饭
Inner meaning: Rice
Outer meaning: Rice alternatives, for example, noodles, bread, also called 主食 which means the main food to fill yourself
Extended meaning: Food you eat at a certain time, breakfast, lunch, or dinner.
"你吃饭了吗?" means Have you eaten (breakfast, lunch, or dinner, depends on the time you are asked)
菜
Inner meaning: vegetable
Outer meaning: food eaten along with 饭, for example, vegetables, eggs, fish, and meals. Also called 副食.
Extended meaning: Dishes
你做饭吗? means Do you cook, but people usually won't say 你做菜吗? instead, 你会做菜吗? Using a microwave is not 做菜, it is not cooking, though it indeed fills yourself, so it is only 做饭.
食
Inner meaning: 吃 in written language
Outer meaning: Food in written language
餐
Inner meaning: breakfast, lunch, and dinner in written language
早饭 = 早餐