Fix reporting of failures for clone_repository
Force polygamy to have a config dir, and a config repo within that dir.

This allows polygamy to keep configuration files (generated from the
application) in a directory, while keeping the users polygamy repository also
within that directory.

This also removes support for using a simple json file for configuration
directly in the path you want to run polygamy from. This may annoy some, but
allows us to support many more features, such as repository groups.