Random question: Did you just hand-cut the svg code for the graph on the left side of the page? I took a quick look through the source code and didn't see any evidence of a specific tool.

The reason I ask is that that kind of behavior, where you click on the node and it highlights the paths to that node but grays out everything else, is super useful for complicated architecture diagrams where you want to put a ton of stuff in one diagram, but still be able to see where edges go when you have a big spider web of connections. I've been looking for diagramming software that would create these clickable kinds of diagrams for my company, but haven't found anything that exactly fits the bill (Most tools I've found generate static diagrams, and some mind mapping software I've seen doesn't totally fit the bill, either).