* 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
