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It is possible to have a package declaration with annotations. See bug 86167. It should be possible to find references inside these annotations.
Fixed and released in HEAD. See bug 83804 for details...
Seems to fail verification for 3.1 M7 using build I20050509-2010 + jdt.core HEAD.
You're right :-( In fact I made search working for Javadoc in package-info but not for annotations!
*** Bug 94718 has been marked as a duplicate of this bug. ***
Fixed. Missed to look at compilation unit package annotations while reporting matches... [jdt-core-internal] Changes done in MatchLocator.reportMatching(CompilationUnitDeclaration,boolean) Test case added in JavaSearchBugsTests
Verified for 3.1 M7 using build I20050509-2010 + jdt.core HEAD-20050512.