I think your needs are directed towards “literature notes” and “project notes” (in the terms from the helpful “Smart Notes” book). I tend to use Obsidan for “permanent notes” - those ideas/small chunks of text that I will return to and mull over in a number of projects. For the lit notes and project notes that I think you are talking about, it seems like Devonthink would be the product you are looking for. It is a heavier program than obsidian (and $$), but is so flexible. It will search anything that is searchable, and if you use GoodNotes as suggested above, your annotations could be ocr’d and easily indexed (or imported by Hazel). I tend to have a very eclectic mix in DT (PDFs, word documents, quick back of the napkin handwritten notes, etc.). But when they are worked on (as suggested by @JohnAtl), they get revisited with keywords, links, etc, in Obsidian.
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