Bring 3 cups of water and 1/2 teaspoon of the salt to a boil in a medium saucepan; add barley. Cover saucepan and simmer barley until tender, about 30 to 35 minutes; drain.Meanwhile, heat oil in a large nonstick skillet over medium-high heat; add squash and cook, stirring often, until it's starting to soften--about five minutes. Add the onion and red pepper and cook for an additional 3 minutes.Stir in apple, garlic, thyme, black pepper and remaining 1/4 teaspoon of salt. Cook, stirring, until apple is almost tender, about 2 minutes; stir in broth, scraping bottom of skillet with a wooden spoon to loosen any browned bits. Stir in cooked barley; toss over low heat to mix and coat. Remove from heat and serve. Yields about 1 cup per serving.*To make this vegetarian, use vegetable broth in place of the chicken broth.