All the light goes through the processed end of the rod. Yes, many new colors of light are created inside the glass resonator. For a single color going in, often times ~1000 new colors come out. A nice feature of microresonator combs is that the spacing between teeth is large enough to easily separate them using standard optical telecommunication equipment (e.g. WDM filter or a diffraction grating).
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So, in use, is the 'raw' laser light injected into the fat end of the rod, and the combed light emitted from the processed end? Are new wavelengths actually generated (i.e., would a green laser produce blue and red light), or is the green light combed into a series of extremely narrow green bandwidths within the original bandwidth? How would a specific wavelength 'nano-band' (a single tooth) be selected for analysis or use?