I like your todo/done and the nesting, that’s super handy!
I personally use zim (https://zim-wiki.org/) to keep my notes and the files sync between my various machines using syncthing. Zim is not fancy but it has worked well for me.
I create one zim page per topic and then normally I’ll write a header for each day I’m working on that thing and then write my notes for that day. Things I need to do still are bolded, then when completed I strike-through them. If I need to find something, I use grep to look through all the zim files (they’re just text files) to find things, especially helpful as sometimes I note hardware issues across multiple topics but they’re on the same hardware type, so grepping for serial numbers or specific phrases works well enough to locate such commonalities.