Annotations meaning notes, highlights, etc.

If they are stored in the file itself, that's news to me. Last time I used it, Okular didn't modify the actual PDF and considered that a feature.

You have to explicitly save the file after making the annotations. I've been doing this for years with Okular, indeed, Okular having out-of-file annotations is news to me :)

Oh, wow. That will make collaboration so much easier. I resorted to Adobe Reader on multiple occasions in the past...

Thanks!