Fix list/kvlist objects not being cleared of default when reading config
Fix list/kvlist objects not being cleared of default when reading config

This addresses REPOS_DIR in the PREFIX/etc/pkg.conf file not overriding
the defaults but causing it to instead append to them.

Fixes #680

skoef/pkg,khorben/pkg,khorben/pkg,khorben/pkg,en90/pkg,Open343/pkg,en90/pkg,junovitch/pkg,skoef/pkg,junovitch/pkg,Open343/pkg