Is an inner courtyard part of Target:Structure?

This just came up at my gaming table.
A magus cast a spell on a small convent, a single Structure (basically, a square with a smaller square "hole" in the middle -- the convent's cloister and inner courtyard). Is the inner courtyard part of the Structure even if technically it's not under the same roof?
In this specific case, it did not matter, but it may crop up again in the future, and I'd like your feedback.

I would say yes. The definition of "Structure" is "everything within a single structure." The courtyard is within the structure, therefore it's affected.

I think so. If it is within you standard Structure size (or the effect has a large enough size modifier to accommodate it) then it is part of that structure.

My take is, unless it is really important for some reason that it is explicitly excluded, I'd include it. However, I would pay attention to size. A structure large enough to include an inner courtyard may be at the upper end of Structure anyway.

I agree.

Unless the sides of the clositer are formed by separate buildings. Typically, one side will be a church/cathedral wall, with the other three sides being formed by the living/working quarters for the monks/canons. In that case, each building would be a separate Structure, and you'd need Boundary to affect the courtyard.

Agreed.

My main worry is size really, cloisters are not exactly small, usually

They are "connected edifices", meaning you can walk from to the others without ever leaving the building, which I think qualifies them for being a single Structure. Size is indeed Structure +1, but that was not a problem in the circumstances.

Well, as far as I can tell, a cloister qualifies as a room (as rooms need not be roofed - height is explicitly irrelevant).
Given how a structure is is defined, I'd argue that a cloister is within a structure.