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I wanted to start the dreaming of a better Modbook with Tom's (arty's) suggestion:
[When a non-drawing application is frontmost] … get the screen to allow layers of handwriting to appear over word documents and pdf files so that handwritten notes / drawings could be made on them for classroom presentations etc.
I really want that functionality. I annotate all my reading and would love to annotate webpages as I read them.
In principle it would be possible to slide a transparent window across the screen that could be written on. The difficulty is correctly associating what is written on the transparent window with a particular location in a Word document or webpage. I'm not sure how to address this. (You'd have to figure out what portion of the document can be seen in its window.) I'll have to think more.
Nonetheless, the transparent drawing window might more straight forwardly provide a way to annotate Keynote or PowerPoint presentations. Using AppleScript, one can figure out which slide is being displayed and associate the annotation with that slide.
Note: I've played with OmniDazzle, a free app, which provides a part of the software we'd need, but the Scribble tool always crashes on me.