You can create some very powerful workflows with dataviewer, properties and templates.

Whatever note taking style you want really, automatically moving them to folders, etc.

I highly recommend using unique notes with tags to start with, you can reorganize it as you need.

I have #snippets for code snippets, #walkthrough, #todo. Theres plugins to automatically move these to folders if you want.

Notes can easily link or embed each other too, so going from bug -> bug -> project isn't an issue. And creating glossaries is super easy with dataviewer.

Bookmarks for glossary's and searching with tags a keywords makes it easy to find what you're looking for even if its in a pile. And properties let you mark things like "completed: false" for todo items.

The best part: All of your notes are markdown, so you can easily move them elsewhere if needed.