A couple of feature requests:
#1:
In annotation files the paths to the annotated files should be workspace or project relative.
I keep several copies of my project workspace, and I use symbolic links for the workspace and project files so that I can have a single set of workspace/project files that can be used over several different copies of the source code.
If the annotations used relative paths, then a workspace.sca could be shared as well.
#2:
The annotation tool window should allow editing of the annotations in place.
In the "Comment" box, the text is read-only, but it should be editable.
In the annotations list box (the center section), most of these fields should be edit-in-place.
Currently, fields like "author" aren't editable at all - they should be.
#3:
All fields in an annotation should be editable, not just the comment.
Author, Date, Type, Version and even Annotation File.