// pwiz/data/common/Diff.hpp
namespace pwiz {
namespace data {
namespace diff {

struct BaseConfig { double precision; };

void diff(const UserParam& a,
          const UserParam& b,
          UserParam& a_b,
          UserParam& b_a,
          const BaseConfig& config);

template <typename object_type, typename config_type = BaseConfig>
struct Diff { ... }

} // namespace diff
} // namespace data
} // namespace pwiz


// pwiz/data/msdata/Diff.hpp
namespace pwiz {
namespace msdata {

struct DiffConfig : public BaseConfig
{
   bool ignoreMetadata, ignoreChromatograms;
}

}
}

namespace pwiz {
namespace data {
namespace diff {

using namespace msdata;

void diff(const Run& a,
          const Run& b,
          Run& a_b,
          Run& b_a,
          const DiffConfig& config);

template <>
struct Diff<SpectrumList, DiffConfig>
{ ... }

} // namespace diff
} // namespace data
} // namespace pwiz