There seems to be some confusion over the new style epiphany bookmarks, they are not hierarchical in the traditional sense, and are still based on tagging bookmarks in topics. What is new however is that the menu will automagically generate a hierarchy based on the topics selected.
The code has been maintained by Peter Harvey for a while now, and he has an excellent page explaining it.
If you have to explain, you’ve failed.
Perhaps this is just a new idea? Better that someone is willing to explain than trying to derive an explanation from an unwieldy handle…