I've no idea why this happens, but if you write this:

@SuppressWarnings(value="unchecked")

then Spoon will not mark java.lang as implicit, and the output will be:

@java.lang.SuppressWarnings(value="unchecked")

Took me an hour of debugging to figure out ... To be clear, the problem is the use of a named element, if you remove the value=, it the annotation type's package gets properly marked as implicit.