Added note about bug in AppConfig that prevents hash keys being specified
on the command line using Getopt::Long.
Added method 'basename_dir' to provide a more consistent public API to an
internal value, changing _basename_dir to be strictly a private use
utility method.

Added test for 'basename_dir' to test suite.
Added entries for 'modcooker.cg' and 'MANIFEST.SKIP' to MANIFEST.