GibbinR: There are no real changes to the annotations from 2.8.1 to 3.3.0. The only change is how the menu and dictionary pop-up are displayed after selecting text in a book. 3.4.1 has a lot of changes to the Annotation list. These are not complete, but overall are an improvement. There are some changes in the annotation entry screen as well. When these are finished, they will be good changes.
As to annotation bugs, I don't think any have been fixed. The ordering of annotations in epubs definitely hasn't.
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