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

tests/ModelContextProtocol.Tests/DiagnosticTests.cs

@@ -139,16 +139,10 @@ public class DiagnosticTests
 
         await using (McpServer server = McpServer.Create(serverTransport, new()
             {
-                Capabilities = new()
-                {
-                    Tools = new()
-                    {
-                        ToolCollection = [
-                            McpServerTool.Create((int amount) => amount * 2, new() { Name = "DoubleValue", Description = "Doubles the value." }),
-                            McpServerTool.Create(() => { throw new Exception("boom"); }, new() { Name = "Throw", Description = "Throws error." }),
-                        ],
-                    }
-                }
+                ToolCollection = [
+                    McpServerTool.Create((int amount) => amount * 2, new() { Name = "DoubleValue", Description = "Doubles the value." }),
+                    McpServerTool.Create(() => { throw new Exception("boom"); }, new() { Name = "Throw", Description = "Throws error." }),
+                ]
             }))
         {
             serverTask = server.RunAsync(TestContext.Current.CancellationToken);