Chickens will scratch and eat anything green and eatable, the tomato plants wont make it long enough to bear fruit if you plant it anywhere that they can get to it. When i first made my chicken yard, it was full of weeds and ginger lillys had almost taken it over, they were also growing outside the yard. now i have bare dirt yard with all of the surrounding vegetation eaten all around the yard as far as they can stick their necks out of the wire, so if you want to plant anything around the chicken run, be sure your fence is a very mesh wire at least along the bottom, so they cannot stick their heads out and eat it all. You have to remember a chickens life is all about scratching and pecking, thats all they do all day. I live in Florida so i have a lot of Spanish moss in my trees, i experimented with feeding that to them, they love it. When i weed my garden or flower beds i take the weeds to them also, leftovers from the kitchen, greens from the garden all go to the chickens. Also if you decide to let them run free for a while, i do mine sometimes about an hour before sunset, so they dont do too much damage before they go into the coop on their own. anyway if you have a garden or flower bed it needs to be protected. But i still love my girls and are about to get another batch soon.