The have gf bread in an open basket right below normal bread. I ended up standing in line for 10 minutes to place an order then asked if they had any sort of separate area for gf food production. They answer I got was basically no. I left without trying anything. Better safe than sorry. It was very disappointing because they had quite a wide selection of items and I was very hungry at the time.
They have a prominently posted sign with a gluten disclaimer. I'm not super-sensitive, so I ordered food anyway, and asked the server to be extra-careful about keeping my meal uncontaminated. She told me the food prep area was very small and that bread is on every surface; additionally, because they are a bakery, there is flour dust everywhere. She said that even when they take extra precautions for celiacs, people have gotten sick. I decided to skip breakfast and just have tea. I was disappointed, but really appreciated her honesty. Better hungry than sick!
Best spot in Eugene for freshly made GF bread. In summer, they have a pizza night once a month, amazing. I have celiac and haven't been bothered but they have signs posted saying their GF food is not meant for those with serious gluten sensitivities.