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Here we revisit the thermodynamics of the Kitaev quantum spin liquid realized on the honeycomb lattice. We address two main questions: First, we investigate whether there are observable thermodynamic signatures of the topological Majorana boundary modes of the Kitaev honeycomb model. We argue that for the time-reversal invariant case the residual low-temperature entropy is the primary thermodynamic signature of these Majorana edge modes, and verify using large-scale Monte Carlo simulations that this residual entropy is present in the full Kitaev model. When time-reversal symmetry is broken, the Majorana edge modes are potentially observable in more direct thermodynamic measurements such as the specific heat, though only at temperatures well below the bulk gap. % Second, we study the energetics, and the corresponding thermodynamic signatures, of the flux excitations in the Kitaev model. Specifically, we study the flux interactions on both cylinder and torus geometries numerically, and quantify their impact on the thermodynamics of the Kitaev spin liquid by using a polynomial fit for the average flux energy as a function of flux density and extrapolating it to the thermodynamic limit. By comparing this model to Monte Carlo simulations, we find that flux interactions have a significant quantitative impact on the shape and the position of the low-temperature peak in the specific heat.