fix: Return JSON-RPC protocol errors for unknown tools

[bzsurbhi]

Return JSON-RPC protocol errors for unknown tools

Motivation and Context

The MCP server was returning tool execution errors for unknown tools instead of proper JSON-RPC protocol errors. This caused issues where Unknown tools were treated as tool execution failures rather than protocol-level errors

Before(Tool execution error):

{
  "jsonrpc": "2.0",
  "id": 3,
  "result": {
    "content": [{"type": "text", "text": "Unknown tool: invalid_tool_name"}],
    "isError": true
  }
}

After(Protocol error):

{
  "jsonrpc": "2.0",
  "id": 3,
  "error": {
    "code": -32601,
    "message": "Unknown tool: invalid_tool_name"
  }
}

Modified the tool call handler in src/mcp/server/lowlevel/server.py to:

• Check for unknown tools after retrieving from cache
• Raise McpError with METHOD_NOT_FOUND (-32601) error code for unknown tools

How Has This Been Tested?

• Added unit test
• Verified with a server and client example

Breaking Changes

This is a breaking change that corrects the error handling behavior:

• Unknown tools now return JSON-RPC protocol errors
• Valid tools that fail during execution still return tool execution errors
• Input validation errors continue to work as before
• Warning logs are still generated for unknown tools during lookup

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation update

Checklist

• I have read the MCP Documentation
• My code follows the repository's style guidelines
• New and existing tests pass locally
• I have added appropriate error handling
• I have added or updated documentation as needed

Additional context