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The easiest way to use your own BSDFs would be to add a loop that rewrites mapping.rad sometime after the translation but before all the Radiance simulation crap happens. Actually I'd just do it right before calculateDaylightCoeffecients. Were you to embark on this today, I'd recommend you just hack this, and simply rewrite mapping.rad using full path(s) to the BSDF(s) you want to use. OpenStudio 2.0's API will have much better support for accessing files and assigning and referencing them in measures. At that point, I think the right answer would be to change the measure interface to allow users to specify the BSDFs in the GUI.
Speaking of hacks, you had also asked about the purpose of the air.bsdf file in your earlier comment. This is basically a unit matrix that passes all the flux through the window interface, unaltered. It's used for calculating the illuminance for a window group's "shades up" condition. This way we only have to compute one 3-phase pair of daylight coefficients per (shaded) window group. We sacrifice a bit of accuracy (the perfectly specular transmission is being smeared out to the 145 Klems hemispherical subdivisions) in the interest of speed and conservation of disk space. For windows with no shades, we simply do a "single phase" daylight coefficient calc for flux at the points of interest (with the actual glazing in the windows). The best solution for shaded windows is to use the 5-phase methodology but that comes with its own issues and challenges in the context of a GUI and what we were trying (and funded) to do. So, the basic workflow is dumbed down a bit and it is what it is. The beauty is it's all there in the repository and you are welcome to improve it. I look forward to seeing what you come up with! Please let us know if you have more questions as you get into it.