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MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n[![CI](https://github.com/semanticintent/semantic-wake-intelligence-mcp/actions/workflows/ci.yml/badge.svg)](https://github.com/semanticintent/semantic-wake-intelligence-mcp/actions/workflows/ci.yml)\n[![Tests](https://img.shields.io/badge/tests-70%20passing-brightgreen.svg)](https://github.com/semanticintent/semantic-wake-intelligence-mcp)\n[![TypeScript](https://img.shields.io/badge/TypeScript-5.8-blue.svg)](https://www.typescriptlang.org/)\n[![Node.js](https://img.shields.io/badge/Node.js-20.x-green.svg)](https://nodejs.org/)\n\n[![Semantic Intent](https://img.shields.io/badge/Pattern-Semantic%20Intent-blue.svg)](https://github.com/semanticintent)\n[![Reference Implementation](https://img.shields.io/badge/Status-Reference%20Implementation-green.svg)](https://github.com/semanticintent/semantic-wake-intelligence-mcp)\n[![Hexagonal Architecture](https://img.shields.io/badge/Architecture-Hexagonal-purple.svg)](docs/ARCHITECTURE.md)\n[![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg)](CONTRIBUTING.md)\n[![Code of Conduct](https://img.shields.io/badge/Code%20of%20Conduct-Contributor%20Covenant-blue.svg)](CODE_OF_CONDUCT.md)\n\n\u003e **Wake Intelligence: 3-Layer Temporal Intelligence for AI Agents**\n\u003e\n\u003e A production-ready Model Context Protocol (MCP) server implementing a temporal intelligence \"brain\" with three layers: **Past** (causality tracking), **Present** (memory management), and **Future** (predictive pre-fetching).\n\u003e\n\u003e Reference implementation of Semantic Intent as Single Source of Truth patterns with hexagonal architecture.\n\n## 📚 Table of Contents\n\n- [Wake Intelligence Brain Architecture](#-wake-intelligence-brain-architecture)\n- [What Makes This Different](#-what-makes-this-different)\n- [Quick Start](#-quick-start)\n- [Architecture](#-architecture)\n- [Features](#features)\n- [Testing](#-testing)\n- [Database Setup](#database-setup)\n- [Contributing](#-contributing)\n- [Security](#-security)\n- [License](#license)\n\n## 🧠 Wake Intelligence Brain Architecture\n\nWake Intelligence implements a **3-layer temporal intelligence system** that learns from the past, manages the present, and predicts the future:\n\n### **Layer 1: Causality Engine (Past - WHY)**\nTracks **WHY** contexts were created and their causal relationships.\n\n**Features:**\n- ✅ Causal chain tracking (what led to what)\n- ✅ Dependency auto-detection from temporal proximity\n- ✅ Reasoning reconstruction (\"Why did I do this?\")\n- ✅ Action type taxonomy (decision, implementation, refactor, etc.)\n\n**Use Cases:**\n- Trace decision history backwards through time\n- Understand why a context was created\n- Identify context dependencies automatically\n- Reconstruct reasoning from past sessions\n\n### **Layer 2: Memory Manager (Present - HOW)**\nManages **HOW** relevant contexts are right now based on temporal patterns.\n\n**Features:**\n- ✅ 4-tier memory classification (ACTIVE, RECENT, ARCHIVED, EXPIRED)\n- ✅ LRU tracking (last access time + access count)\n- ✅ Automatic tier recalculation based on age\n- ✅ Expired context pruning\n\n**Memory Tiers:**\n- **ACTIVE**: Last accessed \u003c 1 hour ago\n- **RECENT**: Last accessed 1-24 hours ago\n- **ARCHIVED**: Last accessed 1-30 days ago\n- **EXPIRED**: Last accessed \u003e 30 days ago\n\n**Use Cases:**\n- Prioritize recent contexts in search results\n- Automatically archive old contexts\n- Prune expired contexts to save storage\n- Track context access patterns\n\n### **Layer 3: Propagation Engine (Future - WHAT)**\nPredicts **WHAT** contexts will be needed next for proactive optimization.\n\n**Features:**\n- ✅ Composite prediction scoring (40% temporal + 30% causal + 30% frequency)\n- ✅ Pattern-based next access estimation\n- ✅ Observable prediction reasoning\n- ✅ Staleness management with lazy refresh\n\n**Prediction Algorithm:**\n- **Temporal Score (40%)**: Exponential decay based on last access time\n- **Causal Score (30%)**: Position in causal chains (roots score higher)\n- **Frequency Score (30%)**: Logarithmic scaling of access count\n\n**Use Cases:**\n- Pre-fetch high-value contexts for faster retrieval\n- Cache frequently accessed contexts in memory\n- Prioritize contexts by prediction score\n- Identify patterns in context usage\n\n### **Temporal Intelligence Flow:**\n\n```\n┌─────────────────────────────────────────────────────────────┐\n│                   WAKE INTELLIGENCE BRAIN                    │\n├─────────────────────────────────────────────────────────────┤\n│                                                               │\n│  LAYER 3: PROPAGATION ENGINE (Future - WHAT)                │\n│  ┌─────────────────────────────────────────────────────┐    │\n│  │ • Predicts WHAT will be needed next                 │    │\n│  │ • Composite scoring (temporal + causal + frequency) │    │\n│  │ • Pre-fetching optimization                         │    │\n│  └─────────────────────────────────────────────────────┘    │\n│                            ▲                                  │\n│  LAYER 2: MEMORY MANAGER (Present - HOW)                    │\n│  ┌─────────────────────────────────────────────────────┐    │\n│  │ • Tracks HOW relevant contexts are NOW              │    │\n│  │ • 4-tier memory classification                      │    │\n│  │ • LRU tracking + automatic tier updates             │    │\n│  └─────────────────────────────────────────────────────┘    │\n│                            ▲                                  │\n│  LAYER 1: CAUSALITY ENGINE (Past - WHY)                     │\n│  ┌─────────────────────────────────────────────────────┐    │\n│  │ • Tracks WHY contexts were created                  │    │\n│  │ • Causal chain tracking                             │    │\n│  │ • Dependency auto-detection                         │    │\n│  └─────────────────────────────────────────────────────┘    │\n│                                                               │\n└─────────────────────────────────────────────────────────────┘\n```\n\n**Benefits:**\n- 🎯 **Learn from the past**: Understand causal relationships\n- 🎯 **Optimize the present**: Manage memory intelligently\n- 🎯 **Predict the future**: Pre-fetch what's needed next\n- 🎯 **Observable reasoning**: Every decision is explainable\n- 🎯 **Deterministic algorithms**: No black-box predictions\n\n## 🎯 What Makes This Different\n\nThis isn't just another MCP server—it's a **reference implementation** of proven semantic intent patterns:\n\n- ✅ **Semantic Anchoring**: Decisions based on meaning, not technical characteristics\n- ✅ **Intent Preservation**: Semantic contracts maintained through all transformations\n- ✅ **Observable Properties**: Behavior anchored to directly observable semantic markers\n- ✅ **Domain Boundaries**: Clear semantic ownership across layers\n\nBuilt on research from [Semantic Intent as Single Source of Truth](https://github.com/semanticintent), this implementation demonstrates how to build maintainable, AI-friendly codebases that preserve intent.\n\n---\n\n## 🚀 Quick Start\n\n### Prerequisites\n\n- Node.js 20.x or higher\n- Cloudflare account (free tier works)\n- Wrangler CLI: `npm install -g wrangler`\n\n### Installation\n\n1. **Clone the repository**\n   ```bash\n   git clone https://github.com/semanticintent/semantic-wake-intelligence-mcp.git\n   cd semantic-wake-intelligence-mcp\n   ```\n\n2. **Install dependencies**\n   ```bash\n   npm install\n   ```\n\n3. **Configure Wrangler**\n\n   Copy the example configuration:\n   ```bash\n   cp wrangler.jsonc.example wrangler.jsonc\n   ```\n\n   Create a D1 database:\n   ```bash\n   wrangler d1 create mcp-context\n   ```\n\n   Update `wrangler.jsonc` with your database ID:\n   ```jsonc\n   {\n     \"d1_databases\": [{\n       \"database_id\": \"your-database-id-from-above-command\"\n     }]\n   }\n   ```\n\n4. **Run database migrations**\n   ```bash\n   # Local development\n   wrangler d1 execute mcp-context --local --file=./migrations/0001_initial_schema.sql\n\n   # Production\n   wrangler d1 execute mcp-context --file=./migrations/0001_initial_schema.sql\n   ```\n\n5. **Start development server**\n   ```bash\n   npm run dev\n   ```\n\n### Deploy to Production\n\n```bash\nnpm run deploy\n```\n\nYour MCP server will be available at: `semantic-wake-intelligence-mcp.\u003cyour-account\u003e.workers.dev`\n\n## 📚 Learning from This Implementation\n\nThis codebase demonstrates semantic intent patterns throughout:\n\n### Architecture Files:\n- **[src/index.ts](src/index.ts)** - Dependency injection composition root (74 lines)\n- **[src/domain/](src/domain/)** - Business logic layer (ContextSnapshot, ContextService)\n- **[src/application/](src/application/)** - Orchestration layer (handlers and protocol)\n- **[src/infrastructure/](src/infrastructure/)** - Technical adapters (D1, AI, CORS)\n- **[src/presentation/](src/presentation/)** - HTTP routing layer (MCPRouter)\n\n### Documentation \u0026 Patterns:\n- **[migrations/0001_initial_schema.sql](migrations/0001_initial_schema.sql)** - Schema with semantic intent documentation\n- **[src/types.ts](src/types.ts)** - Type-safe semantic contracts\n- **[SEMANTIC_ANCHORING_GOVERNANCE.md](SEMANTIC_ANCHORING_GOVERNANCE.md)** - Governance rules and patterns\n- **[REFACTORING_PLAN.md](REFACTORING_PLAN.md)** - Complete refactoring documentation\n\nEach file includes comprehensive comments explaining **WHY** decisions preserve semantic intent, not just **WHAT** the code does. \n\n## Connect to Cloudflare AI Playground\n\nYou can connect to your MCP server from the Cloudflare AI Playground, which is a remote MCP client:\n\n1. Go to https://playground.ai.cloudflare.com/\n2. Enter your deployed MCP server URL (`remote-mcp-server-authless.\u003cyour-account\u003e.workers.dev/sse`)\n3. You can now use your MCP tools directly from the playground!\n\n## Connect Claude Desktop to your MCP server\n\nYou can also connect to your remote MCP server from local MCP clients, by using the [mcp-remote proxy](https://www.npmjs.com/package/mcp-remote). \n\nTo connect to your MCP server from Claude Desktop, follow [Anthropic's Quickstart](https://modelcontextprotocol.io/quickstart/user) and within Claude Desktop go to Settings \u003e Developer \u003e Edit Config.\n\nUpdate with this configuration:\n\n```json\n{\n  \"mcpServers\": {\n    \"semantic-context\": {\n      \"command\": \"npx\",\n      \"args\": [\n        \"mcp-remote\",\n        \"http://localhost:8787/sse\"  // or semantic-wake-intelligence-mcp.your-account.workers.dev/sse\n      ]\n    }\n  }\n}\n```\n\nRestart Claude and you should see the tools become available.\n\n## 🏗️ Architecture\n\nThis project demonstrates **Domain-Driven Hexagonal Architecture** with clean separation of concerns:\n\n```\n┌─────────────────────────────────────────────────────────┐\n│                   Presentation Layer                     │\n│              (MCPRouter - HTTP routing)                  │\n└────────────────────┬────────────────────────────────────┘\n                     │\n┌────────────────────▼────────────────────────────────────┐\n│                  Application Layer                       │\n│     (ToolExecutionHandler, MCPProtocolHandler)          │\n│              MCP Protocol \u0026 Orchestration                │\n└────────────────────┬────────────────────────────────────┘\n                     │\n┌────────────────────▼────────────────────────────────────┐\n│                    Domain Layer                          │\n│         (ContextService, ContextSnapshot)                │\n│                 Business Logic                           │\n└────────────────────┬────────────────────────────────────┘\n                     │\n┌────────────────────▼────────────────────────────────────┐\n│                Infrastructure Layer                      │\n│    (D1ContextRepository, CloudflareAIProvider)          │\n│           Technical Adapters (Ports \u0026 Adapters)         │\n└─────────────────────────────────────────────────────────┘\n```\n\n### Layer Responsibilities:\n\n**Domain Layer** ([src/domain/](src/domain/)):\n- Pure business logic independent of infrastructure\n- `ContextSnapshot`: Entity with validation rules\n- `ContextService`: Core business operations\n\n**Application Layer** ([src/application/](src/application/)):\n- Orchestrates domain operations\n- `ToolExecutionHandler`: Translates MCP tools to domain operations\n- `MCPProtocolHandler`: Manages JSON-RPC protocol\n\n**Infrastructure Layer** ([src/infrastructure/](src/infrastructure/)):\n- Technical adapters implementing ports (interfaces)\n- `D1ContextRepository`: Cloudflare D1 persistence\n- `CloudflareAIProvider`: Workers AI integration\n- `CORSMiddleware`: Cross-cutting concerns\n\n**Presentation Layer** ([src/presentation/](src/presentation/)):\n- HTTP routing and request handling\n- `MCPRouter`: Routes requests to appropriate handlers\n\n**Composition Root** ([src/index.ts](src/index.ts)):\n- Dependency injection\n- Wires all layers together\n- 74 lines (down from 483 - **90% reduction**)\n\n### Benefits:\n\n- ✅ **Testability**: Each layer independently testable\n- ✅ **Maintainability**: Clear responsibilities per layer\n- ✅ **Flexibility**: Swap infrastructure (D1 → Postgres) without touching domain\n- ✅ **Semantic Intent**: Comprehensive documentation of WHY\n- ✅ **Type Safety**: Strong TypeScript contracts throughout\n\n## Features\n\n### Core Context Management\n- **save_context**: Save conversation context with AI-powered summarization and auto-tagging\n- **load_context**: Retrieve relevant context for a project (with Layer 2 LRU tracking)\n- **search_context**: Search contexts using keyword matching (with Layer 2 access tracking)\n\n### Wake Intelligence Layer 1: Causality (Past)\n- **reconstruct_reasoning**: Understand WHY a context was created\n- **build_causal_chain**: Trace decision history backwards through time\n- **get_causality_stats**: Analytics on causal relationships and action types\n\n### Wake Intelligence Layer 2: Memory (Present)\n- **get_memory_stats**: View memory tier distribution and access patterns\n- **recalculate_memory_tiers**: Update tier classifications based on current time\n- **prune_expired_contexts**: Automatic cleanup of old, unused contexts\n\n### Wake Intelligence Layer 3: Propagation (Future)\n- **update_predictions**: Refresh prediction scores for a project\n- **get_high_value_contexts**: Retrieve contexts most likely to be accessed next\n- **get_propagation_stats**: Analytics on prediction quality and patterns\n\n## 🧪 Testing\n\nThis project includes comprehensive unit tests with **70 tests** covering all architectural layers.\n\n### Run Tests\n\n```bash\n# Run all tests\nnpm test\n\n# Run tests in watch mode\nnpm run test:watch\n\n# Run tests with UI\nnpm run test:ui\n\n# Run tests with coverage report\nnpm run test:coverage\n```\n\n### Test Coverage\n\n- ✅ **Domain Layer**: 15 tests (ContextSnapshot validation, ContextService orchestration)\n- ✅ **Application Layer**: 10 tests (ToolExecutionHandler, MCP tool dispatch)\n- ✅ **Infrastructure Layer**: 20 tests (D1Repository, CloudflareAIProvider with fallbacks)\n- ✅ **Presentation Layer**: 12 tests (MCPRouter, CORS, error handling)\n- ✅ **Integration**: 13 tests (End-to-end service flows)\n\n### Test Structure\n\nTests are co-located with source files using the `.test.ts` suffix:\n\n```\nsrc/\n├── domain/\n│   ├── models/\n│   │   ├── ContextSnapshot.ts\n│   │   └── ContextSnapshot.test.ts\n│   └── services/\n│       ├── ContextService.ts\n│       └── ContextService.test.ts\n├── application/\n│   └── handlers/\n│       ├── ToolExecutionHandler.ts\n│       └── ToolExecutionHandler.test.ts\n└── ...\n```\n\nAll tests use **Vitest** with mocking for external dependencies (D1, AI services).\n\n### Continuous Integration\n\nThis project uses **GitHub Actions** for automated testing and quality checks.\n\n**Automated Checks on Every Push/PR:**\n- ✅ TypeScript compilation (`npm run type-check`)\n- ✅ Unit tests (`npm test`)\n- ✅ Test coverage reports\n- ✅ Code formatting (Biome)\n- ✅ Linting (Biome)\n\n**Status Badges:**\n- CI status displayed at top of README\n- Automatically updates on each commit\n- Shows passing/failing state\n\n**Workflow Configuration:** [.github/workflows/ci.yml](.github/workflows/ci.yml)\n\nThe CI pipeline runs on Node.js 20.x and ensures code quality before merging.\n\n## Database Setup\n\nThis project uses Cloudflare D1 for persistent context storage.\n\n### Initial Setup\n\n1. **Create D1 Database**:\n   ```bash\n   wrangler d1 create mcp-context\n   ```\n\n2. **Update `wrangler.jsonc`** with your database ID:\n   ```jsonc\n   {\n     \"d1_databases\": [\n       {\n         \"binding\": \"DB\",\n         \"database_name\": \"mcp-context\",\n         \"database_id\": \"your-database-id-here\"\n       }\n     ]\n   }\n   ```\n\n3. **Run Initial Migration**:\n   ```bash\n   wrangler d1 execute mcp-context --file=./migrations/0001_initial_schema.sql\n   ```\n\n### Local Development\n\nFor local testing, initialize the local D1 database:\n\n```bash\nwrangler d1 execute mcp-context --local --file=./migrations/0001_initial_schema.sql\n```\n\n### Verify Schema\n\nCheck that tables were created successfully:\n\n```bash\n# Production\nwrangler d1 execute mcp-context --command=\"SELECT name FROM sqlite_master WHERE type='table'\"\n\n# Local\nwrangler d1 execute mcp-context --local --command=\"SELECT name FROM sqlite_master WHERE type='table'\"\n```\n\n### Database Migrations\n\nAll database schema changes are managed through versioned migration files in [`migrations/`](migrations/):\n\n- `0001_initial_schema.sql` - Initial context snapshots table with semantic indexes\n\nSee [migrations/README.md](migrations/README.md) for detailed migration management guide.\n\n## License\n\nThis project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.\n\n## 🔬 Research Foundation\n\nThis implementation is based on the research paper **\"Semantic Intent as Single Source of Truth: Immutable Governance for AI-Assisted Development\"**.\n\n### Core Principles Applied:\n\n1. **Semantic Over Structural** - Use meaning, not technical characteristics\n2. **Intent Preservation** - Maintain semantic contracts through transformations\n3. **Observable Anchoring** - Base behavior on directly observable properties\n4. **Immutable Governance** - Protect semantic integrity at runtime\n\n### Related Resources:\n\n- [Research Paper](https://github.com/semanticintent) (coming soon)\n- [Semantic Anchoring Governance](SEMANTIC_ANCHORING_GOVERNANCE.md)\n- [semanticintent.dev](https://semanticintent.dev) (coming soon)\n\n## 🤝 Contributing\n\nWe welcome contributions! This is a **reference implementation**, so contributions should maintain semantic intent principles.\n\n### How to Contribute\n\n1. **Read the guidelines**: [CONTRIBUTING.md](CONTRIBUTING.md)\n2. **Check existing issues**: Avoid duplicates\n3. **Follow the architecture**: Maintain layer boundaries\n4. **Add tests**: All changes need test coverage\n5. **Document intent**: Explain WHY, not just WHAT\n\n### Contribution Standards\n\n- ✅ Follow semantic intent patterns\n- ✅ Maintain hexagonal architecture\n- ✅ Add comprehensive tests\n- ✅ Include semantic documentation\n- ✅ Pass all CI checks\n\n**Quick Links:**\n- [Contributing Guide](CONTRIBUTING.md) - Detailed guidelines\n- [Code of Conduct](CODE_OF_CONDUCT.md) - Community standards\n- [Architecture Guide](docs/ARCHITECTURE.md) - Design principles\n- [Security Policy](SECURITY.md) - Report vulnerabilities\n\n### Community\n\n- 💬 [Discussions](https://github.com/semanticintent/semantic-wake-intelligence-mcp/discussions) - Ask questions\n- 🐛 [Issues](https://github.com/semanticintent/semantic-wake-intelligence-mcp/issues) - Report bugs\n- 🔒 [Security](SECURITY.md) - Report vulnerabilities privately\n\n## 🔒 Security\n\nSecurity is a top priority. Please review our [Security Policy](SECURITY.md) for:\n\n- Secrets management best practices\n- What to commit / what to exclude\n- Reporting security vulnerabilities\n- Security checklist for deployment\n\n**Found a vulnerability?** Email: security@semanticintent.dev \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsemanticintent%2Fsemantic-wake-intelligence-mcp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsemanticintent%2Fsemantic-wake-intelligence-mcp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsemanticintent%2Fsemantic-wake-intelligence-mcp/lists"}