[ahpearce]

It's not quite a fully fledged knowledge base, but https://bear.app/ is pretty great if you're on the Apple ecosystem. Definitely ticks all of your boxes, minus change tracking. Really simple and markdown based with a straightforward tag system.

[kingkongjaffa]

I used bear when I was writing my thesis it was really good to just write, my process was to write chapters in Bear and typeset properly in LaTeX.

I think over the year I spent 8 months in research/discovery mode making notes and writing in Bear.

The final few months I was focused on the act of authoring rather than the act of research and put it all in LaTeX in the end.