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Sometimes when you want to rename a file in the project browser, it will be renamed, but another file will be shown in the palette with its name being the previous name of the file. If you click on any of them, you the new renamed file will be opened. You wait for about 10 seconds and close the projects palette, then open it up again and the false file isn't there anymore! Checked it in a PHP Project, but it doesn't look like it's anything related to the PHP Plugin!
Unless you can reproduce the problem in 6.9.1, let's assume this is a duplicate of bug 184854. *** This bug has been marked as a duplicate of bug 184854 ***