To me the main choice you make for a knowledge base is the linking structure: do you want just an unorganized pile, a web, something hierarchical, or something linear? In general CS/programming people prefer less structured forms like webs (as can be seen in these comments), while physics/math people prefer the opposite. For example, the Stacks and Kerodon projects are huge collaborative knowledge bases for certain subfields, but they're organized like a standard textbook.
This is partly because physics/math people prefer more stable software, since they don't have time to keep up with or build the latest thing. LaTeX has been stable for decades. Furthermore, the material in physics and math really is more ordered and hierarchical, while CS seems to have a broader, more organic structure from its youth.
I love the linear format, and I'd encourage you to try it too. It requires no special software. It forces you to think about what is most foundational, and how certain insights lead directionally to others -- issues which you can ignore if you give yourself the freedom of a web. And as you move forward to more advanced things, spaced repetition of the more foundational things will happen automatically.