The Eclipse Java compiler can process Javadoc comments. Search reports references in doc comments, and refactoring updates these references as well. This feature is controlled from the Java > Compiler > Javadoc preference tab (or set for an individual project using Project > Properties > Java Compiler > Javadoc).

When turned on, malformed Javadoc comments are marked in the Java editor and can be fixed using Edit > Quick Fix (Ctrl+1):