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I share some similar sentiments with the author and I developed a personal note-taking system which has automatic linking based on the collocational word. You can think of it as sort of like an inverted mind mapping software.
link: https://github.com/Tanami/maja
I think a shortcoming of my software and other people’s note-taking software is poor integration of time.. if I could modify my system so I could in effect make some commentary of the changes in the word files I think that would be a much more productive process than simply being able to visualise the changes as a static thing.