Review, Annotate, Collaborate With GoodReader For iPad
The app asks you if you want to save annotations to the original file or a separate copy before committing the first change. As a general practice, I always save to a separate file, leaving the original copy in a pristine condition.
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Once an annotation is committed, tapping it brings up options for highlighted or other text markings (underlines and freeform drawings for example) or ...
... the annotation itself in the case of pop-up text notes.
Tapping the double page book icon in the middle of the options bar at the bottom of the display brings up list of bookmarks, outlines, and annotations, available in a single place.
The annotated document, annotation summary, or both can be emailed and printed from the document view mode by tapping the right-pointing arrow near the right side of the options bar list at the bottom of the display.