Why is there both a config and a configuration directory?

The <tt>config</tt> directory has always contained Virgo configuration files. When Virgo Nano and its support for p2 provisioning was introduced in Virgo 3.5.0, a <tt>configuration</tt> directory was added (see bug 324991 for details). The directory name <tt>configuration</tt> in the install's root is used by default in p2.

The Configuration chapter of the Virgo User Guide makes it clear which configuration goes in each directory.