I ate in a place with 鮎ラーメン. The store employee can't explain it but I think it's something to do with the cut of the 鮎. It was butterfly cutted.
For cutting what would be the kanji for go-to. 毎? 丸毎 shortcut for the marugoto?
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丸ごと means "whole" and ごと is usually written in kana. By "butterfly" I guess you mean what would be called 鮎のひらき, which means the fish would be "cleaned" (gutted) but skin, bones, head, fins, etc. would not be removed.
I guess the store employee was trying to explain to you that you would be served the whole fish, rather than a filet.