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When a PHP project has a (PHPUnit) test folder defined, rename refactorings and usages seem to ignore the files below that folder. When I move the cursor on some class name or public/protected property and choose "find usages" or "refactor > rename", only occurrences inside the "Source Files" (virtual) sub-tree of the "Projects" view are reported. When I mark the same symbol inside a PHPUnit test in the "Test Files" sub-tree, occurrences are reported correctly (i. e. both in "Test Files" and "Source Files"). Reproducible on multiple platforms ever since PHP refactoring beyond the current file first appeared in Netbeans.
*** This bug has been marked as a duplicate of bug 217991 ***