We present a semiconductor master equation technique to study the input/output characteristics of coherent photon transport in a semiconductor waveguide-cavity system containing a single quantum dot. We use this approach to investigate the effects of photon propagation and anharmonic cavity-QED for various dot-cavity interaction strengths, including weakly-coupled, intermediately-coupled, and strongly-coupled regimes. We demonstrate that for mean photon numbers much less than 0.1, the commonly adopted weak excitation (single quantum) approximation breaks down, even in the weak coupling regime. As a measure of the anharmonic multiphoton-correlations, we compute the Fano factor and the correlation error associated with making a semiclassical approximation. We also explore the role of electron--acoustic-phonon scattering and find that phonon-mediated scattering plays a qualitatively important role on the light propagation characteristics. As an application of the theory, we simulate a conditional phase gate at a phonon bath temperature of $20 $K in the strong coupling regime.
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