The semantic tree is built with the semtree plugin (see docs for details).It is defined by the documents in the index doctype markdown files. It forms a conceptual hierarchy with the purpose of orienting one within the concepts of a site.

In case it needs repeating:

“It is important to view knowledge as a sort of semantic tree. Make sure you understand the fundamental principles, i.e., the trunk and big branches before you get into the leaves/details or there is nothing for them to hang on to.”

~ Elon Musk