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Rename file should invoke Refactor -> Rename for php files.
Looks like something has been changed in Eclipse, and now refactoring is enabled on all resources in PHP projects. Due this is not possible to rename file outside .buildpath :(
New Gerrit change created: https://git.eclipse.org/r/155001
Gerrit change https://git.eclipse.org/r/155001 was merged to [master]. Commit: http://git.eclipse.org/c/pdt/org.eclipse.pdt.git/commit/?id=8a3f15e22d828aa54f32f3f1b6be78a65e40d6dd