Breaking leftover dir folders for configs in generated packages

In case a configuration package is generated from an existing repository due to the serialization logic for each nt:file representing a configuration there is also a .dir folder (with an embedded .content.xml declaring nodetype etc.) as a sibling.
The configuration handlers only handle the binaries but don't recognize the sibling structures which will make them remain in the package and therefore render the packages invalid as the binary belonging to the nt:file is being stripped out.

To prevent this (rare but existing) edge case the Configuration handler should also detect the dir folder and drop it from assembly in the target package as well.