Registering an agricultural building

I would speak to the câmara municipal - both elements are likely to require their involvement, and it may be possible to wrap up the licensing for the barn at the same time.  However, they may reasonably want to legalise the structure as-is, and then consider the residential licensing once the building is in a relevant condition (and depending on whether they feel it's appropriate).  In any event, speak to them as the first step.  It's likely to be helpful to have any relevant evidence of how long it's existed, its condition, etc; as well as your plans for how you'd use it residentially-speaking (perhaps downplaying any changes you may wish to make, without actually misrepresenting things).