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With 2012.11.27, I could do a template like "/path/to/%(uploader)s/%(title)s.%(ext)s" and it would save it in the appropriate folder.
With 2012.11.28, it now saves it as path_to_%(uploader)s/%(title)s.%(ext)s within the current directory. So, now there's no way to specify the path in which to save the file.