1145719 - Puppet directory import now respects the 'remove_missing' configuration setting

https://bugzilla.redhat.com/show_bug.cgi?id=1145719
I think it makes more sense to move the check if we should do this to the caller instead of it being inside the method. The name of the method implies that it removes the missing modules, and as a caller I'd be surprised if it checked a setting to see if it should do this or not.