Description

Custom tools registered via [McpForUnityTool] attribute are discovered and work correctly in HTTP transport mode, but are not available when using stdio transport mode.

Steps to Reproduce

1. Create a custom tool in a Unity project:

using MCPForUnity.Editor.Tools;
using MCPForUnity.Editor.Helpers;
using Newtonsoft.Json.Linq;

namespace PkgUnityMcp.Editor.Tools
{
    [McpForUnityTool("test_ping",
        Description = "Simple test tool that returns a pong.")]
    public static class McpPingTool
    {
        public static object HandleCommand(JObject @params)
        {
            string message = @params?["message"]?.ToString() ?? "pong";
            return new SuccessResponse($"test_ping reply: {message}", new
            {
                reply = message,
                source = "custom_tool"
            });
        }
    }
}

2. Wait for compilation to complete
3. Connect via stdio mode
4. Attempt to call test_ping - tool is not found (Unknown or unsupported command type: test_ping)
5. Switch to HTTP mode
6. Call test_ping via execute_custom_tool - works correctly, returns {"reply": "hello from Claude Code", "source": "custom_tool"}

Expected Behavior

Custom tools should be discoverable and callable in both stdio and HTTP transport modes.

Actual Behavior

• HTTP mode: Custom tools are discovered and work correctly
• stdio mode: Custom tools are not registered. Calling them returns Unknown or unsupported command type

Environment

• MCP for Unity: 9.4.8-beta.3
• Unity: 2021.3.58f1
• Client: Claude Code
• OS: Windows 11