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
For a single type, eclipse offers the 'Add import' action (Shift+Ctrl+M). It does exactly what you want - with the big, big limitation: you have to place the cursor on a type and it will only affect that 'selected' occurrence.
But maybe this action can be used in a scripted/global method. A JDT plugin could crawl through the AST and call this action on every type it finds.
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.