Understand file and folder structure with shopify extensions

Shopify Partner
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Specifically in reference to: https://shopify.dev/docs/apps/functions/input-output/variables-queries, is set-metafield.graphql its own file? Which directory should it live in inside the extension? I'm finding the documentation often assumes I know a lot of shopify tenets without really explaining the nitty gritty. 


I do have a couple extensions already running, as well as a cart validation extension already running that I want to use this with. Basically, it's not a question about how to get extensions working, but a question on how to interpret Shopify documentation that is very often referencing file names without showing where it expects them to be.


I'm really just trying to let a user dictate which collections my extensions works on instead of hardcoding those.

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