Remove Duplicate MCP Implementations and Consolidate on mcp_tools.py

[Acuspeedster]

Issue Description

We currently have multiple implementations of MCP (Model-Compiler-Processor) functionality spread across several files in the codebase, causing confusion, maintenance overhead, and potential inconsistencies. The main MCP implementation should be consolidated in mcp_tools.py, which already contains the most up-to-date implementation.

Problem

• mcp_server.py is marked as deprecated but still remains in the codebase, providing redundant functionality
• mcp_service.py contains business logic that could be refactored to work with the unified MCP implementation
• Several example files are using different MCP implementations, leading to inconsistent usage patterns
• The MCP server is configured in multiple places, making configuration changes error-prone

Proposed Solution

• Remove mcp_server.pycompletely, as noted in its own header comment: "DEPRECATED: This file is deprecated. All MCP functionality has been moved to app/mcp_tools.py."
• Update docker-compose.ymland other configuration files to use only the MCP implementation from mcp_tools.py
• Refactor mcp_service.py to be used by mcp_tools.py without duplicating the MCP server setup
• Update all examples to use the consistent MCP implementation
• Ensure the standalone MCP tools from mcp_tools.py work with both the CLI and the API endpoints

Benefits

• Simplified codebase with a single source of truth for MCP implementation
• Easier maintenance and updates to MCP functionality
• Consistent MCP experience across all integration points
• Reduced code duplication and potential for bugs
• Clearer implementation path for new MCP tools
• Implementation Details

Implementation Details

Key files that need updates:

• mcp_tools.py - Ensure it fully supports all required functionality
• mcp_service.py - Refactor business logic to work with the new structure
• run_mcp_server.py - Update to use the mcp_tools implementation
• mcp_client_example.py- Ensure it works with the consolidated implementation
• mcp-proxy-config.json- Update to reference the correct endpoints

Related Components

This change affects:

• MCP server initialization
• MCP tool registration
• MCP client examples
• Docker configuration
• Continuous integration tests

Acceptance Criteria

• All MCP functionality works correctly through mcp_tools.py
• No references to the deprecated MCP server implementation remain
• All tests pass with the consolidated implementation
• Documentation is updated to reflect the changes
• Docker builds and runs correctly with the updated implementation

Tasks

• Remove mcp_server.py
• Update MCP configuration in Docker setup
• Refactor mcp_service.py
• Update example files
• Fix any broken tests
• Update documentation

[Acuspeedster]

closed with : #12