If you’ve recently downloaded a newer version of MU, you may have noticed on a fresh install that the plugins folder and the mu-plugins folder are not there. Or, maybe you’ve seen them referenced, and finding them not where they are supposed to be, got horribly confused. 🙂 No worries.
There are not there because in the latest system they are empty, and thus not created in the zip. There are no default files included in either folder anymore, leaving that up to the site admins.
Just create them on the server, and you’ll be good to go.