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When running "Organize imports" (only one I tried) on the current package, the folders in this package are also analysed. I expect it would only analyse the single package. Running it on "org.netbeans.modules.refactoring.java" now analyses the whole project.
Changeset: fc5b46497c98 Author: Jan Becicka <jbecicka@netbeans.org> Date: 2012-02-15 15:44 Message: Issue #206841 - Inspect and Transform handles packages recursively
Integrated into 'main-golden', will be available in build *201202170400* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress) Changeset: http://hg.netbeans.org/main-golden/rev/fc5b46497c98 User: Jan Becicka <jbecicka@netbeans.org> Log: Issue #206841 - Inspect and Transform handles packages recursively