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References in Javadoc comments (like the @see tag) should be altered when renaming a package. (Same with renaming a single class or a method but I didn't check whether it does it or not)
Rename of javadoc is already implemented for method and class rename. Unfortunately not for move class nor package rename. Tomasi, do you plan to implement it?
Rename of parameter names in method declarations does not rename @param tags in preceding Javadoc - tested in Netbeans 6.7.1 p.s. this bug is 4.5 years old!
brutzman: rename of @param works even in NB 6.7.1 using Menu/Refactoring/Rename with apply on comments. The instant rename with ctrl+R was implemented in NB 6.8, see issue 102669. BTW there is a lot of open issues volunteers are welcome! The reliable refactoring of references in javadoc tags (@see, @link, ...) is not possible without a class index over all javadocs that is not and most likely is not going to be implemented. What jbecicka mentioned is a full text search and replace in javadocs of files where some occurrence of the refactored element was found. As a workaround for package renames you can import the class and use just simple name as the reference in tags if possible.
This old bug may not be relevant anymore. If you can still reproduce it in 8.2 development builds please reopen this issue. Thanks for your cooperation, NetBeans IDE 8.2 Release Boss