# folder-mcp Implementation Plan
## Phase 0: Current State & Required Changes Overview
### **What We Have Now (Foundation)**
✅ **Comprehensive MCP Server**: Advanced v2.0 endpoint system (redesigned December 2024)
✅ **9 Production MCP Endpoints**: Complete document intelligence API
✅ **Claude Desktop Integration**: Fully working with 277 tests passing
✅ **Simple Transport Architecture**: MCP via stdio (local)
✅ **Real Integration Testing**: Comprehensive test suite with actual business documents
✅ **File Processing Pipeline**: PDF, DOCX, XLSX, PPTX, TXT, MD with embeddings
✅ **FAISS Vector Search**: Semantic search with Ollama GPU acceleration
✅ **Document Chunking**: Smart chunking with overlap for context preservation
✅ **Rich Metadata System**: Location info, content snippets, structured responses
✅ **Advanced TUI Framework**: Ink-based components (BorderedBox, NavigationBar, etc.)
### **Current MCP Endpoints (Core Product)**
✅ **`search`** - Semantic & regex search with rich metadata and location info
✅ **`get_document_outline`** - Extract document structure (chapters, sections, slides)
✅ **`get_document_data`** - Flexible content retrieval with metadata
✅ **`list_folders` / `list_documents`** - Directory navigation with filtering
✅ **`get_sheet_data`** - Excel/CSV data extraction with sheet selection
✅ **`get_slides`** - PowerPoint content extraction with slide numbers
✅ **`get_pages`** - PDF page-level access with precise targeting
✅ **`get_embedding`** - Vector embedding access for advanced integrations
✅ **`get_status`** - System health monitoring and capabilities reporting
❌ **LLM-Optimized Documentation** - Each endpoint needs usage documentation and better error messages
### **Final MCP Endpoints (After LLM Optimization) - 13 Total**
1. **`search`** - Enhanced with answer/locate/explore modes for LLM Q&A
2. **`explore_topics`** - NEW: Topic discovery and clustering for codebase understanding
3. **`get_context`** - NEW: Intelligent context assembly within token limits
4. **`find_code_examples`** - NEW: Practical code usage discovery
5. **`get_related`** - NEW: Document relationship navigation
6. **`get_document_outline`** - Structure navigation with summaries
7. **`get_document_data`** - Enhanced with section/page/slide parameters (absorbs get_pages/get_slides)
8. **`list_folders`** - Folder browsing with metadata
9. **`list_documents`** - Enhanced with document type detection
10. **`get_sheet_data`** - Structured Excel/CSV data as JSON
11. **`get_status`** - System health and capabilities
12. **`help`** - NEW: LLM-optimized endpoint documentation
13. **~~get_embedding~~** - REMOVED: No LLM use case
14. **~~get_pages~~** - MERGED into get_document_data
15. **~~get_slides~~** - MERGED into get_document_data
### **What We Need to Build**
❌ **Configuration System**: Comprehensive configuration architecture driving all features
❌ **Intelligent Embedding System**: Flexible backends with hardware optimization
❌ **Enhanced Search**: Add answer/locate/explore modes to search endpoint for LLM Q&A
❌ **Topic Discovery**: New `explore_topics` endpoint with semantic clustering
❌ **Context Assembly**: New `get_context` endpoint for intelligent content aggregation
❌ **Code Examples**: New `find_code_examples` endpoint for practical usage discovery
❌ **Relationship Mapping**: New `get_related` endpoint for document navigation
❌ **Help System**: New `help` endpoint with LLM-optimized documentation
❌ **Enhanced Document Data**: Add `section` parameter to `get_document_data`, merge in pages/slides functionality
❌ **Endpoint Consolidation**: Remove `get_embedding`, merge `get_pages`/`get_slides` into `get_document_data`
❌ **LLM-Optimized Documentation**: Usage documentation and error messages for all endpoints
❌ **Daemon Process**: Configuration-aware background service managing single multi-folder MCP server
❌ **Multi-Folder MCP Server**: Extend current server to handle multiple folders via configuration
❌ **Admin TUI**: Configuration-driven management interface
❌ **CLI/TUI Parity**: Identical functionality with configuration at the core
❌ **Auto-Start**: Configurable daemon startup behavior
❌ **SSE Remote Access**: Express server with /mcp/sse endpoint for remote connections
❌ **Cloudflare Tunnel**: Simple remote access without port forwarding
### **Architecture Transformation**
```bash
# FROM: Manual single-folder with fixed backend
node dist/mcp-server.js ~/Documents
# → 9 MCP endpoints serve one folder with Ollama-only embeddings
# TO: Configuration-driven multi-folder with intelligent backends
folder-mcp # Reads ~/.folder-mcp/config.yaml
Daemon → Single MCP Server → Multiple folders (from config)
├── ~/Documents/.folder-mcp/
├── ~/Projects/.folder-mcp/
└── ~/Photos/.folder-mcp/
# → 13 MCP endpoints serve configured folders (enhanced + new)
# → Intelligent backend selection (Ollama, direct, auto)
# → Pre-computed clustering for topic discovery
# → Simple transports: stdio (local) or SSE (remote)
```
### **Current Strengths to Build Upon**
✅ **Working MCP Endpoints**: 9 endpoints handle documents and code effectively (will enhance and expand to 13)
✅ **Embedding Pipeline**: Ollama integration with GPU acceleration
✅ **Document Chunking**: Smart chunking with overlap for context
✅ **Rich Metadata System**: Location info, content snippets, structured responses
✅ **Token Management**: Proper pagination and response sizing for LLMs
✅ **Error Handling**: Robust error recovery and validation
✅ **Performance**: Optimized for large documents and complex queries
✅ **Real-World Tested**: 36+ business documents in test suite validate functionality
## Configuration Architecture
**Core Philosophy**: Configuration drives flexibility throughout the system. Every aspect of folder-mcp is configurable, with smart defaults that work out-of-the-box while enabling deep customization for power users.
### Configuration System (After Phase 7)
1. **Defaults**: `config-defaults.yaml` with sensible defaults
2. **User Config**: `~/.folder-mcp/config.yaml` for user overrides
3. **CLI Arguments**: Command-line flags for temporary overrides
**Schema-Driven**: Configuration structure defined by schemas that drive both validation and UI generation
### Configuration Principles
- **Progressive Disclosure**: Simple users see simple options, advanced users can access everything
- **Strategy Pattern**: All major components pluggable via configuration
- **Feature Flags**: Enable/disable features without code changes
- **Performance Tuning**: Every performance parameter exposed in config
- **Zero Config**: Works perfectly with no configuration file
- **Config Validation**: Comprehensive validation with helpful error messages
- **Live Reload**: Changes apply without restart where possible
- **Smart Defaults**: Sensible defaults that maximize functionality
- **Simple Transport**: Following Crawl4AI, only stdio and SSE transports supported
### Core Configuration Structure
The configuration system uses a flat YAML structure with these main sections:
- **general**: Basic settings (autoStart, logLevel, telemetry)
- **daemon**: Process management (port, pidFile, healthCheck, autoRestart)
- **embeddings**: Backend selection (ollama, direct, auto) with hardware optimization
- **search**: Core search and clustering configuration
- **transport**: Simple transports only (stdio for local, SSE for remote)
- **authentication**: API key-based authentication
- **folders**: Default settings and per-folder overrides
- **performance**: Resource limits and monitoring
- **ui**: Theme and display preferences for CLI/TUI
- **features**: Feature flags for new capabilities
Configuration follows simple override: config-defaults.yaml → config.yaml → CLI Arguments
**Note**: Phase 7 replaces the original 6-source hierarchical system with this simplified approach
### Configuration Usage Examples
```bash
# Override via CLI arguments
FOLDER_MCP_EMBEDDINGS_BACKEND=direct folder-mcp add ~/Documents
# Override via CLI flags
folder-mcp --config ~/.folder-mcp/prod.yaml add ~/Documents
folder-mcp --embeddings-backend ollama --log-level debug
# Query current configuration
folder-mcp config get embeddings.backend
folder-mcp config set search.clustering.enabled true
folder-mcp config validate
# Enable new features
folder-mcp config set features.topicDiscovery true
# Remote access setup
folder-mcp auth create "My Claude Desktop" # Creates API key
folder-mcp tunnel setup # Interactive Cloudflare setup
```
## Component Definitions & Terminology
This section establishes the common terminology used throughout this document, with emphasis on configuration-driven components.
### Core Components
**Configuration Manager**
The central component that loads, validates, merges, and provides configuration to all other components. It handles the simple two-file system (defaults and user config), validation via schemas, and live reloading. The Configuration Manager is the first component initialized and drives the behavior of all other components.
**Daemon**
A configuration-aware background process that runs continuously and manages the lifecycle of a single multi-folder MCP server. The daemon's behavior is entirely driven by configuration, including auto-start behavior, health check intervals, and restart policies.
**MCP Server**
A single process that serves multiple folders via the Model Context Protocol. The MCP server's capabilities, performance characteristics, and behavior are determined by configuration. It dynamically loads folder-specific configurations and adjusts its behavior accordingly. The server provides 13 endpoints for comprehensive document intelligence, including enhanced search with answer modes, topic discovery, context assembly, and relationship navigation.
**Express Server**
A lightweight HTTP server built with Express.js (a minimal web framework for Node.js) that provides remote access to the MCP server via Server-Sent Events (SSE). Following Crawl4AI's proven pattern, it exposes three endpoints: `/health` for monitoring, `/` for basic info, and `/mcp/sse` for the MCP protocol. Uses simple Bearer token authentication. Express is chosen for its simplicity, widespread adoption, and excellent SSE support.
**Embedding System**
The modular system responsible for generating vector embeddings from text. It supports multiple backends (Ollama, direct sentence-transformers, auto-selection) chosen via configuration. The system adapts to available hardware and memory constraints for optimal performance.
**Search System**
A FAISS-based vector search system with pre-computed clustering for topic discovery. The search system provides both specific search capabilities and topic exploration through two distinct endpoints, with behavior driven by configuration.
**Transport System**
Simple, proven transport mechanisms optimized for LLM consumption: stdio for local connections and Server-Sent Events (SSE) for remote access. Following Crawl4AI's pattern, the system deliberately avoids WebSockets and other complex abstractions in favor of battle-tested simplicity. Remote access uses Express.js with specific endpoints (/health, /mcp/sse) and Bearer token authentication. The transport choice is based on extensive analysis of how LLMs actually consume MCP services - prioritizing reliability, simplicity, and streaming capabilities over bidirectional communication that LLMs don't need.
**CLI (Command Line Interface)**
The command-line tool that users invoke via `folder-mcp`. The CLI respects all configuration sources and provides flags to override any configuration option. It includes commands to inspect and modify configuration.
**TUI (Terminal User Interface)**
The interactive, full-screen terminal interface built with existing Ink framework. The TUI's appearance, behavior, and capabilities are configuration-driven, including theme, animation settings, and update intervals.
**Admin Screen (Management Console)**
The main TUI screen that displays all shared folders in a table format with their status, model, and port information. The layout and information displayed are configurable.
**Configuration Wizard**
The initial TUI flow that guides users through creating their first configuration file. It uses progressive disclosure to show only relevant options based on user choices.
### Operational Terms
**Configuration Profile**
A named set of configuration values that can be activated for different scenarios (development, production, resource-constrained, etc.).
**Configuration Override**
A configuration value specified at runtime that takes precedence over file-based configuration.
**Feature Flag**
A configuration setting that enables or disables specific functionality without code changes. Features can be toggled based on readiness, user preference, or system capabilities.
**Strategy Selection**
Configuration-driven selection of implementation strategies (e.g., embedding backend, clustering algorithm, transport protocol).
**Embedding Backend**
The implementation used to generate embeddings. Options include "ollama" (existing), "direct" (new sentence-transformers), or "auto" (automatic selection).
**Cluster ID**
Pre-computed identifiers assigned during indexing that group similar content. Two types: semantic (by meaning) and folder (by location). These enable fast topic discovery without runtime clustering overhead.
## Project Goal
Create a configuration-driven daemon-based system that manages multiple MCP servers for shared folders, with TUI/CLI interfaces, intelligent model selection, and 13 LLM-optimized endpoints including enhanced search with answer modes, topic discovery, context assembly, code examples, relationship navigation, and comprehensive help - all designed for optimal LLM consumption patterns.
## System Architecture
```
┌─────────────────────────────────────────────────────────┐
│ User Interfaces │
├───────────────────────────┬─────────────────────────────┤
│ CLI │ TUI │
│ (headless) │ (interactive) │
│ │ │
│ folder-mcp add ~/docs │ ┌─┐ Management Console │
│ folder-mcp config set │ │ │ - Add/remove folders │
│ folder-mcp status │ │ │ - View status │
│ folder-mcp tunnel │ │ │ - Configure settings │
│ │ └─┘ - Real-time updates │
└───────────────────────────┴─────────────────────────────┘
│
┌───────▼────────┐
│ Configuration │
│ Manager │
└───────┬────────┘
│
┌────▼────┐
│ Daemon │ ← Driven by Config
│ Process │ (~/.folder-mcp/)
└────┬────┘
│ Manages
▼
┌───────────────┐
│ MCP Server │ ← Multi-folder
└───────┬───────┘ stdio (local)
│
├─────────────────┐
│ │
Local │ Remote │
(stdio)│ (SSE)│
│ │
▼ ▼
┌───────────────┐ ┌───────────────┐
│ Claude Desktop│ │ Express Server│
│ VS Code │ │ :3000/mcp/sse│
│ Cursor │ │ → Cloudflare│
└───────────────┘ └───────────────┘
│
┌───────────┴────────────┐
│ 13 MCP Endpoints │
│ ┌─────────────────┐ │
│ │ - search │ │
│ │ - explore_topics│ │
│ │ - get_context │ │
│ │ - find_code_ex. │ │
│ │ - get_related │ │
│ │ - get_doc_* │ │
│ │ - list_* │ │
│ │ - get_sheet_* │ │
│ │ - get_status │ │
│ │ - help │ │
│ └─────────────────┘ │
└───────────┬────────────┘
│
┌───────────────────┼───────────────────┐
▼ ▼ ▼
[~/Documents] [~/Projects] [~/Photos]
.folder-mcp/ .folder-mcp/ .folder-mcp/
├── vectors/ ├── vectors/ ├── vectors/
├── embeddings/ ├── embeddings/ ├── embeddings/
└── metadata/ └── metadata/ └── metadata/
```
### Component Responsibilities
**Configuration Manager**
- Load and merge configuration from all sources
- Validate configuration against schema
- Provide configuration to all components
- Handle live configuration updates
- Manage configuration settings
**Daemon Process**
- Configuration-driven lifecycle management
- Auto-start based on configuration
- Health monitoring with configurable intervals
- Process recovery with configurable policies
- Performance monitoring per configuration
**CLI Interface**
- Parse command arguments and configuration overrides
- Display configuration-aware help
- Provide configuration management commands
- Support all operations with config overrides
**TUI Interface**
- Render UI based on configuration (theme, style)
- Provide configuration editing interface
- Display configuration-driven status information
- Enable real-time configuration updates
**MCP Server**
- Serve all 13 endpoints (search, explore_topics, get_context, find_code_examples, get_related, get_document_*, list_*, get_sheet_data, get_status, help)
- Enhanced search with answer/locate/explore modes
- Support multiple embedding backends
- Apply folder-specific configurations
- Honor performance settings
- Communicate via stdio (local) or SSE (remote)
**Express Server** (for remote access)
- Serve MCP protocol over SSE at `/mcp/sse`
- Provide health check at `/health`
- Handle API key authentication
- Support CORS for web clients
- Integrate with Cloudflare tunnel
**Embedding System**
- Provide modular backends (Ollama, direct sentence-transformers, auto)
- Automatic hardware detection and optimization
- Memory-adaptive batch processing
- Configuration-driven backend selection
**Search System**
- FAISS-based vector search with pre-computed clustering
- Two search endpoints: specific (search) and discovery (explore_topics)
- Smart result ranking and filtering
- Configuration-driven behavior
## UX-Led Development Philosophy
**Core Principle**: Every feature is designed from the user experience first, then implemented to support that experience, with configuration enabling different user preferences.
### **Development Approach**
1. **Configuration First**: Design configuration schema before implementation
2. **Best Defaults**: Choose defaults that enable maximum functionality
3. **CLI/TUI Parity**: Both interfaces expose same configuration options
4. **Progressive Disclosure**: Simple config for simple needs, advanced for power users
5. **User Story Driven**: Each feature starts with user configuration needs
6. **Adaptive Planning**: Configuration schema evolves with learnings
### **Configuration-Driven UX**
- **Templates**: Example configurations for common use cases
- **Wizards**: Interactive configuration for complex settings
- **Validation**: Helpful error messages for configuration issues
- **Defaults**: Smart defaults that work without configuration
- **Validation**: Schema-based validation for all settings
## Phase 1: MCP Endpoint Redesign ✅ COMPLETED (December 2024)
**📋 [Detailed Phase Plan](completed/Phase-1.mcp-endpoint-redesign.md)**
**Goal**: Replace current MCP endpoints with streamlined, LLM-friendly API
**Why**: Original endpoints were too granular, requiring LLMs to orchestrate complex workflows. The redesign creates intent-driven endpoints that complete user journeys efficiently while respecting token limits.
**Implementation Summary**:
This phase successfully transitioned the MCP server from a tool-centric, low-level API to a user-intent-driven and LLM-friendly interface with 8 streamlined endpoints, token-aware pagination, rich search results, and comprehensive test coverage.
**Key Achievements**:
- **Complete Endpoint Redesign**: 8 new streamlined endpoints (search, get_document_outline, get_document_data, list_folders/documents, get_sheet_data, get_slides, get_pages, get_embedding, get_status)
- **Test Coverage**: 34/34 MCP endpoint tests + 6/6 integration tests + 12/12 performance tests passing
- **Real-World Validation**: 36 business documents in test suite including Marketing, Finance, Engineering, and Legal documents
- **Production Ready**: Full server validation with operational file watching and endpoint responses
## Phase 2: Real Folder-Oriented Tests ✅ COMPLETED (June 2025)
**📋 [Detailed Phase Plan](completed/Phase-2.robust-real-folder-oriented-tests-implementation.md)**
**Goal**: Replace mock-based tests with real folder-oriented tests using actual files and real cache directories
**Why**: Existing tests used mocks and fake data instead of testing against real files, meaning system functionality wasn't actually validated.
**Implementation Summary**:
Achieved **100% real integration testing** with zero tolerance for mocks. All tests now run against actual documents, create real cache directories, and perform real indexing operations.
**Key Achievements**:
- **Real File Testing**: All 137+ integration tests run against actual business documents
- **Zero Mock Tolerance**: 95% compliance achieved - only legitimate mocks for error simulation remain
- **Real Embeddings**: Production-ready Ollama API integration with actual vector generation
- **Complete Coverage**: All 10 user stories from PRD tested with comprehensive real data workflows
- **Performance Benchmarks**: Real-world performance measurements (0.3ms/file processing, 645+ embeddings/sec)
## Phase 3: TUI Design & Implementation ✅ COMPLETED (2025)
**📋 [Detailed Phase Plan](completed/Phase-3.tui-design-and-implementation-plan.md)**
**Goal**: Create groundbreaking terminal user interface with Claude Code-level polish
**Why**: Needed intuitive TUI for configuration management with smooth animations and modern design.
**Implementation Summary**:
Built a complete TUI framework with React Ink components, responsive design, and sophisticated animation system that exceeds modern GUI application standards.
**Key Achievements**:
- **Visual Demo System**: Complete interactive showcase of all design elements
- **Animation Framework**: Breathing progress bars, focus transitions, and smooth state changes
- **Responsive Design**: Intelligent adaptation to terminal size with breakpoint system
- **Component Architecture**: Reusable components (BorderedBox, GenericListPanel, ConfigurationItems)
- **Claude Code Polish**: Interface that feels as polished as professional GUI applications
## Phase 4: TUI Components Development ✅ COMPLETED (July 2025)
**📋 [Detailed Phase Plan](completed/Phase-4.tui-components-development.md)**
**Goal**: Extend TUI framework with comprehensive configuration components
**Why**: Needed full configuration management capabilities with validation, file pickers, selections, and destructive operation confirmations.
**Implementation Summary**:
Built production-ready TUI component library with sophisticated features including validation, file navigation, confirmation dialogs, and responsive layouts.
**Key Achievements**:
- **TextInput Validation**: Number, email, IP, regex validation with visual error states
- **SelectionListItem**: Radio/checkbox selections with vertical/horizontal layouts and metadata display
- **FilePickerListItem**: Real file system navigation with security and cross-platform support
- **Destructive Confirmations**: Inline confirmation dialogs with severity levels and smart button states
- **Animation Components**: AnimationContainer and ProgressBar with responsive behavior
- **Zero TypeScript Errors**: Complete elimination of 397 TypeScript errors while maintaining full functionality
## Phase 5: TypeScript Error Elimination ✅ COMPLETED (July 2025)
**📋 [Detailed Phase Plan](completed/Phase-5.tui-eliminate-all-dev-errors.md)**
**Goal**: Systematically eliminate all TypeScript errors while maintaining fully functional TUI
**Why**: 397 TypeScript errors needed resolution to ensure code quality and maintainability.
**Implementation Summary**:
Achieved zero TypeScript errors through systematic error categorization and resolution while maintaining complete TUI functionality.
**Key Achievements**:
- **Complete Error Resolution**: 397 → 0 errors (100% elimination)
- **Systematic Approach**: Module resolution, component errors, type safety, compatibility, and optional properties
- **No Regression**: TUI remained fully functional throughout the process
- **Architecture Compliance**: All fixes maintained clean architecture boundaries
## Phase 6: Configuration Foundation & CLI/TUI Parity ✅ COMPLETED (July 2025)
**📋 [Detailed Phase Plan](completed/Phase-6-Configuration-Foundation-plan.md)**
**Goal**: Establish comprehensive configuration system as foundation for all features
**Why**: Need unified configuration system driving all functionality with CLI/TUI parity.
**Implementation Summary**:
Built complete configuration architecture with hierarchical loading, validation, hot reload, and daemon-based service management.
**Key Achievements**:
- **Configuration Architecture**: Hierarchical system (defaults → system → user → environment → runtime)
- **Event-Driven Daemon**: Background service with health monitoring and auto-restart (127 tests passing)
- **Multi-Folder MCP Server**: Extended server for multiple folder support with real-data testing
- **CLI Command Suite**: Full configuration management commands (42 tests passing)
- **Unified System**: Single configuration foundation driving all components
## Phase 7: Configuration System Overhaul ✅ COMPLETED (July 2025)
**📋 [Detailed Phase Plan](completed/Phase-7-configuration-system-overhaul-plan.md)**
**Goal**: Replace complex 6-source configuration with simple schema-driven system
**Why**: Original system was too complex; needed simple 2-file system with schema-driven UI generation.
**Implementation Summary**:
Successfully replaced complex configuration with elegant 2-file system and schema-driven interface generation.
**Key Achievements**:
- **Simplified Architecture**: config-defaults.yaml → config.yaml → CLI arguments (from 6-source system)
- **Schema-Driven UI**: Automatic TUI generation from configuration schemas
- **Clean Separation**: User configurations (YAML) vs system constants (JSON)
- **Test Cleanup**: Removed old system tests, implemented new validation system
- **Maintainable Codebase**: Clear architecture with proper DI boundaries
**User Stories**:
- **As a user, I want sensible defaults**: System works without any configuration
- **As a user, I want to customize behavior**: Easy configuration for common needs
- **As a power user, I want full control**: Every aspect configurable
- **As a user, I want to add a folder to be shared**: `folder-mcp add ~/Documents`
- **As a user, I want to see all shared folders**: `folder-mcp list`
- **As a user, I want to check configuration**: `folder-mcp config get`
## Phase 8: Unified Application Flow ✅ COMPLETED (January 2025)
**📋 [Detailed Phase Plan](completed/Phase-8-Unified-Application-Flow-plan.md)**
**Goal**: Create unified application experience combining all components into cohesive, production-ready system
**Why**: Transform from single-folder proof-of-concept into complete multi-folder indexing system with unified TUI interface.
**Implementation Summary**:
Phase 8 achieved a complete architectural transformation, far exceeding the original scope. What began as "Enhanced UX & Core Features" became a comprehensive system rewrite delivering a production-ready multi-folder indexing platform.
**Major Infrastructure Achievements**:
- **✅ Multi-Folder Multi-Model System**: Complete support for multiple folders with different embedding models
- **✅ Unified TUI Application**: Full-featured terminal interface with wizard, management, and real-time status
- **✅ Daemon-Centric Architecture**: WebSocket-based daemon with persistent state and multi-client support
- **✅ Python Embeddings Pipeline**: GPU-accelerated embeddings with 8 supported models and hardware detection
- **✅ SQLite-vec Vector Storage**: Production-ready vector database with persistent storage per folder
- **✅ Dynamic Model Selection**: Hardware-aware defaults with sequential processing and intelligent switching
- **✅ Real-time Progress Reporting**: Live status updates during indexing with detailed progress tracking
**Quality & Testing Achievements**:
- **✅ Zero Test Failures**: 905+ tests passing with comprehensive coverage
- **✅ Cross-Platform Support**: Windows, macOS, and Linux compatibility
- **✅ Performance Optimization**: GPU acceleration, model caching, memory management
- **✅ Error Recovery**: Graceful degradation and comprehensive error handling
**User Experience Transformation**:
- **✅ Intelligent First-Run**: Wizard with smart defaults and hardware detection
- **✅ Real-Time Management**: Live folder status with progress bars and validation
- **✅ Multi-Client Architecture**: Multiple TUI instances with WebSocket synchronization
- **✅ Production-Ready CLI**: Complete command-line interface with folder management
**Technical Foundation Built**:
The complete technical foundation for all future development including configuration architecture, process management, keep-alive systems, graceful shutdown, WebSocket communication, error recovery, and extensible design supporting additional features and deployment options.
## Phase 9: Perfect Indexing & Semantic Enhancement ✅ PARTIALLY COMPLETED (September 2025)
**Goal**: Perfect indexing, embeddings creation, semantic key phrases extraction, and multi-folder MCP endpoints support
**Why**: Phase 8 built multi-folder infrastructure. Phase 9 was intended to perfect the semantic quality AND connect MCP endpoints to the multi-folder system.
**What Completed**: Perfect semantic extraction pipeline with enhanced keyword quality, document-level aggregation, and multi-model optimization.
**What Was Cut Off**: MCP endpoints recreation to work with multi-folder system - moved to separate phase for focused implementation.
**Implementation Summary**:
Phase 9 achieved outstanding semantic quality improvements with research-validated techniques, but was strategically cut off after completing the indexing foundation to allow focused work on MCP endpoints separately.
**Key Achievements**:
- **✅ Enhanced Semantic Extraction**: KeyBERT and advanced clustering delivering >80% multiword phrases (vs previous 11% single words)
- **✅ Document-Level Aggregation**: Every document has pre-computed semantic metadata with 93%+ extraction confidence
- **✅ Model Excellence**: All 5 curated models (BGE-M3, E5-Large, MiniLM, E5-ONNX variants) optimized with model-specific configurations
- **✅ Quality Transformation**: >90% domain-specific topics (vs previous 29% generic), realistic readability scores (40-60 vs broken 3-11)
- **✅ Performance Optimization**: <2x processing time despite major quality improvements
- **✅ Database Storage**: Rich semantic metadata stored persistently for fast navigation access
**Deferred to Next Phase**:
- ❌ **MCP Endpoints Multi-Folder Integration**: Connecting endpoints to Phase 8's multi-folder infrastructure
- ❌ **Multi-Folder Search**: Cross-folder search and folder-aware operations
- ❌ **Folder-Aware Responses**: MCP responses that understand multi-folder context
**Strategic Decision**: Cut Phase 9 after indexing completion to create focused, manageable phases rather than one massive implementation.
## Phase 10: Semantic Endpoint Navigation ✅ COMPLETED (September-October 2025)
**Goal**: Transform folder-mcp from basic file server into intelligent knowledge navigator that LLMs can explore semantically
**Why**: Phase 9 built perfect semantic foundation. Phase 10 leverages this to create LLM-native navigation where every endpoint returns rich semantic metadata enabling informed decisions without wasting context.
**What**: Built comprehensive semantic navigation system with 9 production endpoints providing exploration, search, and content retrieval capabilities.
**Implementation Summary**:
Phase 10 delivered a complete semantic navigation system with dual search paths (exploration vs search), rich metadata at every level, and context-efficient responses optimized for LLM consumption.
**Key Achievements**:
- **✅ 9 Production Endpoints**: Complete semantic navigation API with exploration and search paths
- **✅ Dual Search System**: Separate endpoints for content search (chunk-level) vs document discovery (document-level)
- **✅ Rich Semantic Metadata**: Pre-computed key phrases, readability scores, and document summaries at every navigation level
- **✅ Context-Efficient Design**: Pagination, continuation tokens, and smart defaults prevent overwhelming LLM context
- **✅ Hybrid Search**: Combines semantic similarity with exact term matching for technical precision
- **✅ Download URLs**: Pre-generated time-limited tokens embedded in all file-referencing responses
- **✅ Cross-Platform Paths**: Auto-normalization handles Unix/Windows/mixed path formats
- **✅ Performance**: All endpoints <200ms using pre-computed Phase 9 semantic data
- **✅ Zero Bugs**: Comprehensive A2E validation found no issues, database integrity verified
**Endpoints Created** (9 total):
**Discovery & Navigation** (5 endpoints):
1. **`get_server_info`** - Server capabilities and endpoint discovery with usage hints
2. **`list_folders`** - List all indexed folders with aggregated key phrases and recent files
3. **`explore`** - ls-like hierarchical navigation with subdirectories AND files, semantic context per location
4. **`list_documents`** - Path-aware document listing with pagination (default 20 docs to preserve context)
5. **`get_document_metadata`** - Document structure with chunk-level key phrases for section discovery
**Content Retrieval** (2 endpoints):
6. **`get_chunks`** - Targeted chunk extraction by ID after metadata exploration
7. **`get_document_text`** - Clean text extraction with character-based pagination, formatting loss warnings
**Search** (2 endpoints):
8. **`search_content`** - Chunk-level semantic search with hybrid scoring (semantic concepts + exact terms)
9. **`find_documents`** - Document-level topic discovery using document embeddings
**Key Design Decisions**:
- **Exploration vs Search**: Two distinct navigation paths for different LLM needs
- **Content-First Search**: `search_content` returns full chunk content (not just IDs) to eliminate round trips
- **Flat Chunk Results**: Search returns ranked chunks across all documents (not grouped by file)
- **No download_file Endpoint**: Download URLs pre-generated and embedded in all file references
- **Model-Independent Scoring**: Removed fixed min_score thresholds - works across all embedding models
- **Two-Phase Indexing**: Chunk embeddings (Sprint 7.5 vec0) + document embeddings (Sprint 9)
**Navigation Patterns**:
```
Exploration: get_server_info → list_folders → explore → get_document_text
Search: get_server_info → search_content → get_chunks or get_document_text
Discovery: get_server_info → find_documents → get_document_text
```
**Success Criteria Met**:
- ✅ All endpoints respond in <200ms using pre-computed data
- ✅ 75% reduction in unnecessary content retrieval through smart pagination
- ✅ Semantic metadata enables intelligent LLM decision-making
- ✅ Both exploration and search paths validated end-to-end
- ✅ Zero bugs found during comprehensive integration testing
**📋 [Detailed Phase Plan](completed/Phase-10-Semantic-Endpoint-Navigation-EPIC.md)**
## Phase 11: Complete App Interface
**Goal**: Build complete 4-screen TUI application
**Why**: Core functionality is complete. Need professional multi-screen interface for production use.
**4-Screen Architecture**:
| Screen | Purpose |
|--------|---------|
| **Manage Folders** | Add/remove folders, model selection, indexing status |
| **Connect** | Local MCP setup (JSON configs for Claude Desktop, VSCode, etc.) |
| **Activity Log** | Live logs, indexing events, daemon health |
| **Settings** | Theme, log verbosity, default model |
**Sprints**:
- Sprint 1 ✅: Navigation Framework (landscape/portrait adaptive, arrow-key switching)
- Sprint 2 ✅: Settings Screen (Theme, Log Verbosity settings)
- Sprint 3 ✅: Default Model System (FMDM integration, Settings UI, Wizard simplification, CLI integration)
- Sprint 4 ✅: Activity Log Screen (Progress River model, real-time daemon events, code review fixes)
- Sprint 5 ✅: Connect Screen (9 MCP clients: Claude Desktop, Claude Code, Cursor, Windsurf, Codex CLI, Cline, Qwen Code, GitHub Copilot CLI, VS Code)
**Components**: All screens use existing tested components (GenericListPanel, SelectionListItem, TextListItem, ButtonsRow, LogItem). NO new components needed.
**Success Criteria**: 4 functional screens with responsive layouts and keyboard navigation.
## Phase 12: Remote Access (Connect Screen Enhancement)
**Goal**: Add remote access capabilities to the Connect screen built in Phase 11
**Why**: Users want to access their knowledge base from anywhere, not just locally.
**What** (Additions to Connect Screen):
- Enable/disable remote access toggle (SelectionListItem)
- Cloudflare tunnel setup wizard
- Custom domain configuration
- Authentication settings (API keys)
- Connection status indicator
- Remote connection string (when enabled)
**Backend Work**:
- Express server with SSE endpoint at `/mcp/sse`
- Cloudflare tunnel integration
- API key authentication
- Public URL generation for file downloads
**Current REST API Endpoints (14 total - 13 implemented, 1 planned)**:
**System & Health**:
- `GET /api/v1/health` - Health check endpoint
- `GET /api/v1/server/info` - Server information and capabilities
- `GET /api/v1` and `GET /api` - API root information
**Folder Operations**:
- `GET /api/v1/folders` - List all configured folders with status
- `GET /api/v1/folders/:folderPath/explore` - Navigate folder hierarchy with ls-like interface
**Document Discovery**:
- `GET /api/v1/folders/:folderPath/documents` - List documents in folder with metadata
- `POST /api/v1/folders/:folderPath/find_documents` - Document-level semantic search ✅ COMPLETED (Phase 10 Sprint 9)
**Document Content Retrieval**:
- `GET /api/v1/folders/:folderPath/documents/:filePath` - Get full document with all chunks
- `GET /api/v1/folders/:folderPath/documents/:filePath/metadata` - Get document metadata with chunk list
- `POST /api/v1/folders/:folderPath/documents/:filePath/chunks` - Retrieve specific chunks by ID
- `GET /api/v1/folders/:folderPath/documents/:filePath/text` - Get extracted plain text with pagination
- `GET /api/v1/folders/:folderPath/documents/:filePath/outline` - Get document structure outline
**Search Operations**:
- `POST /api/v1/folders/:folderPath/search_content` - Chunk-level semantic search with hybrid scoring (Sprint 8)
**File Download**:
- `GET /api/v1/download` - Token-based file download for remote access
- Maintain token-based authentication for security
- Support WebFetch tool compatibility for file retrieval
- Security configuration (API keys, rate limiting, audit logging)
- VSCode MCP integration optimization
**Success Criteria**: Users can securely access their knowledge base remotely with proper authentication.
## Phase 13: Release 1.0 - Production System & Advanced Features
**Goal**: Deliver complete production-ready system with advanced capabilities
**Why**: Combine production system management with advanced features for comprehensive 1.0 release.
**What**:
- **Production System Management**: Enhanced daemon process management, multi-agent connection support, OS integration (auto-start on boot)
- **Advanced LLM Features**: New endpoints (`explore_topics`, `get_context`, `find_code_examples`, `get_related`, `help`)
- **Extended Capabilities**: Broader file format support, code intelligence features, performance optimizations
- **Versioning & Installation**: Semantic versioning, npm registry publishing, update notifications
- **CI/CD Pipeline**: Automated testing, building, and deployment pipeline for reliable releases
- **Release Readiness**: Complete testing, documentation, and release automation
**Success Criteria**: Complete production system with advanced features and automated CI/CD pipeline ready for 1.0 release.
## Phase 14: Public Release
**Goal**: Deliver polished public release with comprehensive documentation
**Why**: Make the system publicly available with professional documentation and support materials.
**What**:
- Comprehensive user documentation and guides
- API reference and developer documentation
- Cross-platform compatibility verification
- Public release preparation and distribution
**Success Criteria**: Polished system ready for public use with complete documentation.
## Success Metrics
1. **Feature Completeness**: All 13 MCP endpoints fully functional
2. **Ease of Use**: 90% of users succeed with default settings
3. **Search Effectiveness**: Enhanced search modes deliver relevant results
4. **LLM Integration**: Endpoints optimized for AI consumption
5. **Performance**: Fast indexing and search across large repositories
6. **Reliability**: Production-ready with monitoring and resilience
7. **Flexibility**: Power users can customize all aspects
8. **Performance Impact**: <5% overhead from configuration system
9. **LLM Optimization**: Transport layer optimized for LLM consumption patterns
10. **LLM Usability**: LLMs can use endpoints effectively without exploration
11. **Error Recovery Rate**: LLMs successfully recover from 90%+ of errors
12. **Documentation Quality**: Users and LLMs find documentation helpful
---
*This plan has completed Phase 10 (Semantic Endpoint Navigation), as Phases 1-10 represent the substantial work already completed. Phase 9 was partially completed with outstanding semantic enhancement work (indexing, embeddings, and document-level aggregation) but was strategically cut off before MCP endpoints work to create focused phases. Phase 10 then completed the semantic navigation system with 9 production endpoints. This plan follows configuration-driven development principles where every feature is designed to be configurable from the start. The configuration system is not an afterthought but the core architectural principle that enables flexibility, customization, and future extensibility. The upcoming phases build systematically: Phase 11 (TUI rebuild) → Phase 12 (remote access) → Phase 13+ (production release & advanced features). Smart defaults ensure the system works excellently out-of-the-box while providing deep customization for power users. The plan is designed to evolve - after each phase completion, we review learnings and update future phases to ensure this document remains our single source of truth throughout the project.*
