In this third example the “imparfait” is a “background” tense; it is used to communicate information about the setting; the explanation below comes from the following reference;

A1) L’imparfait de l’arrière-plan ou de l’action secondaire : il s’applique à des procès secondaires d’arrière plan, contrairement au passé simple qui est réservé à l’évocation des événements de premier plan.

The plus-que-parfait is a possible choice within the general tone set by the imparfait; however you introduce a slight difference and that is that at the time when the wind stopped the trees had been bared, whereas the imparfait means that this action of pulling the leaves off the trees was going on and had not necessarily been completed (there might still be leaves left). It dépends on what you want to say.

LPH gave a good answer. Just to complete it a little:

First of all, keep in mind that the passé composé is used for a fact. Something punctual, or at least the conclusion of something that lasted. Whereas the imparfait is for something that lasts in time and serves as a background for something else.

1) This is the most regular of the sentences you provided. We have 2 facts in the past. One is anterior to the other. We need the passé composé for the most recent and the plus-que-parfait for the other one.

2) Here, this could be the same things. 2 facts, one being anterior to the other. We could use passé composé and then plus-que-parfait. But the author chose the imparfait for the same reason that you might say: in -365, the temple that took the Greek 120 years of time and energy was being taken down by Érostrate, instead of in -365 Érostrate destroyed a temple. You are not just talking about a blunt fact, but more about a tragedy that, with a bit of imagination, you might almost see happening before your eyes.

3) Here, depuis deux jours dénudait les arbres is just the background for the action cesser. The tenses are perfectly regular.