In JDK 9, annotations on package-infos are only reported during the first annotation processing round. They are handled correctly with JDK 8.

=== P.java
import java.util.Set;
import javax.annotation.processing.AbstractProcessor;
import javax.annotation.processing.RoundEnvironment;
import javax.annotation.processing.SupportedAnnotationTypes;
import javax.lang.model.SourceVersion;
import javax.lang.model.element.PackageElement;
import javax.lang.model.element.TypeElement;

@SupportedAnnotationTypes("*")
public class P extends AbstractProcessor {

  @Override
  public SourceVersion getSupportedSourceVersion() {
    return SourceVersion.latestSupported();
  }

  private int i = 0;

  @Override
  public boolean process(Set<? extends TypeElement> annotations, RoundEnvironment roundEnv) {
    PackageElement p = processingEnv.getElementUtils().getPackageElement("p");
    System.err.println("[" + i++ + "] p: " + p.getAnnotationMirrors());
    return false;
  }
}
=== p/T.java
package p;
class T {}
=== p/package-info.java
@Deprecated
package p;
===

With JDK 1.8.0_162-ea-b03, the annotations on the package 'p' are reported during both annotation processing rounds:

$ javac P.java p/package-info.java
$ javac -sourcepath : -cp . -processor P p/T.java
[0] p: @java.lang.Deprecated
[1] p: @java.lang.Deprecated

With JDK 9.0.1+11, the annotations on the package 'p' are only reported during the first annotation processing round:

$ javac P.java p/package-info.java
$ javac -sourcepath : -cp . -processor P p/T.java
[0] p: @java.lang.Deprecated
[1] p: