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The type filter allows forbidden and discouraged references to be hidden from suggestion. However, it still suggests types that are annotated with a @Deprecated annotation. In a Java project that has JUnit 4 installed, the organise imports for this code shows both 'junit.framework.Assert' and 'org.junit.Assert'. Unfortunately this lexicographic order presents the deprecated type first. public Bug { Assert a; } There should be an option to hide deprecated types from the Filter Types dialog, and organise imports should not suggest junit.framework.Assert in the first place.
"Type Filters" can be enhanced with an option to filter deprecated types.
See also bug 250284. Deprecation is very different from ordinary type filters, since the set of filtered elements is not constant and not user-defined. It can be confusing if a type suddenly doesn't show up any more because someone else has marked it as deprecated. A better solution would be a generalization of bug 250284 that allows to lower the relevance of deprecated proposals everywhere (Open Type, Organize Imports, Content Assist, Quick Fixes). I think the number of types/packages that should really be filtered everywhere is quite low. And these can easily be added to type filters on a case-by-case basis.