The semantic tree is built with the jekyll-semtree plugin (see docs for details) and are the building blocks for the tree graph. 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.”