We are aware of your work flow. In 6.0, the File/File as are not avaible when you are in Object type tab. The Code edtior is object-based support, not file based yet. We plan to add file based support to the Code editor in future release.
In 6.0, To save a package into a file, You don’t need to copy and paste…you first need to use the Generate DDL script option. You can click on the “generate DDL script” button (next to the Sate DB button) on the code editor toolbar to get the extracted DDL. I know the work flow is a bit different to 5.5 but we decided to follow this work flow to avoid some issues with saving objects. In addition, you can review the (actual) script before saving to file.
Hope this helps. Please let us know if the work flow in 6.0 would work for you.