--- Comment #8 from ederag <> ---
The okular developers have done a great job in general,
so the following is just an idea, not prying at all.

Here is a possible design that would clarify saving with annotations,
while bringing back the great external annotations as an option:
- keep two groups of annotations:  internal/external
  (saved inside / saved outside document).
  This is possible since annotations overlap is already accepted.
- global option to direct new annotations to internal or external by default.
  (and create an individual annotation property for that,
   so that it is possible to change an annotation destination at any time.
   This would also be a way to help migration if so desired
- Potential concern:
  When an internal annotation is saved, the document size changes,
  so the external annotations file name, based on size, has to be updated.
  The number of annotation files might increase a lot ?
  not in the standard use cases: 
  in my case, a pdf with an existing internal annotation
  is just complemented with external annotations. No pdf file change.
  Opposite use case is no external annotations at all. No problem either.
  For an unlikely hybrid workflow, it should be possible to
  provide a mean to chose between 
  copying or just moving the external annotation file.
  => not blocking at all, actually.

>From a user perspective this looks like the best of both worlds,
but of course, that would complexify the code,
and I do not know the internals of okular;
that might be even too difficult to implement and maintain.

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