Migraine aura is a fully reversible condition that either precedes or commences with the onset of head pain. 

It affects up to 20% of migraineurs, and in some rarer cases my appear without headache.

It is now understood to be related to a phenomenon called "cortical spreading depression". This tsunami of decreased blood flow causes decreased nerve activity in the brain. It begins in the occipital lobe (visual cortex) and spreads to the front quite slowly (estimated 3mm/minute).
First observed in animals in the 1940's, recent MRI and PET scan studies show it is a common feature of aura.

Is this the brains way of limiting the overactivity coming from the trigeminocervical nucleus? A lot remains to be understood about the relationship between different aspects of migraine.

Typical aura may involve:
Visual disturbance: bright flashing lights, zig zag lines, 
scotoma (loss of part of visual 
field/blind spot), difficulty focussing
Paraesthesia - pins and needles/tingling, numbness
Parosmia - altered smell
Dysarthria - difficulty speaking
Dysphagia - difficulty swallowing
Dysgeusia - altered taste
Hypokinesia - decreased muslce function
Paramnesia - deja vu, Jamaiv vu
Auditory hallucinations - tinnitus, buzzing
Altered cognitive function

It should be noted that if any of these symptoms appear for the first time, or they are regular features but do not fully resolve you should seek and assessment with a medical practitioner. However rare, any of these can be signs of more significant pathology and appropriate investigation is warranted.

"My neck isn't involved - I don't get a sore neck. I know my migraines come from stress/eating chocolate/drinking red wine."

What of these triggers? Is it an allergy? How can it be your neck if you eat something and get a migraine?

There are many different triggers for chronic headache and migraine. Many in the form of ingestants (wine, chocolate), strong smells, bright lights, and most commonly stress.

A common method of treating migraine or chronic headache is to keep a diary and try to identify your triggers, and hopefully you can find one or two that are predictable and that you can actually control - the lucky few. For the rest there are either too many triggers, or there isn't a consistent pattern, or you can't avoid them (i.e. driving, stress).
All to often the "avoid the triggers" or "just relax" doesn't work.

So what do all these factors have in common? The trigeminocervical nucleus in the brainstem. 

When we all eat certain foods particular chemicals in them have an effect on the lining of our mouth. Bright lights affect our cornea's, and strong smells affect the lining of our nose and sinuses. All of this normal information is relayed through the trigeminal nerve into the brainstem.

Now, we know from our earlier look into the science behind headache and migraine that a common factor in ALL headache types in an overactive brainstem. Effectively, it is sitting there like a powder keg, and the "buzz" coming in from the trigger is the "spark". The spark tips the activity over the "headache threshold" and BOOM! Migraine.

"But I have been told it is an allergy? No. An allergic reaction is your body mounting an immune response to a foreign invader. We know what allergies look like. Give someone peanuts who can't have them, cat fur, bee stings.......we see different types of allergies all the time, and what they provoke is an immune response. Your body says "Get it out".
We don't see an immune response in these cases. We just see the product of adding more information to an overloaded brainstem. Stress will do the same thing coming in through the cervical nerves.

We also know that in 80% of sufferers the upper neck is a major contributor to this overactivity, and has a treatable condition commonly overlooked by most clinicians. They just aren't trained to look for it.

In many cases after successful treatment, people again become able to tolerate wine, cheeses, chocolate........this is the true miracle of what I do. ;-)

The science is clear.

Check your neck.