docs: reorganize documentation files and update Docker build process

CHANGELOG.md

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-# Changelog
-
-All notable changes to this project will be documented in this file.
-
-## [2.3.0] - 2024-12-06
-
-### Added
-- **HTTP Remote Deployment**: Single-user HTTP server for remote access
-  - Stateless architecture for simple deployments
-  - Bearer token authentication
-  - Compatible with mcp-remote adapter for Claude Desktop
-  - New HTTP mode scripts and deployment helper
-- **Universal Node.js Compatibility**: Automatic database adapter fallback system
-  - Primary adapter: `better-sqlite3` for optimal performance
-  - Fallback adapter: `sql.js` (pure JavaScript) for version mismatches
-  - Automatic detection and switching between adapters
-  - No manual configuration required
-- Database adapter abstraction layer (`src/database/database-adapter.ts`)
-- Version detection and logging for troubleshooting
-- sql.js dependency for pure JavaScript SQLite implementation
-- HTTP server implementation (`src/http-server.ts`)
-- Deployment documentation and scripts
-
-### Changed
-- Updated all database operations to use the adapter interface
-- Removed Node.js v20.17.0 requirement - now works with ANY version
-- Simplified Claude Desktop setup - no wrapper scripts needed
-- Enhanced error messages for database initialization
-- Made all MCP tool handlers async for proper initialization
-
-### Fixed
-- NODE_MODULE_VERSION mismatch errors with Claude Desktop
-- Native module compilation issues in restricted environments
-- Compatibility issues when running with different Node.js versions
-- Database initialization race conditions in HTTP mode
-
-### Technical Details
-- Better-sqlite3: ~10-50x faster (when compatible)
-- sql.js: ~2-5x slower but universally compatible
-- Both adapters maintain identical API and functionality
-- Automatic persistence for sql.js with 100ms debounced saves
-- HTTP server uses StreamableHTTPServerTransport for MCP compatibility
-
-## [2.2.0] - 2024-12-06
-
-### Added
-- PropertyExtractor class for dedicated property/operation extraction
-- NodeRepository for proper JSON serialization/deserialization  
-- Support for @n8n/n8n-nodes-langchain package (59 AI nodes)
-- AI tool detection (35 tools with usableAsTool property)
-- Test suite for critical node validation
-- Comprehensive documentation (README, SETUP, CHANGELOG)
-- Example configuration files for Claude Desktop
-- Node.js v20.17.0 wrapper scripts for compatibility
-
-### Fixed
-- Empty properties/operations arrays (now 98.7% nodes have properties)
-- Versioned node detection (HTTPRequest, Code properly identified)
-- Documentation mapping for nodes with directory-based docs
-- Critical node validation (httpRequest, slack, code all pass)
-
-### Changed
-- Refactored parser to handle instance-level properties
-- Updated MCP server to use NodeRepository
-- Improved rebuild script with validation
-- Enhanced database schema with proper typing
-
-### Metrics
-- 458 total nodes (100% success rate)
-- 452 nodes with properties (98.7%)
-- 265 nodes with operations (57.9%) 
-- 406 nodes with documentation (88.6%)
-- 35 AI-capable tools detected
-- All critical nodes validated
-
-## [2.1.0] - 2025-01-08
-
-### Added
-- Remote deployment capabilities via HTTP/JSON-RPC transport
-- Domain configuration through environment variables (`MCP_DOMAIN`)
-- Bearer token authentication for remote access
-- Comprehensive remote deployment documentation
-- PM2 and Nginx configuration examples
-- HTTP server mode (`npm run start:http`)
-
-### Enhanced
-- Support for both local (stdio) and remote (HTTP) deployment modes
-- Production deployment guide for VM/cloud environments
-- Claude Desktop configuration for remote servers
-
-## [2.0.0] - 2025-01-08
-
-### Major Refactoring
-- **BREAKING CHANGE**: Refocused project to serve only n8n node documentation
-- Removed all workflow execution and management features
-- Removed bidirectional n8n-MCP integration
-- Simplified to be a read-only documentation server
-
-### Added
-- SQLite database with full-text search (FTS5) for node documentation
-- Integration with n8n-docs repository for official documentation
-- Automatic example workflow generation for each node type
-- Comprehensive node information including:
-  - Source code
-  - Official documentation
-  - Usage examples
-  - Properties schema
-  - Credential definitions
-
-### New MCP Tools
-- `list_nodes` - List available nodes with filtering
-- `get_node_info` - Get complete node information
-- `search_nodes` - Full-text search across nodes
-- `get_node_example` - Get example workflow for a node
-- `get_node_source_code` - Get only source code
-- `get_node_documentation` - Get only documentation
-- `rebuild_database` - Rebuild entire node database
-- `get_database_statistics` - Database statistics
-
-### Infrastructure
-- New database schema optimized for documentation storage
-- `DocumentationFetcher` for n8n-docs repository integration
-- `ExampleGenerator` for creating node usage examples
-- `NodeDocumentationService` for database management
-
-## [1.1.0] - 2024-01-07
-
-### Added
-- Node source code extraction capability via `get_node_source_code` tool
-- List available nodes functionality with `list_available_nodes` tool
-- `NodeSourceExtractor` utility for file system access to n8n nodes
-- Resource endpoint `nodes://source/{nodeType}` for accessing node source code
-- Docker test environment with mounted n8n node_modules
-- Comprehensive test suite for AI Agent node extraction
-- Test documentation in `docs/AI_AGENT_EXTRACTION_TEST.md`
-
-### Enhanced
-- MCP server can now access and extract n8n node implementations
-- Support for extracting credential definitions alongside node code
-- Package metadata included in extraction results
-
-## [1.0.0] - 2024-01-07
-
-### Initial Release
-- Complete n8n-MCP integration implementation
-- MCP server exposing n8n workflows as tools, resources, and prompts
-- Custom n8n node for connecting to MCP servers
-- Bidirectional data format conversion bridge
-- Token-based authentication system
-- Comprehensive error handling and logging
-- Full test coverage for core components
-- Docker support with production and development configurations
-- Installation scripts for n8n custom node deployment
-
-### MCP Tools
-- `execute_workflow` - Execute n8n workflows
-- `list_workflows` - List available workflows
-- `get_workflow` - Get workflow details
-- `create_workflow` - Create new workflows
-- `update_workflow` - Update existing workflows
-- `delete_workflow` - Delete workflows
-- `get_executions` - Get execution history
-- `get_execution_data` - Get execution details
-
-### MCP Resources
-- `workflow://active` - Active workflows
-- `workflow://all` - All workflows
-- `execution://recent` - Recent executions
-- `credentials://types` - Credential types
-- `nodes://available` - Available nodes
-
-### MCP Prompts
-- `create_workflow_prompt` - Workflow creation
-- `debug_workflow_prompt` - Workflow debugging
-- `optimize_workflow_prompt` - Workflow optimization
-- `explain_workflow_prompt` - Workflow explanation