A project has a library jar with com.foo.InterfaceA
There is a source folder with com.foo.ImplementationA class. Trying to rename com.foo to com.bar makes IDEA present a dialog with pointers to the package in a jar as well. However, trying to proceed fails, as IDEA can't modify the jar (and shouldn't). As a result a refactoring fails. In a worst case scenario, the result is an incomplete refactoring, throwing a project into a mess.
IDEA may still present a dialog with jar links, but it must not prevent source packages from being renamed in the current project.
If this sounds like a valid bug, I'm happy to file a JIRA, just let me know.