There is no one fit all way.
First, structuring you notes in s tree like structures using folders is a valid approach (independent on real files structure).
Second, some people, including me, expect that their notes can live longer that tools, in this case it makes sense to not rely on tool features too much.
@gelberhut @biscotty @obsidianmd I agree with gelberhut. Folders are to organization as plaintext is to data, and are one of the keys to a files-first, future-proofing approach. #Obsidian could break and refuse to open, and I could still navigate my notes in any file manager and open and use them in any text or #markdown editor. That’s going to be a lot harder to do if you’ve dumped all of your thousands or tens of thousands of notes in root. #PKM
@EpiphanicSynchronicity @gelberhut @biscotty @obsidianmd I do both: indexes and MOCs and individual projects are organised into directory structures, "cards" go into one folder with little organisation but only after they're tagged or linked into the indexes in ways I'm pretty sure I can access if/when #obsidian passes.
@Colman @gelberhut @biscotty @obsidianmd I use MOCs, tags, etc., too. #Obsidian lets you link freely across folders, which don’t constrain you from using other organizational methods concurrently.