I know for lots of people, knowledge mgmt setups are as important as editing setups. The recent outgrowth of notebook libraries (clerk) is a fun demonstration to witness. I think like all good tools your system should inspire the work you do with it.
Personally I’ve been agnostic to the narrower use cases because I’m taking notes on more than clojure and programming. For specific software, I have enjoyed Trilium for some years. It’s a single-author electron app wrapping note file navigation around ckeditor panes.
Obsidian with pandoc makes notes remarkably fun when you can go from nothing to good-looking content across formats in seconds.
Trilium, extensibility has a manual flair and its hotkey support is superior. Obsidian’s plugins have an active community, it’s easier, hotkey navigation is patchy and their pure focus on markdown limits how complex formatting can be. The killer features between the two, in Trilium I love note cloning, property inheritance, and how parent nodes can be leaves (Obsidian, reflecting directory structure, folders ≠ notes).
Still I’ve never gone all the way with manual latex setups. If people here use any of those type of systems (*tex?) for building/working with programming knowledge I’d love to know why, how, with what.