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It depends on what you are doing with the annotations, if Annotations Plugin or Kobo Utilities plugin (both in Calibre and both work) is most suitable.
Annotations Plugin: Can fetch for ALL books and puts result in book Custom Metadata. Works for other things than Kobo.
Kobo Utilities: Quickly fetches for selected book. Best suited for copy/paste into an external file per book, such as when proof editing one large novel.
AFAIK, "davidfor" maintains both of these.
There may be a third method in Calibre.
It's only with the Sony eReader that I DON'T use Calibre for Annotations, and its PC application is only Windows/Mac and horrid. So I use Calibre and Kobo as I have entirely migrated to Linux after nearly 30 years, though I've done Linux servers since 1998.
I only occasionally use the Kindle for annotation.
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