When a holistic practitioner begins working with a new patient, the first dietary step is to complete a form of an elimination diet. This means that you are eliminating the foods most people are sensitive to, such as dairy and grains. Depending upon your current clinical picture, you may need to exclude more items.
If you know that you are autoimmune, you would further modify your elimination diet to exclude foods most autoimmune patients react to = nightshades, eggs and nuts.
If your total cholesterol is above 250, you would want to follow a Mediterranean versus of the elimination diet, otherwise you may follow the Paleo diet which promotes saturated fats.
In addition to removing foods that you may be, or are sensitive to, you would want to eat as nutrient-dense as possible. Part of repairing the digestive tract is not making it assimilate and process foods that provide little, or no nutritive gain.
The Paleo Diet is a nutrient-dense, anti-inflammatory diet. To clarify, when I say Paleo diet, I am not referencing the diet of our ancestors in the Paleolithic times.