@SebMacV & @benoit.pointet, I have similar goals w.r.t an academic reading / note taking workflow. Having atomic notes that are self-contained is key so that these knowledge elements can be filtered & gathered independently, reused, and arranged in new ways. With https://keypoints.app I‘m currently trying to develop a Mac app that supports this workflow. I plan to deeply integrate it with DEVONthink so that users can use DT‘s unique features to further work with their notes.
Here‘s a short demo screencast that shows a new note being created from a PDF highlight which is then tagged, rated, labeled, commented on and cross-linked:
More info is available in these threads: