Onion Fly

Today I discovered onion fly on my - onions! I never saw maggots, just brown pupae. I peeled back the layers of infested skin. My question is - have I saved them or do I have to bin them? I did bin some that were obviously infested all the way through. If I've saved them - what about the root - do I cut off mega short - to ensure none remain there and same goes for leaves. Last year I cut off roots and leaves because I didn't know otherwise - they stored OK but to be fair we were making onion everything so they only lasted until end September max anyway. Also - what do I know do to the soil?