It's common practice for step 1 of seeing your naturopathic doctor for autoimmune disorders such as Hashimoto's, psoriasis and ankylosing spondylitis, to be an entire diet overhaul. Most practitioners will tend towards using the Elimination Diet, which keeps you eating an appropriate number of calories but steers you towards hypoallergenic, whole food choices by cutting out things that are often triggering or allergenic, e.g. gluten containing grains, dairy, eggs, nightshades, sugar, alcohol, caffeine.
There's a lot to share with a patient as a doctor when recommending the Elimination Diet, and so often times a precise definition of how exactly this will be useful in helping your illness will go by the wayside. I came across this really excellent video (albeit more for the 'information coper' than those of us who don't need to know every detail of how things work) from nutritionist and gluten expert Joe Rignola that does a pretty good job at explaining what we're doing for our immune system when we take highly reactive foods like gluten out. Check it out!