github.com/nahisaho/YATA.git
-cd YATA
-
-# Create Python environment
-uv venv
-source .venv/bin/activate  # Linux/macOS
-# or .venv\Scripts\activate  # Windows
-
-# Install dependencies
-uv pip install -e ".[dev]"
-```
-
----
-
-## CLI Usage
-
-### musubix Command
-
-Main command for project management:
-
-```bash
-# Initialize project
-musubix init <project-name>
-
-# Available templates
-musubix init my-project --template typescript
-musubix init my-project --template node
-musubix init my-project --template react
-
-# Help
-musubix --help
-
-# Version
-musubix --version
-```
-
-### Design Commands *(v3.1.0 NEW!)*
-
-```bash
-# Generate C4 design from requirements
-musubix design generate <file>
-
-# Validate design patterns
-musubix design validate <file>
-
-# REQ↔DES traceability validation
-musubix design traceability
-musubix design traceability --min-coverage 80   # Set coverage threshold
-musubix design traceability --require-full      # Require 100% coverage
-```
-
-### Code Generation Commands *(v3.1.0 NEW!)*
-
-```bash
-# Generate code from C4 design
-musubix codegen generate <file> --output src/
-
-# Generate status transition code from spec
-musubix codegen status <spec>                   # Union type (default)
-musubix codegen status <spec> --enum            # Enum type
-musubix codegen status <spec> --no-validator    # Skip validation functions
-musubix codegen status <spec> --no-helpers      # Skip helper functions
-```
-
-### Scaffold Commands *(v3.1.0 Enhanced!)*
-
-```bash
-# DDD project scaffolding
-musubix scaffold domain-model <name>
-
-# With entities
-musubix scaffold domain-model <name> -e "User,Order"
-
-# With Value Objects
-musubix scaffold domain-model <name> -v "Price,Email"
-
-# With status machines
-musubix scaffold domain-model <name> -s "Order,Task"
-
-# Combined options
-musubix scaffold domain-model myproject -e "User,Order" -v "Price,Email" -s "Order"
-```
-
-### musubix-mcp Command
-
-Start MCP server for AI platform integration:
-
-```bash
-# Start with stdio transport (default)
-musubix-mcp
-
-# Start with SSE transport
-musubix-mcp --transport sse --port 3000
-
-# Help
-musubix-mcp --help
-
-# Version
-musubix-mcp --version
-```
-
----
-
-## Quick Start
-
-### Basic TypeScript Usage
-
-```typescript
-import { 
-  createRequirementsService,
-  createDesignService,
-  createValidationService 
-} from 'musubix';
-
-// Create services
-const requirements = createRequirementsService();
-const design = createDesignService();
-const validation = createValidationService();
-
-// Add requirement (EARS format)
-const req = requirements.addRequirement({
-  id: 'REQ-001',
-  text: 'When a user logs in, the system shall authenticate the user',
-  priority: 'high',
-  acceptanceCriteria: [
-    'JWT token shall be returned on successful login',
-    'Error message shall be displayed on failure'
-  ]
-});
-
-// Create design
-const des = design.createComponent({
-  id: 'DES-001',
-  name: 'AuthModule',
-  type: 'component',
-  requirements: ['REQ-001'],
-  decisions: ['Use JWT authentication']
-});
-
-// Validate
-const result = validation.validate({
-  requirements: [req],
-  designs: [des]
-});
-
-console.log(result.compliant); // true or false
-```
-
-### SDD Workflow Overview
-
-```
-┌─────────────────┐
-│   Requirements  │ EARS format requirements
-└────────┬────────┘
-         ↓
-┌─────────────────┐
-│     Design      │ C4 Architecture + ADR
-└────────┬────────┘
-         ↓
-┌─────────────────┐
-│     Tasks       │ Traceable implementation tasks
-└────────┬────────┘
-         ↓
-┌─────────────────┐
-│   Validation    │ 9 Articles compliance check
-└─────────────────┘
-```
-
----
-
-## SDD Workflow
-
-### Phase 1: Requirements (EARS Format)
-
-Use EARS (Easy Approach to Requirements Syntax) format for requirements:
-
-```typescript
-const requirements = createRequirementsService();
-
-// Pattern: "When <trigger>, the system shall <response>"
-const loginReq = requirements.addRequirement({
-  id: 'REQ-001',
-  text: 'When a user enters valid credentials, the system shall issue an authentication token',
-  priority: 'high',
-  acceptanceCriteria: [
-    'Token shall be valid for 24 hours',
-    'Token shall include user information'
-  ]
-});
-
-// Pattern: "While <state>, the system shall <behavior>"
-const sessionReq = requirements.addRequirement({
-  id: 'REQ-002',
-  text: 'While a session is active, the system shall maintain user state',
-  priority: 'medium'
-});
-
-// Get all requirements
-const allReqs = requirements.getAllRequirements();
-console.log(`Total requirements: ${allReqs.length}`);
-```
-
-### Phase 2: Design (C4 + ADR)
-
-#### C4 Model
-
-Design at 4 levels:
-
-```typescript
-const design = createDesignService();
-
-// Level 1: Context
-const system = design.createContainer({
-  id: 'SYS-001',
-  name: 'MUSUBIX System',
-  type: 'system',
-  description: 'Neuro-Symbolic AI-based SDD platform'
-});
-
-// Level 2: Container
-const apiServer = design.createContainer({
-  id: 'CON-001',
-  name: 'API Server',
-  type: 'container',
-  parent: 'SYS-001',
-  technology: 'Node.js + Express'
-});
-
-// Level 3: Component
-const authModule = design.createComponent({
-  id: 'COMP-001',
-  name: 'Authentication Module',
-  type: 'component',
-  parent: 'CON-001',
-  requirements: ['REQ-001']
-});
-```
-
-#### ADR (Architecture Decision Record)
-
-Document technical decisions:
-
-```typescript
-const adr = design.createADR({
-  id: 'ADR-001',
-  title: 'JWT for Authentication',
-  context: 'Need to select stateless authentication method',
-  decision: 'Use JWT',
-  status: 'accepted',
-  consequences: [
-    'Positive: Stateless, scalable',
-    'Negative: Token revocation requires additional implementation'
-  ],
-  relatedRequirements: ['REQ-001']
-});
-```
-
-### Phase 3: Tasks
-
-Break down requirements and designs into implementation tasks:
-
-```typescript
-const tasks = createTaskService();
-
-// Create task linked to requirements
-const task = tasks.createTask({
-  id: 'TASK-001',
-  title: 'Implement JWT authentication',
-  description: 'Implement JWT-based authentication module',
-  requirements: ['REQ-001'],
-  designs: ['COMP-001'],
-  estimatedHours: 4,
-  acceptanceCriteria: [
-    'Login API endpoint completed',
-    'JWT generation/validation tests passing'
-  ]
-});
-
-// Track progress
-tasks.updateProgress('TASK-001', {
-  status: 'in-progress',
-  completedItems: ['Login API endpoint completed']
-});
-```
-
-### Phase 4: Validation
-
-Check compliance with 9 Constitutional Articles:
-
-```typescript
-const validation = createValidationService();
-
-// Full validation
-const result = validation.validateAll({
-  requirements: requirements.getAllRequirements(),
-  designs: design.getAllDesigns(),
-  tasks: tasks.getAllTasks()
-});
-
-// Check results
-console.log('Compliant:', result.compliant);
-console.log('Score:', result.score);
-
-// Check details by Article
-result.articleResults.forEach(article => {
-  console.log(`Article ${article.number}: ${article.passed ? '✓' : '✗'}`);
-  if (!article.passed) {
-    console.log('  Issues:', article.issues);
-  }
-});
-```
-
----
-
-## Self-Learning System
-
-MUSUBIX includes a self-learning system that improves through feedback collection and pattern extraction.
-
-### Learning CLI Commands
-
-```bash
-# View learning status dashboard
-musubix learn status
-
-# Record feedback on an artifact
-musubix learn feedback <artifact-id> --type accept|reject|modify --artifact-type requirement|design|code|test --reason "explanation"
-
-# List learned patterns
-musubix learn patterns
-
-# Manually register a pattern
-musubix learn add-pattern <name> --category code|design|requirement|test --action prefer|avoid --description "pattern description"
-
-# Remove a pattern
-musubix learn remove-pattern <pattern-id>
-
-# Get context-based recommendations
-musubix learn recommend --artifact-type code
-
-# Apply decay to unused patterns
-musubix learn decay
-
-# Export learning data (v1.4.0 enhanced)
-musubix learn export --output learning-data.json
-# Options:
-#   --privacy-filter         Remove sensitive data (API keys, passwords)
-#   --patterns-only          Export patterns only (exclude feedback)
-#   --feedback-only          Export feedback only (exclude patterns)
-#   --min-confidence <n>     Minimum confidence threshold (0-1)
-
-# Import learning data with merge strategy (v1.4.0 enhanced)
-musubix learn import learning-data.json
-# Options:
-#   --merge-strategy <skip|overwrite|merge>  How to handle duplicates
-#   --dry-run                                Preview without applying
-#   --patterns-only                          Import patterns only
-#   --feedback-only                          Import feedback only
-```
-
-### Programmatic Usage
-
-```typescript
-import { createLearningEngine } from '@nahisaho/musubix-core';
-
-const learningEngine = createLearningEngine();
-
-// Record feedback
-await learningEngine.recordFeedback({
-  type: 'accept',
-  artifactType: 'code',
-  artifactId: 'AUTH-001',
-  reason: 'Good implementation of JWT authentication'
-});
-
-// Get recommendations
-const recommendations = await learningEngine.getRecommendations({
-  artifactType: 'code',
-  context: 'authentication'
-});
-
-// Export learning data
-const data = await learningEngine.exportData();
-```
-
-### Pattern Extraction
-
-Patterns are automatically extracted when similar feedback is recorded multiple times (default threshold: 3).
-
-```typescript
-// Patterns gain confidence with each occurrence
-// High-confidence patterns (≥70%) appear in recommendations
-const stats = await learningEngine.getStats();
-console.log(`Total patterns: ${stats.totalPatterns}`);
-console.log(`High confidence patterns: ${stats.highConfidencePatterns}`);
-```
-
----
-
-## C4 Code Generation
-
-Generate TypeScript skeleton code from C4 design documents.
-
-### CLI Usage
-
-```bash
-# Generate code from C4 design
-musubix codegen generate design-c4.md --output src/
-
-# With specific language
-musubix codegen generate design-c4.md --output src/ --language typescript
-```
-
-### Generated Code Structure
-
-From a C4 design with components like:
-
-| ID | Name | Type | Description |
-|----|------|------|-------------|
-| auth | AuthService | component | Authentication |
-
-MUSUBIX generates:
-
-```typescript
-// auth-service.ts
-export interface IAuthService {
-  authenticate(credentials: { username: string; password: string }): Promise<{ token: string }>;
-  validate(token: string): Promise<boolean>;
-}
-
-export class AuthService implements IAuthService {
-  async authenticate(credentials: { username: string; password: string }): Promise<{ token: string }> {
-    // TODO: Implement authenticate
-    throw new Error('Not implemented');
-  }
-  
-  async validate(token: string): Promise<boolean> {
-    // TODO: Implement validate
-    throw new Error('Not implemented');
-  }
-}
-
-export function createAuthService(): IAuthService {
-  return new AuthService();
-}
-```
-
----
-
-## Interactive REPL Mode
-
-*(New in v1.5.0, Enhanced in v1.6.0)*
-
-MUSUBIX provides an interactive REPL (Read-Eval-Print-Loop) shell for real-time command execution and exploration.
-
-### Starting REPL
-
-```bash
-# Start interactive REPL
-musubix repl
-
-# With custom history file
-musubix repl --history ~/.musubix-repl-history
-
-# Without colors
-musubix repl --no-color
-```
-
-### REPL Features
-
-| Feature | Description |
-|---------|-------------|
-| Command completion | TAB completion for commands, options |
-| History navigation | UP/DOWN arrows, history search |
-| Session variables | `$name=value` to set, `$name` to reference |
-| Output formatting | JSON, YAML, Table auto-formatting |
-| CLI integration | Execute any CLI command directly |
-
-### Basic Usage
-
-```bash
-musubix> help                          # Show all commands
-musubix> help requirements             # Show command details
-musubix> requirements analyze input.md # Execute CLI command
-musubix> $project=my-app               # Set session variable
-musubix> design generate $project      # Use variable in command
-musubix> history                       # Show command history
-musubix> exit                          # Exit REPL
-```
-
-### Session Variables
-
-```bash
-# Set variables
-musubix> $req=REQ-001
-musubix> $file=./docs/requirements.md
-
-# Use in commands
-musubix> requirements validate $file
-musubix> trace impact $req
-
-# Special variable: $_ holds last result
-musubix> requirements analyze input.md
-musubix> $_                           # Access last result
-```
-
-### Output Formats
-
-```bash
-# Auto-detect best format (default)
-musubix> learn status
-
-# Force JSON output
-musubix> set format json
-musubix> learn patterns
-
-# Force YAML output
-musubix> set format yaml
-
-# Force table output
-musubix> set format table
-```
-
-### History Management
-
-```bash
-# Show recent commands
-musubix> history
-
-# Search history (Ctrl+R style)
-musubix> history search requirements
-
-# Clear history
-musubix> history clear
-```
-
-### REPL Components
-
-| Component | Purpose |
-|-----------|---------|
-| `ReplEngine` | Main REPL controller |
-| `CommandCompleter` | TAB completion provider |
-| `HistoryManager` | Command history persistence |
-| `SessionState` | Variable storage |
-| `OutputFormatter` | JSON/YAML/Table output |
-| `PromptRenderer` | Dynamic prompt display |
-
----
-
-## YATA Local
-
-*(New in v1.6.3)*
-
-YATA Local provides a high-performance, SQLite-based local knowledge graph with built-in inference capabilities. Designed for single-user, offline scenarios where data sovereignty and speed are critical.
-
-### Features
-
-| Feature | Description |
-|---------|-------------|
-| **SQLite Storage** | WAL mode for concurrent reads, single-writer |
-| **Full-Text Search** | FTS5-based triple search |
-| **Graph Traversal** | BFS/DFS with depth control |
-| **Inference Engine** | 4 OWL-lite rules (transitivity, symmetry, inverse, domain/range) |
-| **Constraints** | 4 validation rules (cardinality, disjoint, unique, required) |
-| **ACID Transactions** | Full transaction support |
-
-### Installation
-
-```bash
-npm install @nahisaho/yata-local
-```
-
-### Quick Start
-
-```typescript
-import { YataLocal } from '@nahisaho/yata-local';
-
-// Initialize with default config
-const yata = new YataLocal('./knowledge.db');
-await yata.initialize();
-
-// Add triples
-await yata.addTriple({
-  subject: 'Person:john',
-  predicate: 'hasParent',
-  object: 'Person:mary'
-});
-
-// Query triples
-const results = await yata.query({
-  subject: 'Person:john',
-  predicate: 'hasParent'
-});
-
-// Full-text search
-const searchResults = await yata.search('john parent');
-
-// Graph traversal (BFS)
-const ancestors = await yata.traverse('Person:john', 'hasParent', {
-  direction: 'outgoing',
-  maxDepth: 5,
-  algorithm: 'bfs'
-});
-
-// Clean up
-await yata.close();
-```
-
-### Inference Engine
-
-YATA Local supports four OWL-lite inference rules:
-
-| Rule | Description | Example |
-|------|-------------|---------|
-| **Transitivity** | If A→B and B→C then A→C | hasAncestor is transitive |
-| **Symmetry** | If A→B then B→A | friendOf is symmetric |
-| **Inverse** | If A→B via P then B→A via P⁻¹ | hasChild ↔ hasParent |
-| **Domain/Range** | Type inference from predicate | hasAge implies Person |
-
-```typescript
-// Run inference
-const inferred = await yata.infer();
-console.log(`Inferred ${inferred.length} new triples`);
-```
-
-### Constraints
-
-```typescript
-// Define constraints
-await yata.addConstraint({
-  type: 'cardinality',
-  predicate: 'hasSpouse',
-  max: 1
-});
-
-// Validate
-const violations = await yata.validate();
-if (violations.length > 0) {
-  console.error('Constraint violations:', violations);
-}
-```
-
-### Configuration Options
-
-```typescript
-const yata = new YataLocal('./knowledge.db', {
-  // WAL mode for better concurrency (default: true)
-  walMode: true,
-  
-  // Enable FTS5 search (default: true)
-  enableSearch: true,
-  
-  // Auto-run inference on writes (default: false)
-  autoInfer: false,
-  
-  // Journal mode (default: 'wal')
-  journalMode: 'wal'
-});
-```
-
----
-
-## YATA Global
-
-*(New in v1.6.3)*
-
-YATA Global is a distributed knowledge graph platform for team collaboration. It provides REST API access to shared knowledge graphs with offline support and intelligent synchronization.
-
-### Features
-
-| Feature | Description |
-|---------|-------------|
-| **REST API** | Full CRUD operations via HTTP |
-| **Offline Cache** | SQLite-based local cache |
-| **Sync Engine** | Push/Pull with conflict resolution |
-| **Conflict Resolution** | Last-write-wins or custom strategies |
-| **Authentication** | API key-based auth |
-| **Batch Operations** | Bulk triple operations |
-
-### Installation
-
-```bash
-npm install @nahisaho/yata-global
-```
-
-### Quick Start
-
-```typescript
-import { YataGlobal } from '@nahisaho/yata-global';
-
-// Initialize client
-const yata = new YataGlobal({
-  endpoint: 'https://yata.example.com/api',
-  apiKey: 'your-api-key',
-  graphId: 'project-knowledge'
-});
-
-await yata.initialize();
-
-// Add triples (batched)
-await yata.addTriples([
-  { subject: 'Task:001', predicate: 'assignedTo', object: 'User:alice' },
-  { subject: 'Task:001', predicate: 'status', object: 'in-progress' }
-]);
-
-// Query with filters
-const tasks = await yata.query({
-  predicate: 'assignedTo',
-  object: 'User:alice'
-});
-
-// Clean up
-await yata.close();
-```
-
-### Offline Support
-
-YATA Global supports offline-first operation with automatic synchronization:
-
-```typescript
-const yata = new YataGlobal({
-  endpoint: 'https://yata.example.com/api',
-  apiKey: 'your-api-key',
-  graphId: 'project-knowledge',
-  
-  // Offline configuration
-  offlineMode: true,
-  cachePath: './yata-cache.db',
-  syncInterval: 60000  // Auto-sync every 60 seconds
-});
-
-// Works offline - cached locally
-await yata.addTriple({
-  subject: 'Note:001',
-  predicate: 'content',
-  object: 'Important meeting notes'
-});
-
-// Manual sync when online
-await yata.sync();
-```
-
-### Conflict Resolution
-
-```typescript
-const yata = new YataGlobal({
-  // ... other options
-  
-  conflictStrategy: 'last-write-wins',  // Default
-  // or: 'server-wins', 'client-wins', 'manual'
-  
-  onConflict: async (local, remote) => {
-    // Custom resolution logic
-    console.log('Conflict detected:', local, remote);
-    return remote;  // Prefer remote version
-  }
-});
-```
-
-### Sync Status
-
-```typescript
-// Check sync status
-const status = await yata.getSyncStatus();
-console.log(`Pending changes: ${status.pendingPush}`);
-console.log(`Last sync: ${status.lastSyncAt}`);
-
-// Force full sync
-await yata.sync({ force: true });
-```
-
-### When to Use YATA Local vs YATA Global
-
-| Use Case | Recommended |
-|----------|-------------|
-| Personal knowledge base | YATA Local |
-| Single-user application | YATA Local |
-| Privacy-sensitive data | YATA Local |
-| Team collaboration | YATA Global |
-| Cross-device access | YATA Global |
-| Shared project knowledge | YATA Global |
-| Offline-first with sync | YATA Global |
-
----
-
-## KGPR - Knowledge Graph Pull Request
-
-*(v1.6.4)*
-
-KGPR (Knowledge Graph Pull Request) enables safe sharing of knowledge graphs from YATA Local to YATA Global using a GitHub PR-like workflow.
-
-### Workflow
-
-```
-┌─────────────┐     ┌──────────────┐     ┌───────────────┐
-│ YATA Local  │ ──► │ KGPR (Draft) │ ──► │ YATA Global   │
-│ (Local KG)  │     │ (Extract)    │     │ (Review/Merge)│
-└─────────────┘     └──────────────┘     └───────────────┘
-
-Status Flow:
-draft → open → reviewing → approved/changes_requested → merged/closed
-```
-
-### Privacy Levels
-
-| Level | Filtered Content |
-|-------|------------------|
-| `strict` | File paths, URLs, credentials, all metadata |
-| `moderate` | File paths, URLs, credentials |
-| `none` | No filtering |
-
-### CLI Commands
-
-```bash
-# Create a KGPR
-musubix kgpr create -t "Add authentication patterns"
-
-# Preview diff before creating
-musubix kgpr diff --namespace myproject --privacy moderate
-
-# List KGPRs
-musubix kgpr list
-
-# Submit KGPR for review
-musubix kgpr submit <id>
-
-# Show KGPR details
-musubix kgpr show <id>
-
-# Close without merging
-musubix kgpr close <id>
-```
-
-### MCP Tools
-
-| Tool | Description |
-|------|-------------|
-| `kgpr_create` | Create KGPR from local knowledge graph |
-| `kgpr_diff` | Preview diff before creating KGPR |
-| `kgpr_list` | List all KGPRs |
-| `kgpr_submit` | Submit KGPR for review |
-| `kgpr_review` | Review KGPR (approve/changes_requested/commented) |
-
-### Example Usage
-
-```bash
-# 1. Preview what will be shared
-musubix kgpr diff --privacy strict
-
-# 2. Create KGPR with description
-musubix kgpr create -t "Share React patterns" -d "Learned patterns from project-x"
-
-# 3. Review the KGPR
-musubix kgpr show KGPR-001
-
-# 4. Submit for review
-musubix kgpr submit KGPR-001
-```
-
----
-
-## YATA Platform Enhancements
-
-*(v1.7.0)*
-
-Version 1.7.0 introduces significant enhancements to the YATA platform with 5 major features.
-
-### Phase 1: Index Optimization
-
-Optimized query performance for YATA Local with composite indexes.
-
-```typescript
-import { IndexOptimizer } from '@nahisaho/yata-local';
-
-const optimizer = new IndexOptimizer(database);
-
-// Analyze and create optimal indexes
-const analysis = await optimizer.analyzeQueryPatterns();
-const created = await optimizer.createOptimalIndexes();
-
-// Check index health
-const health = await optimizer.checkIndexHealth();
-```
-
-**Key Features:**
-- Composite index creation for common query patterns
-- Index health monitoring with fragmentation detection
-- Automatic optimization recommendations
-
-### Phase 2: Enhanced Export Pipeline
-
-Powerful export capabilities with incremental export and multiple formats.
-
-```typescript
-import { ExportPipeline } from '@nahisaho/yata-local';
-
-const pipeline = new ExportPipeline(database);
-
-// Full export
-const fullData = await pipeline.exportFull({ namespace: 'myproject' });
-
-// Incremental export (changes since last export)
-const changes = await pipeline.exportIncremental({
-  since: lastExportTimestamp,
-  format: 'json'
-});
-
-// Export with transformation
-const transformed = await pipeline.exportWithTransform({
-  format: 'rdf',
-  includeMetadata: true
-});
-```
-
-**Supported Formats:**
-- JSON (default)
-- RDF/Turtle
-- N-Triples
-- Custom transformers
-
-### Phase 3: Global Sync Integration
-
-Seamless synchronization between YATA Local and YATA Global.
-
-```typescript
-import { GlobalSyncClient, SyncEngine } from '@nahisaho/yata-global';
-
-const client = new GlobalSyncClient({
-  endpoint: 'https://yata-global.example.com',
-  offlineMode: true
-});
-
-// Initialize sync
-await client.initialize();
-
-// Push local changes
-const syncResult = await client.sync({
-  namespace: 'myproject',
-  direction: 'push'
-});
-
-// Pull updates from global
-await client.sync({
-  namespace: 'shared-patterns',
-  direction: 'pull'
-});
-```
-
-**Features:**
-- Offline-first with automatic sync
-- Conflict resolution strategies
-- Selective namespace sync
-- Framework pattern repository
-
-### Phase 4: Code Generator Enhancement
-
-Advanced code generation from design documents.
-
-```typescript
-import { CodeGenerator } from '@nahisaho/yata-local';
-
-const generator = new CodeGenerator({
-  language: 'typescript',
-  outputDir: './src/generated'
-});
-
-// Generate from C4 design
-const result = await generator.generateFromC4(designDocument);
-
-// Generate with custom templates
-await generator.generate({
-  template: 'repository-pattern',
-  context: { entityName: 'User' }
-});
-```
-
-**Supported Patterns:**
-- Repository Pattern
-- Service Layer
-- Factory Pattern
-- Domain Events
-- Value Objects
-
-### Phase 5: YATA UI (Web Visualization)
-
-Web-based visualization and management interface for knowledge graphs.
-
-```typescript
-import { YataUIServer, createYataUIServer } from '@nahisaho/yata-ui';
-
-// Create and start server
-const server = createYataUIServer({
-  port: 3000,
-  enableRealtime: true
-});
-
-// Set data provider
-server.setDataProvider(async () => ({
-  nodes: await getEntities(),
-  edges: await getRelationships()
-}));
-
-await server.start();
-console.log(`UI available at ${server.getUrl()}`);
-```
-
-**UI Features:**
-- Interactive graph visualization
-- Real-time updates via WebSocket
-- Namespace filtering
-- Entity/Relationship editing
-- Export/Import functionality
-
-### v1.7.0 Package Summary
-
-| Package | Description |
-|---------|-------------|
-| `@nahisaho/yata-local` | IndexOptimizer, ExportPipeline, CodeGenerator |
-| `@nahisaho/yata-global` | GlobalSyncClient, SyncEngine, CacheManager |
-| `@nahisaho/yata-ui` | YataUIServer, Graph visualization |
-
----
-
-## Formal Verification
-
-*(v1.7.5)*
-
-The `@nahisaho/musubix-formal-verify` package provides formal verification capabilities using the Z3 SMT solver.
-
-### Installation
-
-```bash
-npm install @nahisaho/musubix-formal-verify
-# Optional: Install z3-solver for WebAssembly support
-npm install z3-solver
-```
-
-### Z3 SMT Solver Integration
-
-```typescript
-import { Z3Adapter, PreconditionVerifier, PostconditionVerifier } from '@nahisaho/musubix-formal-verify';
-
-// Create Z3 adapter (auto-selects backend)
-const z3 = await Z3Adapter.create();
-
-// Precondition verification
-const preVerifier = new PreconditionVerifier(z3);
-const result = await preVerifier.verify({
-  condition: { expression: 'amount > 0 && balance >= amount', format: 'javascript' },
-  variables: [
-    { name: 'amount', type: 'Int' },
-    { name: 'balance', type: 'Int' },
-  ],
-});
-
-console.log(result.status); // 'valid' | 'invalid' | 'unknown' | 'error'
-```
-
-### Hoare Triple Verification
-
-```typescript
-// Verify {P} C {Q}
-const postVerifier = new PostconditionVerifier(z3);
-const hoareResult = await postVerifier.verify({
-  precondition: { expression: 'balance >= amount', format: 'javascript' },
-  postcondition: { expression: 'balance_new == balance - amount', format: 'javascript' },
-  preVariables: [{ name: 'balance', type: 'Int' }, { name: 'amount', type: 'Int' }],
-  postVariables: [{ name: 'balance_new', type: 'Int' }],
-  transition: 'balance_new == balance - amount',
-});
-```
-
-### EARS to SMT Conversion
-
-```typescript
-import { EarsToSmtConverter } from '@nahisaho/musubix-formal-verify';
-
-const converter = new EarsToSmtConverter();
-
-// Convert EARS requirements to SMT-LIB2
-const results = converter.convertMultiple([
-  'THE system SHALL validate inputs',           // ubiquitous
-  'WHEN error, THE system SHALL notify user',   // event-driven
-  'WHILE busy, THE system SHALL queue requests', // state-driven
-  'THE system SHALL NOT expose secrets',        // unwanted
-  'IF admin, THEN THE system SHALL allow edit', // optional
-]);
-
-results.forEach(r => {
-  console.log(`Pattern: ${r.formula?.metadata.earsPattern.type}`);
-  console.log(`SMT: ${r.formula?.smtLib2}`);
-});
-```
-
-### Traceability Database
-
-```typescript
-import { TraceabilityDB, ImpactAnalyzer } from '@nahisaho/musubix-formal-verify';
-
-// Create SQLite-based traceability database
-const db = new TraceabilityDB('./trace.db');
-
-// Add nodes
-await db.addNode({ id: 'REQ-001', type: 'requirement', title: 'User Auth' });
-await db.addNode({ id: 'DES-001', type: 'design', title: 'AuthService' });
-await db.addNode({ id: 'CODE-001', type: 'code', title: 'auth.ts' });
-
-// Add traceability links
-await db.addLink({ source: 'DES-001', target: 'REQ-001', type: 'satisfies' });
-await db.addLink({ source: 'CODE-001', target: 'DES-001', type: 'implements' });
-
-// Impact analysis
-const analyzer = new ImpactAnalyzer(db);
-const impact = await analyzer.analyze('REQ-001');
-console.log(`Impacted nodes: ${impact.totalImpacted}`);
-```
-
-### v1.7.5 Package Summary
-
-| Package | Description |
-|---------|-------------|
-| `@nahisaho/musubix-formal-verify` | Z3 integration, Hoare verification, EARS→SMT, TraceabilityDB |
-
-### Supported Variable Types
-
-| Type | Description |
-|------|-------------|
-| `Int` | Integer values |
-| `Real` | Real numbers |
-| `Bool` | Boolean values |
-| `String` | String values |
-| `Array` | Array types |
-| `BitVec` | Bit vectors |
-
----
-
-## Security Analysis
-
-*(v1.8.0)*
-
-The `@nahisaho/musubix-security` package provides comprehensive security analysis capabilities for TypeScript/JavaScript projects.
-
-### Installation
-
-```bash
-npm install @nahisaho/musubix-security
-```
-
-### Vulnerability Scanning
-
-Detects OWASP Top 10 and CWE Top 25 vulnerabilities using AST analysis:
-
-```typescript
-import { VulnerabilityScanner, createSecurityService } from '@nahisaho/musubix-security';
-
-// Scan a single file
-const scanner = new VulnerabilityScanner();
-const vulnerabilities = scanner.scanFile('src/api.ts');
-
-// Scan a directory
-const result = await scanner.scanDirectory('./src');
-console.log(`Found ${result.vulnerabilities.length} vulnerabilities`);
-console.log(`Scanned ${result.scannedFiles} files`);
-```
-
-### Detected Vulnerabilities
-
-| Category | CWE | Severity |
-|----------|-----|----------|
-| SQL Injection | CWE-89 | Critical |
-| Command Injection | CWE-78 | Critical |
-| XSS | CWE-79 | High |
-| Path Traversal | CWE-22 | High |
-| Code Injection | CWE-94 | Critical |
-| NoSQL Injection | CWE-943 | High |
-
-### Secret Detection
-
-Detects hardcoded credentials and sensitive information:
-
-```typescript
-import { SecretDetector } from '@nahisaho/musubix-security';
-
-const detector = new SecretDetector();
-const secrets = detector.scanContent(content, 'config.ts');
-const result = await detector.scan('./src');
-
-console.log(`Found ${result.summary.total} secrets`);
-```
-
-### Detected Secret Types
-
-| Type | Pattern |
-|------|--------|
-| AWS Access Key | `AKIA...` |
-| AWS Secret Key | 40-char base64 |
-| GitHub Token | `ghp_*`, `gho_*`, `ghu_*` |
-| Private Key | PEM format |
-| Database URL | `postgres://`, `mongodb://` |
-| JWT Secret | JWT signing secrets |
-| Stripe Key | `sk_live_*`, `sk_test_*` |
-
-### Taint Analysis
-
-Tracks data flow from user input (sources) to dangerous functions (sinks):
-
-```typescript
-import { TaintAnalyzer } from '@nahisaho/musubix-security';
-
-const analyzer = new TaintAnalyzer();
-const result = analyzer.analyze('./src');
-
-console.log(`Sources: ${result.sources.length}`);
-console.log(`Sinks: ${result.sinks.length}`);
-console.log(`Taint paths: ${result.paths.length}`);
-```
-
-### Dependency Auditing
-
-Integrates with npm audit to detect vulnerable dependencies:
-
-```typescript
-import { DependencyAuditor } from '@nahisaho/musubix-security';
-
-const auditor = new DependencyAuditor();
-const result = await auditor.audit('./project');
-
-console.log(`Critical: ${result.summary.critical}`);
-console.log(`High: ${result.summary.high}`);
-```
-
-### Integrated Security Service
-
-Combines all security analysis features:
-
-```typescript
-import { createSecurityService } from '@nahisaho/musubix-security';
-
-const service = createSecurityService();
-
-// Full security scan
-const result = await service.scan({
-  target: './src',
-  vulnerabilities: true,
-  taint: true,
-  secrets: true,
-  dependencies: true,
-  generateFixes: true,
-});
-
-console.log(`Total vulnerabilities: ${result.summary.totalVulnerabilities}`);
-console.log(`Total secrets: ${result.summary.totalSecrets}`);
-console.log(`Fixes generated: ${result.summary.fixesGenerated}`);
-```
-
-### Report Generation
-
-Generate reports in multiple formats:
-
-```typescript
-// SARIF format (GitHub Code Scanning compatible)
-const sarifReport = await service.generateReport(result, 'sarif');
-
-// Markdown format
-const mdReport = await service.generateReport(result, 'markdown');
-
-// HTML format
-const htmlReport = await service.generateReport(result, 'html');
-```
-
-### CLI Usage
-
-```bash
-# Full security scan
-npx musubix-security scan ./src
-
-# Vulnerability scan only
-npx musubix-security scan ./src --vulnerabilities-only
-
-# Secret detection
-npx musubix-security secrets ./src
-
-# Taint analysis
-npx musubix-security taint ./src
-
-# Dependency audit
-npx musubix-security audit ./project
-
-# Generate SARIF report
-npx musubix-security scan ./src --format sarif --output report.sarif
-```
-
-### v1.8.0 Package Summary
-
-| Package | Description |
-|---------|-------------|
-| `@nahisaho/musubix-security` | Vulnerability scanning, secret detection, taint analysis, dependency auditing |
-
----
-
-## DFG/CFG Extraction
-
-*(v2.0.0)*
-
-The `@nahisaho/musubix-dfg` package provides Data Flow Graph (DFG) and Control Flow Graph (CFG) extraction for TypeScript and JavaScript code analysis.
-
-### Installation
-
-```bash
-npm install @nahisaho/musubix-dfg
-```
-
-### DFG Extraction
-
-Extract data flow graphs from source code:
-
-```typescript
-import { extractDFG, DFGExtractor } from '@nahisaho/musubix-dfg';
-
-// Simple extraction
-const dfg = extractDFG(sourceCode, 'typescript');
-
-// With configuration
-const extractor = new DFGExtractor({
-  includeImplicitFlows: true,
-  trackConstants: true,
-});
-const result = extractor.extract(sourceCode);
-
-console.log(`Nodes: ${result.nodes.length}`);
-console.log(`Edges: ${result.edges.length}`);
-```
-
-### CFG Extraction
-
-Extract control flow graphs:
-
-```typescript
-import { extractCFG, CFGExtractor } from '@nahisaho/musubix-dfg';
-
-const cfg = extractCFG(sourceCode);
-
-// Traverse CFG
-for (const block of cfg.blocks) {
-  console.log(`Block ${block.id}: ${block.statements.length} statements`);
-  console.log(`Successors: ${block.successors.join(', ')}`);
-}
-```
-
-### Def-Use Chain Analysis
-
-Build definition-use chains for variable tracking:
-
-```typescript
-import { analyzeDefUse } from '@nahisaho/musubix-dfg';
-
-const chains = analyzeDefUse(dfg);
-
-for (const chain of chains) {
-  console.log(`Variable: ${chain.variable}`);
-  console.log(`Defined at: line ${chain.definition.line}`);
-  console.log(`Used at: ${chain.uses.map(u => u.line).join(', ')}`);
-}
-```
-
-### Data Dependency Analysis
-
-Analyze data dependencies between statements:
-
-```typescript
-import { analyzeDataDependencies } from '@nahisaho/musubix-dfg';
-
-const deps = analyzeDataDependencies(dfg);
-
-for (const dep of deps) {
-  console.log(`${dep.from} -> ${dep.to}: ${dep.type}`);
-}
-```
-
----
-
-## Lean 4 Integration
-
-*(v2.0.0)*
-
-The `@nahisaho/musubix-lean` package provides integration with the Lean 4 theorem prover for formal verification of requirements.
-
-### Installation
-
-```bash
-npm install @nahisaho/musubix-lean
-```
-
-### EARS to Lean Conversion
-
-Convert EARS requirements to Lean 4 theorems:
-
-```typescript
-import { EarsToLeanConverter } from '@nahisaho/musubix-lean';
-
-const converter = new EarsToLeanConverter();
-
-// Convert EARS requirement
-const earsRequirement = {
-  id: 'REQ-001',
-  type: 'event-driven',
-  trigger: 'user clicks submit',
-  response: 'system saves form data',
-};
-
-const theorem = converter.convert(earsRequirement);
-console.log(theorem.leanCode);
-// theorem REQ_001 : ∀ (s : State), 
-//   user_clicks_submit s → saves_form_data (next s)
-```
-
-### Lean AST Parsing
-
-Parse and manipulate Lean 4 code:
-
-```typescript
-import { LeanParser, LeanAST } from '@nahisaho/musubix-lean';
-
-const parser = new LeanParser();
-const ast = parser.parse(leanCode);
-
-// Traverse AST
-for (const decl of ast.declarations) {
-  if (decl.type === 'theorem') {
-    console.log(`Theorem: ${decl.name}`);
-    console.log(`Statement: ${decl.statement}`);
-  }
-}
-```
-
-### Proof Engine
-
-Execute proofs using Lean 4:
-
-```typescript
-import { LeanProofEngine } from '@nahisaho/musubix-lean';
-
-const engine = new LeanProofEngine({
-  leanPath: '/usr/bin/lean',
-  timeout: 30000,
-});
-
-const result = await engine.prove(theorem);
-
-if (result.success) {
-  console.log('Proof verified!');
-  console.log(`Proof: ${result.proof}`);
-} else {
-  console.log(`Failed: ${result.error}`);
-}
-```
-
-### ReProver Integration
-
-Use ReProver for automated proof search:
-
-```typescript
-import { ReProverClient } from '@nahisaho/musubix-lean';
-
-const reprover = new ReProverClient({
-  endpoint: 'http://localhost:8080',
-  maxDepth: 10,
-});
-
-const proof = await reprover.searchProof(theorem);
-
-if (proof.found) {
-  console.log('Proof found!');
-  console.log(proof.tactics);
-}
-```
-
----
-
-## YATA Scale
-
-*(v2.0.0)*
-
-The `@nahisaho/yata-scale` package provides distributed knowledge graph capabilities with sharding, caching, and synchronization.
-
-### Installation
-
-```bash
-npm install @nahisaho/yata-scale
-```
-
-### High-Level API
-
-Use `YataScaleManager` for simplified access:
-
-```typescript
-import { YataScaleManager } from '@nahisaho/yata-scale';
-
-const yata = new YataScaleManager({
-  shards: 16,
-  cacheConfig: {
-    l1MaxSize: 1000,
-    l2MaxSize: 10000,
-    l3Path: './cache',
-  },
-});
-
-// Store entity
-await yata.putEntity({
-  id: 'entity-1',
-  type: 'Document',
-  properties: { title: 'Example' },
-});
-
-// Query
-const results = await yata.query('SELECT ?s WHERE { ?s rdf:type Document }');
-```
-
-### Sharding
-
-Distribute data across shards using consistent hashing:
-
-```typescript
-import { ShardManager, HashPartitionStrategy } from '@nahisaho/yata-scale';
-
-const shardManager = new ShardManager({
-  shardCount: 16,
-  virtualNodes: 150,
-  strategy: new HashPartitionStrategy(),
-});
-
-// Get shard for entity
-const shard = shardManager.getShardForEntity('entity-id');
-console.log(`Entity assigned to shard ${shard.id}`);
-
-// Rebalance on node changes
-await shardManager.addNode('node-5');
-```
-
-### Multi-Tier Caching
-
-Three-tier caching for optimal performance:
-
-```typescript
-import { CacheManager, L1Cache, L2Cache, L3Cache } from '@nahisaho/yata-scale';
-
-const cache = new CacheManager({
-  l1: new L1Cache({ maxSize: 1000 }),    // LRU cache
-  l2: new L2Cache({ maxSize: 10000 }),   // LFU cache
-  l3: new L3Cache({ path: './cache' }),  // Disk cache
-});
-
-// Cache operations
-await cache.set('key', value, { ttl: 3600 });
-const result = await cache.get('key');
-
-// Invalidation
-await cache.invalidate('key');
-await cache.invalidatePattern('user:*');
-```
-
-### Index Management
-
-Multiple index types for efficient queries:
-
-```typescript
-import { IndexManager, BPlusTreeIndex, FullTextIndex, GraphIndex } from '@nahisaho/yata-scale';
-
-const indexManager = new IndexManager();
-
-// B+ Tree for range queries
-indexManager.addIndex('timestamp', new BPlusTreeIndex());
-
-// Full-text for search
-indexManager.addIndex('content', new FullTextIndex());
-
-// Graph for traversal
-indexManager.addIndex('relationships', new GraphIndex());
-```
-
-### Vector Clock Synchronization
-
-Distributed synchronization with conflict resolution:
-
-```typescript
-import { SyncController, VectorClock, ConflictResolver } from '@nahisaho/yata-scale';
-
-const sync = new SyncController({
-  nodeId: 'node-1',
-  conflictStrategy: 'last-write-wins',
-});
-
-// Synchronize with peers
-await sync.synchronize();
-
-// Manual conflict resolution
-sync.onConflict((conflict) => {
-  console.log(`Conflict on ${conflict.key}`);
-  return conflict.local; // or conflict.remote
-});
-```
-
-### v2.0.0 Package Summary
-
-| Package | Tests | Description |
-|---------|-------|-------------|
-| `@nahisaho/musubix-dfg` | 30 | DFG/CFG extraction, Def-Use analysis |
-| `@nahisaho/musubix-lean` | 151 | Lean 4 theorem proving, EARS conversion |
-| `@nahisaho/yata-scale` | 57 | Distributed sharding, caching, sync |
-| **Total** | **238** | **Phase 1: Deep Symbolic Integration** |
-
----
-
-## Library Learning
-
-*(v2.0.0 NEW!)*
-
-The `@nahisaho/musubix-library-learner` package provides intelligent API pattern extraction and documentation from TypeScript libraries, enabling the system to learn and suggest library usage patterns.
-
-### Installation
-
-```bash
-npm install @nahisaho/musubix-library-learner
-```
-
-### Library Analysis
-
-Analyze and learn patterns from TypeScript libraries:
-
-```typescript
-import { LibraryLearner, LibraryAnalyzer } from '@nahisaho/musubix-library-learner';
-
-const learner = new LibraryLearner();
-
-// Analyze a library
-const patterns = await learner.analyze({
-  libraryName: 'lodash',
-  sourceDir: './node_modules/lodash',
-  includeExamples: true,
-});
-
-console.log(`Found ${patterns.length} API patterns`);
-for (const pattern of patterns) {
-  console.log(`- ${pattern.name}: ${pattern.description}`);
-}
-```
-
-### Pattern Extraction
-
-Extract usage patterns from code examples:
-
-```typescript
-import { PatternExtractor } from '@nahisaho/musubix-library-learner';
-
-const extractor = new PatternExtractor();
-
-const patterns = await extractor.extract({
-  code: sourceCode,
-  libraryContext: 'express',
-});
-
-// Get common patterns
-for (const pattern of patterns) {
-  console.log(`Pattern: ${pattern.type}`);
-  console.log(`Example: ${pattern.example}`);
-  console.log(`Frequency: ${pattern.frequency}`);
-}
-```
-
-### API Documentation Generation
-
-Generate documentation from learned patterns:
-
-```typescript
-import { DocGenerator } from '@nahisaho/musubix-library-learner';
-
-const generator = new DocGenerator();
-
-const docs = await generator.generate({
-  patterns: learnedPatterns,
-  format: 'markdown',
-  includeExamples: true,
-});
-
-await fs.writeFile('API-PATTERNS.md', docs);
-```
-
-### TypeScript Analysis
-
-Deep analysis of TypeScript declarations:
-
-```typescript
-import { TypeScriptAnalyzer } from '@nahisaho/musubix-library-learner';
-
-const analyzer = new TypeScriptAnalyzer();
-
-const analysis = await analyzer.analyze('./src/index.ts');
-
-// Get exported types
-for (const type of analysis.exports) {
-  console.log(`${type.name}: ${type.kind}`);
-  if (type.kind === 'function') {
-    console.log(`  Params: ${type.parameters.join(', ')}`);
-    console.log(`  Returns: ${type.returnType}`);
-  }
-}
-```
-
----
-
-## Neural Search
-
-*(v2.0.0 NEW!)*
-
-The `@nahisaho/musubix-neural-search` package provides semantic code search using embeddings and neural ranking, enabling context-aware code discovery across your codebase.
-
-### Installation
-
-```bash
-npm install @nahisaho/musubix-neural-search
-```
-
-### Semantic Search
-
-Search code by meaning, not just keywords:
-
-```typescript
-import { NeuralSearchEngine } from '@nahisaho/musubix-neural-search';
-
-const search = new NeuralSearchEngine({
-  embeddingModel: 'code-bert',
-  indexPath: './search-index',
-});
-
-// Index your codebase
-await search.index('./src');
-
-// Semantic search
-const results = await search.search({
-  query: 'function that validates email addresses',
-  limit: 10,
-});
-
-for (const result of results) {
-  console.log(`${result.file}:${result.line} (score: ${result.score})`);
-  console.log(`  ${result.snippet}`);
-}
-```
-
-### Code Embeddings
-
-Generate embeddings for code snippets:
-
-```typescript
-import { CodeEmbedder } from '@nahisaho/musubix-neural-search';
-
-const embedder = new CodeEmbedder();
-
-const embedding = await embedder.embed({
-  code: 'function add(a: number, b: number) { return a + b; }',
-  language: 'typescript',
-});
-
-// Compare similarity
-const similarity = embedder.cosineSimilarity(embedding1, embedding2);
-console.log(`Similarity: ${similarity}`);
-```
-
-### Hybrid Search
-
-Combine lexical and semantic search:
-
-```typescript
-import { HybridSearchEngine } from '@nahisaho/musubix-neural-search';
-
-const hybrid = new HybridSearchEngine({
-  lexicalWeight: 0.3,
-  semanticWeight: 0.7,
-});
-
-const results = await hybrid.search({
-  query: 'authentication middleware express',
-  filters: {
-    language: 'typescript',
-    path: 'src/middleware/**',
-  },
-});
-```
-
-### Code Ranking
-
-Neural ranking for search results:
-
-```typescript
-import { CodeRanker } from '@nahisaho/musubix-neural-search';
-
-const ranker = new CodeRanker();
-
-const ranked = await ranker.rank({
-  query: 'parse JSON safely',
-  candidates: searchResults,
-  context: {
-    currentFile: './src/utils.ts',
-    recentFiles: ['./src/api.ts', './src/config.ts'],
-  },
-});
-```
-
----
-
-## Program Synthesis
-
-*(v2.0.0 NEW!)*
-
-The `@nahisaho/musubix-synthesis` package provides neural-guided program synthesis, generating code from specifications using symbolic constraints and neural networks.
-
-### Installation
-
-```bash
-npm install @nahisaho/musubix-synthesis
-```
-
-### Specification-Based Synthesis
-
-Generate code from formal specifications:
-
-```typescript
-import { ProgramSynthesizer } from '@nahisaho/musubix-synthesis';
-
-const synthesizer = new ProgramSynthesizer();
-
-const result = await synthesizer.synthesize({
-  specification: {
-    input: 'array of numbers',
-    output: 'array of numbers (sorted ascending)',
-    constraints: ['stable sort', 'O(n log n) complexity'],
-  },
-  language: 'typescript',
-});
-
-console.log(result.code);
-// function sort(arr: number[]): number[] {
-//   return [...arr].sort((a, b) => a - b);
-// }
-```
-
-### Example-Based Synthesis
-
-Generate code from input/output examples:
-
-```typescript
-import { ExampleBasedSynthesizer } from '@nahisaho/musubix-synthesis';
-
-const synthesizer = new ExampleBasedSynthesizer();
-
-const result = await synthesizer.synthesize({
-  examples: [
-    { input: ['hello', 'world'], output: 'hello world' },
-    { input: ['foo', 'bar', 'baz'], output: 'foo bar baz' },
-  ],
-  language: 'typescript',
-});
-
-console.log(result.code);
-// function join(arr: string[]): string {
-//   return arr.join(' ');
-// }
-```
-
-### Sketch-Based Synthesis
-
-Fill in holes in partial programs:
-
-```typescript
-import { SketchSynthesizer } from '@nahisaho/musubix-synthesis';
-
-const synthesizer = new SketchSynthesizer();
-
-const result = await synthesizer.complete({
-  sketch: `
-    function validate(email: string): boolean {
-      const pattern = ??; // hole to fill
-      return pattern.test(email);
-    }
-  `,
-  constraints: ['must validate common email formats'],
-});
-
-console.log(result.code);
-// const pattern = /^[^\s@]+@[^\s@]+\.[^\s@]+$/;
-```
-
-### Neural-Guided Search
-
-Use neural networks to guide synthesis search:
-
-```typescript
-import { NeuralGuidedSynthesizer } from '@nahisaho/musubix-synthesis';
-
-const synthesizer = new NeuralGuidedSynthesizer({
-  model: 'codegen-2B',
-  beamWidth: 5,
-  maxDepth: 10,
-});
-
-const result = await synthesizer.synthesize({
-  description: 'Parse a CSV string into array of objects with headers as keys',
-  tests: [
-    {
-      input: 'name,age\\nAlice,30\\nBob,25',
-      output: [{ name: 'Alice', age: '30' }, { name: 'Bob', age: '25' }],
-    },
-  ],
-});
-
-if (result.verified) {
-  console.log('All tests pass!');
-  console.log(result.code);
-}
-```
-
-### Synthesis Verification
-
-Verify synthesized code against specifications:
-
-```typescript
-import { SynthesisVerifier } from '@nahisaho/musubix-synthesis';
-
-const verifier = new SynthesisVerifier();
-
-const verification = await verifier.verify({
-  code: synthesizedCode,
-  specification: originalSpec,
-  tests: testCases,
-});
-
-console.log(`Verified: ${verification.passed}`);
-console.log(`Coverage: ${verification.testCoverage}%`);
-for (const issue of verification.issues) {
-  console.log(`Issue: ${issue.message}`);
-}
-```
-
-### v2.0.0 Package Summary
-
-| Package | Tests | Description |
-|---------|-------|-------------|
-| **Phase 1: Deep Symbolic Integration** | | |
-| `@nahisaho/musubix-dfg` | 30 | DFG/CFG extraction, Def-Use analysis |
-| `@nahisaho/musubix-lean` | 151 | Lean 4 theorem proving, EARS conversion |
-| `@nahisaho/yata-scale` | 57 | Distributed sharding, caching, sync |
-| **Phase 2: Advanced Learning** | | |
-| `@nahisaho/musubix-library-learner` | 132 | API pattern extraction, documentation |
-| `@nahisaho/musubix-neural-search` | 144 | Semantic code search, embeddings |
-| `@nahisaho/musubix-synthesis` | 146 | Neural-guided program synthesis |
-| **Total v2.0.0 New** | **660** | **6 new packages** |
-
----
-
-## Advanced Learning Enhancement
-
-*(v2.2.0 NEW!)*
-
-MUSUBIX v2.2.0では、Neural Search、Library Learner、Synthesisの3パッケージに対して高度な学習機能を追加しました。
-
-### Neural Search Enhancement
-
-#### ContextAwareEmbedder
-
-AST構造を認識したコンテキスト埋め込み:
-
-```typescript
-import { ContextAwareEmbedder } from '@nahisaho/musubix-neural-search';
-
-const embedder = new ContextAwareEmbedder({
-  windowSize: 5,
-  includeAST: true,
-});
-
-const embedding = embedder.embed(code, {
-  surrounding: surroundingCode,
-  imports: importStatements,
-});
-```
-
-#### HybridRanker
-
-BM25とベクトル類似度のハイブリッドランキング:
-
-```typescript
-import { HybridRanker } from '@nahisaho/musubix-neural-search';
-
-const ranker = new HybridRanker({ alpha: 0.6 });
-const results = ranker.rank(query, documents);
-```
-
-#### EmbeddingCache
-
-LRU + TTL管理キャッシュ:
-
-```typescript
-import { EmbeddingCache } from '@nahisaho/musubix-neural-search';
-
-const cache = new EmbeddingCache({
-  maxSize: 10000,
-  ttlMs: 3600000,
-});
-
-cache.set('key', embedding);
-const stats = cache.getStats(); // { hits, misses, hitRate }
-```
-
-#### TrajectoryLogger
-
-検索軌跡のロギング:
-
-```typescript
-import { createTrajectoryLogger } from '@nahisaho/musubix-neural-search';
-
-const logger = createTrajectoryLogger();
-logger.logBranch({ depth: 1, score: 0.85, action: 'expand' });
-
-const trajectory = logger.getTrajectory();
-const parquet = logger.export('parquet');
-```
-
-### Library Learner Enhancement
-
-#### SemanticChunker
-
-AST境界認識チャンキング:
-
-```typescript
-import { SemanticChunker } from '@nahisaho/musubix-library-learner';
-
-const chunker = new SemanticChunker({
-  minSize: 50,
-  maxSize: 500,
-  respectBoundaries: true,
-});
-
-const chunks = chunker.chunk(code);
-```
-
-#### PatternVersionManager
-
-Git風バージョン管理:
-
-```typescript
-import { PatternVersionManager } from '@nahisaho/musubix-library-learner';
-
-const manager = new PatternVersionManager();
-manager.commit(pattern, 'Add validation pattern');
-const history = manager.getHistory(patternId);
-manager.rollback(patternId, commitId);
-```
-
-#### MetricsExporter
-
-学習メトリクスのエクスポート:
-
-```typescript
-import { createMetricsExporter } from '@nahisaho/musubix-library-learner';
-
-const exporter = createMetricsExporter(library);
-const json = exporter.export('json');
-const markdown = exporter.export('markdown');
-const summary = exporter.getSummary();
-// { totalPatterns, averageConfidence, healthStatus }
-```
-
-### Synthesis Enhancement
-
-#### MetaLearningEngine
-
-タスク類似度ベースの戦略選択:
-
-```typescript
-import { createMetaLearningEngine } from '@nahisaho/musubix-synthesis';
-
-const meta = createMetaLearningEngine({
-  historySize: 100,
-  similarityThreshold: 0.7,
-});
-
-meta.recordTask(task, result);
-const strategy = meta.selectStrategy(newTask);
-```
-
-#### DSLExtender
-
-パターンからのDSL演算子自動生成:
-
-```typescript
-import { createDSLExtender } from '@nahisaho/musubix-synthesis';
-
-const extender = createDSLExtender(baseDSL);
-const gaps = extender.detectGaps(patterns);
-const suggestions = extender.suggestOperators(gaps);
-```
-
-#### ExampleAnalyzer
-
-例題品質分析:
-
-```typescript
-import { createExampleAnalyzer } from '@nahisaho/musubix-synthesis';
-
-const analyzer = createExampleAnalyzer();
-const quality = analyzer.analyzeQuality(examples);
-const coverage = analyzer.analyzeCoverage(examples, dsl);
-```
-
-#### ExplanationGenerator
-
-合成プログラムの自然言語説明:
-
-```typescript
-import { createExplanationGenerator } from '@nahisaho/musubix-synthesis';
-
-const explainer = createExplanationGenerator();
-const explanation = explainer.generate(program);
-const summary = explainer.summarize(program);
-// "Converts to uppercase"
-```
-
-### v2.2.0 CLI Commands
-
-```bash
-# プログラム合成
-npx musubix synthesize <examples.json>
-npx musubix syn <examples.json>  # エイリアス
-
-# パターンライブラリ管理
-npx musubix library learn <file>
-npx musubix library query <query>
-npx musubix library stats
-npx musubix lib stats  # エイリアス
-```
-
-### v2.2.0 Test Statistics
-
-| EPIC | Tasks | Tests |
-|------|-------|-------|
-| Neural Search | 7 | 138 |
-| Library Learner | 7 | 145 |
-| Synthesis | 6 | 108 |
-| Integration | 4 | 73 |
-| **Total** | **28** | **464** |
-
----
-
-## Performance Optimization
-
-*(v3.1.0)*
-
-Performance utilities for CLI commands and pattern processing.
-
-### Performance Measurement
-
-```typescript
-import {
-  PerformanceTimer,
-  measureAsync,
-  measureSync,
-  PerformanceCollector,
-  createPerformanceCollector,
-  formatPerformanceReport,
-} from '@nahisaho/musubix-core/cli';
-
-// Measure async operation
-const { result, performance } = await measureAsync('api-call', async () => {
-  return await fetchData();
-});
-console.log(`Duration: ${performance.durationMs}ms`);
-
-// Create collector with default baselines
-const collector = createPerformanceCollector();
-collector.addResult(performance);
-
-// Generate and format report
-const report = collector.generateReport();
-console.log(formatPerformanceReport(report));
-// === Performance Report ===
-// Average: 150.25ms
-// Min: 100ms
-// Max: 200ms
-// ✅ cli:init: 300ms (target: 500ms, 60%)
-```
-
-### Lazy Loading
-
-```typescript
-import {
-  createLazyLoader,
-  LazyModuleRegistry,
-  globalLazyRegistry,
-  BatchLoader,
-} from '@nahisaho/musubix-core/cli';
-
-// Lazy module loading
-const heavyModule = createLazyLoader(() => import('./heavy-module'));
-const module = await heavyModule(); // Loads only on first access
-
-// Module registry for multiple lazy modules
-const registry = new LazyModuleRegistry();
-registry.register('parser', () => import('./parser'));
-registry.register('formatter', () => import('./formatter'));
-
-const parser = await registry.get('parser');
-await registry.preload(['parser', 'formatter']);
-
-// Batch loading with deduplication
-const loader = new BatchLoader(async (keys) => {
-  const results = await fetchMany(keys);
-  return new Map(keys.map((k, i) => [k, results[i]]));
-}, 10); // 10ms batch delay
-
-const [a, b, c] = await Promise.all([
-  loader.load('a'),
-  loader.load('b'),
-  loader.load('c'),
-]); // Single batch request
-```
-
-### Pattern Cache
-
-```typescript
-import {
-  LRUCache,
-  PatternCache,
-  globalPatternCache,
-  memoize,
-  memoizeAsync,
-} from '@nahisaho/musubix-core/learning';
-
-// LRU cache with TTL
-const cache = new LRUCache<string, Pattern>({
-  maxSize: 100,
-  ttlMs: 60000, // 1 minute TTL
-});
-cache.set('pattern-1', patternData);
-const pattern = cache.get('pattern-1');
-
-// Get cache statistics
-const stats = cache.getStats();
-// { size: 1, maxSize: 100, hits: 5, misses: 2, hitRatio: 0.71, evictions: 0 }
-
-// Category-based pattern cache
-const patternCache = new PatternCache({ maxSize: 50, ttlMs: 300000 });
-patternCache.set('design', 'singleton', { name: 'Singleton' });
-patternCache.set('code', 'factory', { name: 'Factory' });
-
-// Memoize expensive functions
-const expensiveFn = memoize((x: number) => {
-  // Heavy computation
-  return x * 2;
-});
-
-// Memoize async functions with concurrent call deduplication
-const fetchUser = memoizeAsync(async (id: string) => {
-  return await api.getUser(id);
-});
-```
-
-### Default Performance Baselines
-
-| Operation | Target (ms) | Max (ms) |
-|-----------|-------------|----------|
-| `cli:init` | 500 | 1000 |
-| `cli:validate` | 200 | 500 |
-| `cli:analyze` | 1000 | 2000 |
-| `cli:generate` | 500 | 1000 |
-| `pattern:query` | 100 | 300 |
-| `pattern:extract` | 500 | 1000 |
-| `learning:recommend` | 200 | 500 |
-
----
-
-## MCP Server Integration
-
-### CLI Startup
-
-```bash
-# Default (stdio transport)
-musubix-mcp
-
-# SSE transport
-musubix-mcp --transport sse --port 3000
-
-# WebSocket transport
-musubix-mcp --transport websocket --port 3001
-```
-
-### Programmatic Startup
-
-```typescript
-import { startServer, createMCPServer } from '@nahisaho/musubix-mcp-server';
-
-// Simple startup
-await startServer();
-
-// Startup with options
-const server = createMCPServer({
-  transport: 'sse',
-  port: 3000
-});
-await server.start();
-```
-
-### AI Platform Integration
-
-#### GitHub Copilot (VS Code)
-
-Add to `.vscode/settings.json`:
-
-```json
-{
-  "github.copilot.chat.mcpServers": {
-    "musubix": {
-      "command": "musubix-mcp",
-      "args": ["--transport", "stdio"]
-    }
-  }
-}
-```
-
-#### Claude Desktop
-
-Add to Claude configuration file (`~/.config/claude/config.json` or similar):
-
-```json
-{
-  "mcpServers": {
-    "musubix": {
-      "command": "musubix-mcp",
-      "args": []
-    }
-  }
-}
-```
-
-#### Cursor
-
-Add to `.cursor/mcp.json`:
-
-```json
-{
-  "mcpServers": {
-    "musubix": {
-      "command": "musubix-mcp",
-      "args": ["--transport", "stdio"]
-    }
-  }
-}
-```
-
-### Available MCP Tools
-
-| Tool Name | Description |
-|-----------|-------------|
-| `create_requirement` | Create EARS-format requirement |
-| `validate_requirements` | Validate requirements |
-| `create_design` | Create C4 design element |
-| `create_adr` | Create ADR |
-| `create_task` | Create implementation task |
-| `validate_all` | Full 9 Articles compliance check |
-| `get_traceability` | Get traceability matrix |
-
----
-
-## Symbolic Reasoning
-
-*(v1.2.0 New Feature)*
-
-### Overview
-
-Symbolic reasoning enhances LLM outputs by applying formal verification and knowledge-graph backed reasoning. This hybrid approach (Neuro-Symbolic) combines the creativity of neural networks with the precision of symbolic logic.
-
-### Key Components
-
-| Component | Description |
-|-----------|-------------|
-| `SemanticCodeFilterPipeline` | Filter LLM outputs for code quality |
-| `HallucinationDetector` | Detect and prevent hallucinated outputs |
-| `EarsToFormalSpecConverter` | Convert EARS requirements to formal Z3 specifications |
-| `Z3Adapter` | Interface with Z3 solver for formal verification |
-| `QualityGateValidator` | Validate against 17 quality gate checks |
-
-### Usage
-
-#### Semantic Code Filtering
-
-```typescript
-import { SemanticCodeFilterPipeline } from '@nahisaho/musubix-core';
-
-const pipeline = new SemanticCodeFilterPipeline({
-  enableHallucinationDetection: true,
-  maxRetries: 3
-});
-
-const result = await pipeline.filter({
-  code: generatedCode,
-  context: { language: 'typescript', domain: 'authentication' }
-});
-
-if (result.isValid) {
-  console.log('Code passed validation:', result.filteredCode);
-} else {
-  console.log('Issues found:', result.issues);
-}
-```
-
-#### Hallucination Detection
-
-```typescript
-import { HallucinationDetector } from '@nahisaho/musubix-core';
-
-const detector = new HallucinationDetector();
-
-const analysis = await detector.analyze({
-  response: llmResponse,
-  groundTruth: knownFacts,
-  context: projectContext
-});
-
-console.log('Confidence score:', analysis.confidence);
-console.log('Hallucination risks:', analysis.risks);
-```
-
-#### EARS to Formal Specification
-
-```typescript
-import { EarsToFormalSpecConverter } from '@nahisaho/musubix-core';
-
-const converter = new EarsToFormalSpecConverter();
-
-const formalSpec = await converter.convert({
-  earsRequirement: 'WHEN user clicks login, THE system SHALL authenticate within 2 seconds',
-  requirementId: 'REQ-AUTH-001'
-});
-
-// Returns Z3-compatible specification
-console.log(formalSpec.z3Expression);
-```
-
-#### Quality Gate Validation
-
-```typescript
-import { QualityGateValidator } from '@nahisaho/musubix-core';
-
-const validator = new QualityGateValidator();
-
-const gateResult = await validator.validate({
-  requirements: requirementsList,
-  designs: designDocuments,
-  tasks: taskList
-});
-
-console.log('All gates passed:', gateResult.allPassed);
-console.log('Gate details:', gateResult.gates);
-// 17 quality checks including EARS compliance, traceability, etc.
-```
-
-### Quality Gate Checks
-
-| Gate | Description |
-|------|-------------|
-| EARS Compliance | Requirements follow EARS patterns |
-| Unique IDs | All artifacts have unique identifiers |
-| Traceability | Full traceability chain exists |
-| Design Coverage | All requirements have designs |
-| Task Coverage | All designs have tasks |
-| No Orphans | No orphaned requirements or tasks |
-| Completeness | All required fields are present |
-| ... | And 10 more quality checks |
-
----
-
-## Consistency Validation
-
-*(v1.4.1 New Feature)*
-
-### Overview
-
-Consistency validation ensures data integrity when adding triples to the knowledge graph. Based on OWL constraints, it detects violations before they corrupt the knowledge base.
-
-### Validation Types
-
-| Type | Description | Severity |
-|------|-------------|----------|
-| `disjoint-class-membership` | Instance belongs to disjoint classes | error |
-| `functional-property-violation` | Multiple values for functional property | error |
-| `inverse-functional-violation` | Same value maps to multiple subjects | error |
-| `asymmetric-violation` | Inverse relation exists for asymmetric property | error |
-| `irreflexive-violation` | Self-reference for irreflexive property | error |
-| `duplicate-triple` | Exact duplicate triple | warning |
-| `circular-dependency` | Circular subClassOf chain | error |
-
-### Usage
-
-#### Validated Triple Addition
-
-```typescript
-import { N3Store } from '@nahisaho/musubix-ontology-mcp';
-
-// Enable validation on add
-const store = new N3Store({}, true);
-
-// Add with validation
-const result = store.addTripleValidated({
-  subject: 'http://example.org/Person1',
-  predicate: 'http://example.org/hasMother',
-  object: 'http://example.org/Mother1'
-});
-
-if (!result.success) {
-  console.error('Validation errors:', result.validation.errors);
-}
-```
-
-#### Store-wide Consistency Check
-
-```typescript
-// Check entire store
-const consistency = store.checkConsistency();
-
-if (!consistency.consistent) {
-  for (const violation of consistency.violations) {
-    console.log(`${violation.type}: ${violation.message}`);
-    console.log('Affected triples:', violation.triples);
-  }
-  
-  // Get fix suggestions
-  for (const suggestion of consistency.suggestions) {
-    console.log(`Suggestion: ${suggestion.suggestion}`);
-    console.log(`Auto-fixable: ${suggestion.autoFixable}`);
-  }
-}
-```
-
-#### Direct Validator Usage
-
-```typescript
-import { ConsistencyValidator } from '@nahisaho/musubix-ontology-mcp';
-
-const validator = new ConsistencyValidator({
-  checkDisjointClasses: true,
-  checkFunctionalProperties: true,
-  checkDuplicates: true,
-  checkCircularDependencies: true
-});
-
-// Validate before adding
-const validation = validator.validateTriple(newTriple, existingTriples);
-if (!validation.valid) {
-  console.error(validation.errors);
-}
-
-// Find duplicates
-const duplicates = validator.findDuplicates(allTriples);
-const semanticDuplicates = validator.findSemanticDuplicates(allTriples);
-```
-
----
-
-## Advanced Inference
-
-*(v1.4.5 New Feature)*
-
-### Overview
-
-Advanced Inference provides OWL 2 RL reasoning and Datalog evaluation capabilities for the knowledge graph. It supports materialization of implicit facts, rule-based inference, and human-readable explanations.
-
-### Key Components
-
-| Component | Description |
-|-----------|-------------|
-| `OWL2RLReasoner` | OWL 2 RL profile reasoning with 20+ built-in rules |
-| `DatalogEngine` | Stratified Datalog evaluation engine |
-| `InferenceExplainer` | Natural language explanation generator |
-| `ProgressReporter` | Real-time inference progress tracking |
-
-### OWL 2 RL Reasoning
-
-```typescript
-import { OWL2RLReasoner } from '@nahisaho/musubix-ontology-mcp';
-
-const reasoner = new OWL2RLReasoner({
-  maxIterations: 100,
-  enablePropertyChains: true,
-  enableInverseProperties: true
-});
-
-// Run reasoning on store
-const result = await reasoner.reason(store, {
-  onProgress: (progress) => {
-    console.log(`Iteration ${progress.iteration}: ${progress.newTriples} new triples`);
-  }
-});
-
-console.log(`Inferred ${result.inferredCount} new facts`);
-console.log(`Rules applied: ${result.rulesApplied.join(', ')}`);
-```
-
-### OWL 2 RL Rules
-
-| Rule ID | Name | Description |
-|---------|------|-------------|
-| `prp-dom` | Property Domain | Infer type from property domain |
-| `prp-rng` | Property Range | Infer type from property range |
-| `prp-inv1/2` | Inverse Properties | Infer inverse relationships |
-| `prp-trp` | Transitive Properties | Chain transitive properties |
-| `prp-symp` | Symmetric Properties | Infer symmetric relationships |
-| `cax-sco` | SubClassOf | Propagate class membership |
-| `scm-spo` | SubPropertyOf | Property subsumption |
-| `eq-rep-s/p/o` | SameAs Replacement | Substitute equal individuals |
-
-### Datalog Evaluation
-
-```typescript
-import { DatalogEngine } from '@nahisaho/musubix-ontology-mcp';
-
-const engine = new DatalogEngine();
-
-// Define rules
-const rules = [
-  {
-    head: { predicate: 'ancestor', args: ['?x', '?y'] },
-    body: [
-      { predicate: 'parent', args: ['?x', '?y'] }
-    ]
-  },
-  {
-    head: { predicate: 'ancestor', args: ['?x', '?z'] },
-    body: [
-      { predicate: 'parent', args: ['?x', '?y'] },
-      { predicate: 'ancestor', args: ['?y', '?z'] }
-    ]
-  }
-];
-
-// Evaluate rules
-const result = await engine.evaluate(rules, facts, {
-  onProgress: (progress) => {
-    console.log(`Stratum ${progress.stratum}: evaluating ${progress.rule}`);
-  }
-});
-
-console.log(`Derived ${result.derivedFacts.length} new facts`);
-```
-
-### Inference Explanation
-
-```typescript
-import { InferenceExplainer, ExplanationFormat } from '@nahisaho/musubix-ontology-mcp';
-
-const explainer = new InferenceExplainer(reasoner.getProvenanceLog());
-
-// Get explanation for a specific triple
-const explanation = explainer.explain(
-  'http://example.org/Animal',
-  'rdf:type',
-  'owl:Class',
-  ExplanationFormat.TEXT
-);
-
-console.log(explanation);
-// Output: "Animal is a Class because it is declared as owl:Class via rule cax-sco"
-
-// Generate HTML explanation
-const htmlExplanation = explainer.explain(
-  subject, predicate, object,
-  ExplanationFormat.HTML
-);
-```
-
-### Progress Reporting
-
-```typescript
-import { createProgressReporter } from '@nahisaho/musubix-ontology-mcp';
-
-const reporter = createProgressReporter({
-  onProgress: (info) => {
-    console.log(`Phase: ${info.phase}`);
-    console.log(`Iteration: ${info.iteration}/${info.maxIterations}`);
-    console.log(`Triples: ${info.totalTriples}`);
-    console.log(`New inferences: ${info.newInferences}`);
-  },
-  throttleMs: 500  // Report every 500ms
-});
-
-await reasoner.reason(store, { progressReporter: reporter });
-```
-
----
-
-## YATA Integration
-
-### What is YATA?
-
-**YATA** (Yet Another Thinking Agent) is a knowledge graph management MCP server that stores and retrieves expertise and know-how as structured data. **Note: YATA is a separate Python-based installation.**
-
-### Architecture
-
-```
-┌─────────────────────────────────────────┐
-│           AI Platform                    │
-│    (GitHub Copilot, Claude, etc.)       │
-└─────────────┬───────────────────────────┘
-              │ MCP Protocol
-      ┌───────┴───────┐
-      ↓               ↓
-┌──────────┐   ┌──────────┐
-│ MUSUBIX  │   │   YATA   │
-│   MCP    │   │   MCP    │
-│  Server  │   │  Server  │
-└────┬─────┘   └────┬─────┘
-     │              │
-     ↓              ↓
-┌──────────┐   ┌──────────┐
-│   SDD    │   │ Knowledge│
-│  Engine  │   │   Graph  │
-└──────────┘   └──────────┘
-```
-
-### YATA Client (from MUSUBIX)
-
-```typescript
-import { createYATAClient } from '@nahisaho/musubix-yata-client';
-
-// Create client
-const yata = createYATAClient({
-  endpoint: 'http://localhost:8000',
-  apiKey: process.env.YATA_API_KEY
-});
-
-// Save knowledge
-await yata.addKnowledge({
-  topic: 'jwt-authentication',
-  content: 'Best practices for JWT implementation',
-  tags: ['security', 'authentication'],
-  relatedRequirements: ['REQ-001']
-});
-
-// Search knowledge
-const results = await yata.search({
-  query: 'authentication best practices',
-  limit: 10
-});
-```
-
-### YATA Features
-
-| Feature | Description |
-|---------|-------------|
-| 34 MCP Tools | Read/write/query knowledge graphs |
-| 47 Frameworks | TypeScript, Python, React, etc. |
-| Vector Search | Semantic knowledge search |
-| Relationship Mapping | Connect knowledge nodes |
-
----
-
-## Best Practices
-
-### 1. Requirements Best Practices
-
-✅ **Recommended**:
-- Use EARS format
-- Include verifiable acceptance criteria
-- One function per requirement
-
-❌ **Avoid**:
-- Vague expressions ("appropriately", "quickly", etc.)
-- Multiple functions in one requirement
-- Implementation details in requirements
-
-### 2. Design Best Practices
-
-✅ **Recommended**:
-- Utilize all 4 C4 levels
-- Document important decisions with ADR
-- Maintain traceability to requirements
-
-❌ **Avoid**:
-- Over-detailed initial design
-- Omitting decision rationale
-- Isolated design documents
-
-### 3. Task Management Best Practices
-
-✅ **Recommended**:
-- Granularity within 4 hours
-- Clear links to requirements
-- Explicit completion criteria
-
-❌ **Avoid**:
-- Tasks too large (8+ hours)
-- Tasks without requirement links
-- Vague completion criteria
-
----
-
-## Troubleshooting
-
-### Common Problems and Solutions
-
-#### Requirements Validation Error
-
-```
-Error: EARS format not detected
-```
-
-**Solution**: Include an EARS pattern in your requirement text.
-
-```typescript
-// Before
-const text = 'Implement authentication feature';
-
-// After
-const text = 'When a user logs in, the system shall perform authentication';
-```
-
-#### Traceability Warning
-
-```
-Warning: Requirement REQ-001 has no design reference
-```
-
-**Solution**: Create a design document and link it.
-
-```typescript
-requirementsService.linkDesign('REQ-001', 'DES-001');
-```
-
-#### MCP Server Connection Error
-
-```
-Error: Cannot connect to MCP server
-```
-
-**Solution**:
-1. Verify server is running
-2. Check port number
-3. Check firewall settings
-
-```bash
-# Check server status
-ps aux | grep musubix
-```
-
-#### YATA Connection Error
-
-```
-Error: Cannot connect to YATA endpoint
-```
-
-**Solution**:
-1. Verify endpoint URL
-2. Check API key
-3. Check network settings
-
-```typescript
-const client = createYATAClient({
-  endpoint: 'http://localhost:8000',  // Correct URL
-  apiKey: process.env.YATA_API_KEY    // Verify environment variable
-});
-```
-
----
-
-## Next Steps
-
-- 📚 See [API Reference](./API-REFERENCE.md)
-- 💡 Check [Sample Projects](./examples/)
-- 🤝 Read [Contribution Guide](./CONTRIBUTING.md)
-
----
-
-## Related Documents
-
-| Document | Description |
-|----------|-------------|
-| [INSTALL-GUIDE.md](INSTALL-GUIDE.md) | Detailed installation guide |
-| [API-REFERENCE.md](API-REFERENCE.md) | API reference |
-| [evolution-from-musubi-to-musubix.md](evolution-from-musubi-to-musubix.md) | Evolution from MUSUBI |
-| [overview/MUSUBIX-v2.2.0-Advanced-Learning.md](overview/MUSUBIX-v2.2.0-Advanced-Learning.md) | v2.2.0 Advanced Learning details |
-
----
-
-**Version**: 2.2.0  
-**Last Updated**: 2026-01-08  
-**MUSUBIX Project**