config.xml and package directory can not be in the same level

Path to config.xml is the config dir path which is completly compied to the temp path in case when an installer is generated.

We had users where the environment was that the config.xml file is at the same level like the packages directory, but then the code does strange things.

One thing would be to fix that and copy only needed files, the other and more dirty quick hack would be to check that the package directory is not at the same level like the config.xml file.