But you can't say "Hur lagar du?" in Swedish. It sounds really weird, so you have to specify what you are cooking. "Lagar" kan also mean "fix/repair", you see.

Saying "Hur lagar du?" would be like saying "How do you make?". Something is missing in that sentence.

You should regard "att laga mat" as a phrasal verb meaning "to cook". Like Jungla3 was saying "att laga" means "to repair".

It isn't "hur lagar mat du?", that would be asking "how do you food cook?"

I wrote some about it here: https://www.duolingo.com/comment/8970470

laga mat isn't really a phrasal verb in Swedish, but rather a verb and an object that are both required for the meaning of the phrase. Considering that, what happens in the question is that the subject and the verb switch places, but the object remains in place.

That would be hur kokar du?, but it would mean cook as in boil, not as in preparing food.