plugins/discovery: Fix discovery erasing `persistence_directory` config

Before this change, if a discovery bundle didn't contain configuration
for `persistence_directory`, this would be deleted from the manager's
configuration. When enabling persistence of the discovery bundle this
doesn't make much sense, as the first discovery bundle would erase the
persistence settings.

This change ensures that discovery never erases `persistence_directory`.

Signed-off-by: Benjamin Nørgaard <mail@blacksails.dev>