Really enjoying my experiments with MN, but am very nervous about being essentially trapped within any single application. I realize a lot of the neat cross-document functionality is lost when exporting a single PDF. But, if the annotations aren’t flattened, one’s efforts in annotating a pdf can be carried over into other parts of my ecosystem. For example, I keep my PDFs–currently just highlighted in acrobat, in a bibliography managers (EndNote or BibDesk, depending on what’s caught my fancy most recently).
Thanks for the consideration.