I see you're stepping on the same problem I faced when learning how to use futhark.
The general rule is that opir (first pass) reads the whole C code just lite clang would do, while futhark (second pass) generates wrappers only for the explicitly listed .h files to avoid excessive clutter. TDK, also consider that a proper wrapper is a better solution for the community (AFAIK this is also araq's opinion), but I believe futhark is a great helper for this tast too.
