Clean up namespaces (#410)

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

src/ModelContextProtocol/Configuration/McpServerOptionsSetup.cs

@@ -1,6 +1,6 @@
-using ModelContextProtocol.Server;
 using Microsoft.Extensions.Options;
-using ModelContextProtocol.Utils;
+using ModelContextProtocol;
+using ModelContextProtocol.Server;
 
 namespace Microsoft.Extensions.DependencyInjection;