Clean up namespaces (#410)

No meaningful code changes, just lots of namespace shuffling to have fewer namespaces and to put things in better namespaces.

tests/ModelContextProtocol.TestSseServer/Program.cs

@@ -1,7 +1,6 @@
 using Microsoft.AspNetCore.Connections;
-using ModelContextProtocol.Protocol.Types;
+using ModelContextProtocol.Protocol;
 using ModelContextProtocol.Server;
-using ModelContextProtocol.Utils.Json;
 using Serilog;
 using System.Diagnostics;
 using System.Text;