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Seriously I have been thinking about this lately. I could just keep folders with text files. I could go all in on Apple Notes and just trust Apple completely and never leave the platform.
I looked at DevonThink but I really can't see a difference between just using files and folders vs an actual database.
I tried to use Drafts but I started to realize I was just using it exactly like Notes. Between iCloud Drive, what used to be called iWork, and the Notes app, why do I need anything else? That's supposed to be one of the promises of the Mac after all, good software out of the box.
So what do you like currently as a middle ground, simpler alternative? You seem to imply Apple Notes isn't quite there yet.
I just had a closer look and Notes has an import to notes option which will let me import entire folders, structure and all. What I don't see is any export function other than for individual notes. This is one reason I am reluctant to use anything that uses a database and not standard files I could get at with anything. I don't like the idea of being locked in. Which I suppose is ironic since I'm all in on Apple platforms for my personal use.