Add a simple save option
When an existing file is opened and modified, there should be a simple save option (Ctrl-S). Exporting is completely unintuitive.
What would expect Annotator to do when you use an option like Ctrl-S?
All image annotation tools that I have used in the past allow you to take an image, add annotations to it, and then export that image in whatever format is needed.
Annotator isn't designed to be an image editing tool like Gimp, Pixelmator, or Photoshop. And even those tools have image export features when the image needs to be saved in a standard image format (i.e., PNG, JPEG, GIF, SVG, etc.) Using Ctrl-S in these applications creates a application-specific save file that can all the image to be re-opened at a later date.