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I think a lot of what he did with the physical notes is handled by the digital system. You write out your atomic notes and there is probably some order to them. In a bullet list of notes, they are "linked" by the order of that list. You could have a "head node" and then indent follow-on nodes. Or just keep one flat list (maybe split up by pages.) Then you can inject a node into multiple lists.

Roam Research handles this well with the block lists and block links (linking a block shows the content of the block rather than a link.)

Alternatively, I have found that a combination of OS links (symlinks or hardlinks as you prefer) with markdown files works fine. You can then use a static site creator to create different HTML views. As another view layer, you can manage these files with a file manager. Even better if the file manager can show text previews as large thumbnails. With the file manager, you can also manage the linking and other file operations. Then you can use any editor to edit the files. This is relatively complex, but more flexible while still using flat files.

I have tried to like Obsidian, but it ends up just getting in my way like any other Electron note app which attempts to re-create something that the base OS tooling can handle by itself.

I do like Roam and I have been trialing it along-side my above described flow. My ideal is using Roam for atomic notes and my own system for long form and anything else which isn't "atomic notes." I also won't put anything sensitive in Roam. I have been trialing it for months now but it's still sticking.

I think people who have problems with the idea of the Zettelkasten overthink the parts which they don't really need to think about at all. You don't need to recreate the stuff which the digital system handles for you in the background.

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