If it rains, are there parts of Roots under cover of a roof? Is it still worth the trip?

Absolutely worth the trip.

There are multiple buildings and most things are located inside :)

There is a lot of prepared food inside. Baked goods. Sandwiches. Breads (bagels...). Coffee.

Yes, the others are correct.

Yes a lot is indoors and covered outside

Yes ! Plenty of places to get out of the weather.

Definitely worth the trip, even in the rain and yes, lots of items inside. If memory serves, about 5 buildings worth! As mentioned before - baked goods, breads, sandwiches, fresh meat, deli, soaps, produce, incense, etc. Amazing place!