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Admittedly munit/mcover have a few obscure aspects (and quirks) but from what I see you really misunderstood how it work.
Firstly there is no simple way to do code coverage, and mcover does that using macros. It can be used without munit but munit easily integrates it.
Secondly munit first generates an hxml and some classes, then it won't overwrite them. Except the one class listing the test classes which are detected.
@test
public function testMultiply() : Void
{
MyMath.multiply( 3, 2 )
}