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Example: A.java: public interface A { @Deprecated void foo(); } B.java: public class B implements A { @SuppressWarnings("deprecation") public void foo() { } } A deprecation warning is shown on the implementation of foo() in spite of the @SuppressWarnings annotation. In my opinion, the deprecation warning should not be shown even in absence of a @SuppressWarnings annotation, because an implementation of interface A necessarily has to implement foo(), deprecated or not. I.e. there is nothing to warn about in this situation.
Javac reports override deprecation even if @SuppressWarnings is present on the overriding method - that's why NetBeans hint behave the same. Move @SuppressWarnings("deprecation") to the class decl to suppress deprecations throughout the class. I have some doubts the compiler behaviour is correct, since the javadoc for @SuppressWarnings says that it suppresses warnings for the specific element - so it should be able to suppress deprecation for an individual method. JLahoda may have additional comments on javac (desired) behaviour.
Regarding producing the warning when overriding a deprecated method (without @SuppressWarnings), that is specifically mandated by the JLS to my knowledge (JLS 9.6.4.6.). @SuppressWarnings should obviously suppress the warning, this has been fixed as: https://bugs.openjdk.java.net/browse/JDK-8033421 in JDK 9 codebase. I'll look into backporting options.