May I suggest taking notes by hand? There was at least one study that determined taking notes by hand forces you to summarize the information, and so you end up increasing your recall as a result. (https://www.scientificamerican.com/article/a-learning-secret...)

Humanity survived without apps for quite a long time. I'm not sure though the comparison would yield the same result for information retrieval.

VIM + ((vim)?grep|ack|at|...)

That said. I also liked TiddlyWiki.