Update dependencies and enhance MySQL support

- Add `mysql2` as a dependency for improved MySQL support.
- Update README and documentation to reflect new MySQL execution capabilities.
- Refactor DBeaver client to handle MySQL queries natively, including SSL configuration.
- Introduce workspace path configuration for better user experience.
- Clean up unused dependencies and improve error handling in query execution.

Author: maciej-w

README.md

@@ -33,6 +33,7 @@ A production-ready Model Context Protocol (MCP) server that seamlessly integrate
 - **Schema Management**: Complete DDL operations (CREATE, ALTER, DROP)
 - **Data Export**: CSV, JSON, XML, Excel export formats
 - **Performance Monitoring**: Query execution time tracking
+- **Native Execution**: Direct query support for SQLite, PostgreSQL, and MySQL/MySQL8
 
 ### 🧠 AI-Powered Intelligence
 - **Business Insights**: Track and store analysis insights with tagging
@@ -92,6 +93,7 @@ The server will automatically detect your DBeaver version and use the appropriat
 - Node.js 18+ 
 - DBeaver installed and configured with at least one connection
 - Claude Desktop, Cursor, or another MCP-compatible client
+- For MySQL (including MySQL 8) and most other databases, query execution uses the DBeaver executable in headless mode (set `DBEAVER_PATH` if auto-detection fails)
 
 ## 🛠️ Installation
 
@@ -133,6 +135,7 @@ npm link  # Makes the command available globally
 
 ### Environment Variables
 - `DBEAVER_PATH`: Path to DBeaver executable (auto-detected if not set)
+- `DBEAVER_WORKSPACE`: Path to DBeaver workspace directory (defaults to the standard OS location, e.g. `~/Library/DBeaverData/workspace6` on macOS)
 - `DBEAVER_TIMEOUT`: Query timeout in milliseconds (default: 30000)
 - `DBEAVER_DEBUG`: Enable debug logging (true/false)
 
@@ -305,4 +308,4 @@ MIT License - see LICENSE file for details
 - DBeaver for the amazing database tool
 - The open source community for inspiration and feedback
 
-> **Note**: This project is not officially affiliated with DBeaver or Anthropic. It's designed for real-world production use with AI assistants.
+> **Note**: This project is not officially affiliated with DBeaver or Anthropic. It's designed for real-world production use with AI assistants.

docs-site/docs/getting-started/configuration.md

@@ -43,6 +43,7 @@ To use DBeaver MCP Server with Claude Desktop, add the following to your configu
 
 ### Core Variables
 - `DBEAVER_PATH`: Set a custom path to the DBeaver executable if not auto-detected
+- `DBEAVER_WORKSPACE`: Set a custom path to your DBeaver workspace (useful for non-default workspaces and DBeaver CLI execution)
 - `DBEAVER_TIMEOUT`: Set the query timeout in milliseconds (default: 30000)
 - `DBEAVER_DEBUG`: Set to `true` to enable debug logging
 

docs-site/docs/guides/available-tools.md

@@ -38,6 +38,7 @@ The DBeaver MCP Server provides 14 powerful tools organized into four categories
 ### `execute_query`
 **Description**: Execute SELECT queries (read-only)  
 **Safety Level**: ✅ Safe  
+**Notes**: Queries are executed natively for SQLite, PostgreSQL, and MySQL/MySQL8. Other drivers may fall back to DBeaver headless mode (set `DBEAVER_PATH` if needed).  
 **Parameters**:
 - `connectionId` (required): The ID or name of the DBeaver connection
 - `query` (required): The SQL query to execute (SELECT statements only)
@@ -130,4 +131,4 @@ The DBeaver MCP Server provides 14 powerful tools organized into four categories
 - **⚠️ Schema changes**: Operations that modify database structure
 - **❌ Destructive**: Operations that permanently remove data or objects
 
-All destructive operations require explicit confirmation to prevent accidental data loss. 
+All destructive operations require explicit confirmation to prevent accidental data loss.