Decouple Handlers and Collections from protocol types (#765)

* Decouple Handlers and Collections (e.g. ToolsHandler and ToolsCollection) from Capabilities by promoting them to the options types.

Also, group all handlers in container classes, for server, I decided to move McpServerHandlers down to Mcp.Core and move the NotificationHandlers there too.

Also, Fix ListResourceTemplatesHandler issue.

* Add remarks for empty protocol capability types

* Keep JsonIgnore properties and mark them as Obsolete

* Continue supporting Obsolete members

* Update Obsolete messages to indicate the member will be removed

* Add EditorBrowsable Never to the remaining obsolete members

samples/InMemoryTransport/Program.cs

@@ -10,13 +10,7 @@ await using McpServer server = McpServer.Create(
     new StreamServerTransport(clientToServerPipe.Reader.AsStream(), serverToClientPipe.Writer.AsStream()),
     new McpServerOptions()
     {
-        Capabilities = new()
-        {
-            Tools = new()
-            {
-                ToolCollection = [McpServerTool.Create((string arg) => $"Echo: {arg}", new() { Name = "Echo" })]
-            }
-        }
+        ToolCollection = [McpServerTool.Create((string arg) => $"Echo: {arg}", new() { Name = "Echo" })]
     });
 _ = server.RunAsync();