If you're one of the cool kids, then you use one (or more) of the now long list of what are sometimes called "connective-thinking apps" (e.g., Craft, DEVONthink, Heptabase, Logseq, Notion, Obsidian, Roam, Scrintal, Tana, The Archive, Tinderbox, etc.). This post will talk about PDF-annotation