From @Minecrell - #53

Just tested the new version 1.0.0 and it doesn't generate the old folders of the dependencies anymore. However, for some reason in the JAR file is an empty folder with the name of the file. (In my case GradleTest-1.0-all). This is kinda strange but I don't really mind, but maybe it is just a small mistake that is easily fixable?
Relocations of packages within the source files still generate their old folders in the JAR but as of I don't use that, it's not important to fix (for me).