Thanks for the reply. I can certainly appreciate the difficulties that changing the way annotations are stored could introduce.
Do you have any kind of timeline for CFI support (the next major release, as you say)? Apple thoroughly ruined iBooks in iOS8 by making the reader just a small part of the store (instead of having the store be a small part of the reader). Marvin is great except for this little niggle for me, but it's a show-stopper. I'm a bit obsessive about annotations and retaining them regardless of readers, and it's frustrating to me how much of an afterthought they seem to be for most readers — of course, for most readers the actual reading is an afterthought since they exist as a means to sell products first.
There's no chance of Marvin going open source anytime soon, is there?
It's something I'd happily work on, but rolling my own reader is out of the question, and there aren't any satisfactory open source readers.