This feature is actually part of Eclipse M5 and not directly JBoss Tools but I wanted to mention it because the feature is awesome and it was contributed by us by the great work of Mickael Istria.

In Eclipse M5 the Project Explorer now have a "Projects Presentation" in its view menu. Allowing you to switch from the traditional "Flat" view to the new "Hiearchical". This new option lets you view the projects as they are structured on the filesystem as opposed to one big flat list.