Logseq is as close as it gets. In my humble opinion these tools aren't quite there yet, which is not to say they aren't polished, but that they don't disappear

Logseq is as close as it gets. In my humble opinion these tools aren't quite there yet, which is not to say they aren't polished, but that they don't disappear from view like good tools should. There's still a noticeable impedance mismatch due to having to use their editor, for example, which has its quirks and is different enough to a standard text editor to cause a context switch. But it's open source and it's pretty good.