@brennen Thanks for sharing your approach for handling notes.
Advantages of a code editor with a folder of text files: project drawer (get an overview/toc), searchable (e.g. grep), high probability of files still being readable years later.
I haven't used vimwiki partly from uncertainty about how portable the wiki formatting would be if I later switched apps, compared to writing with markup like ReST (but no internal links). However, it does fit the notebook paradigm well.