Learn Spanish (Latin America): ¡Buen provecho, que disfrutes la comida!

This is the present subjunctive! In Spanish, when you express a wish or hope for someone else starting with que, you must use the subjunctive mood. For an -ar verb like disfrutar, the tú (you) ending changes from -as to -es. You can think of que disfrutes as a short way of saying "I hope that you enjoy".

What does the word provecho literally mean?

Provecho means "benefit" or "advantage". When you say buen provecho to someone who is eating, you are literally wishing them "good benefit" from their food. It is the most common way to say "enjoy your meal" or "bon appétit" in Latin America.

Are buen provecho and que disfrutes la comida always used together like this?

Not necessarily. They mean basically the same thing, so using them together is just an extra polite and warm way to wish someone a good meal. You will often hear native speakers use either phrase completely on its own.

I see que disfrutes, but where is the word for "you"?

The "you" is hidden in the verb! The -es ending on disfrutes tells us exactly who the subject is (the informal "you", tú). While you could grammatically say que tú disfrutes, Spanish speakers almost always drop the subject pronoun in wishes like this because it is already obvious.