I have a project created by others that includes thousands of class files and has the package names explicitly typed out for every reference to any of their classes. It look
I don't know a tool for this use case, but I had to do something similar a few month ago.
Write a script or do a search replace with regex to get rid of the explicitly typed package prefixes.
Than let eclipse do the rest using "organize imports". Ctrl-1
Hint: to avoid ambiguities, setup the classpath with no more than the required libs. For sround about 800 classes I was done in 2 hours.
EDIT: You should know that in Prefeneces/Java/Editor/Save Actions, Organize imports can be configured as save action.