When editing large files, bookmarks are very helpfull. Why not save them in the workspace when I close the file? Next time I work in that file, I could start at the same point without having to set all the bookmarks again.

100% agree!
Actually, I was quite surprised when discovering that my bookmarks were not here when I opened the file next time. Working with large piece of code it would be very nice to have bookmarks saved!
I hope it is not af a big work for NuSphere and they would implement this feature soon!