The project bar allows you to folder organise objects, but currently some dialogs (like new condition/action) still display everything without any folder organisation. It's on our todo list to get folders to display there, but it's a low priority since it's still pretty easy to quickly find objects via the search box.
I'm not so sure about folder-organising variables - I don't see any obvious way to fit it in to the UI. Properties in the properties bar generally aren't drag-and-droppable like the project bar is, so the same method of right-click, making folders and dragging stuff in probably won't work in the properties bar. What would organising variables look like?