This paper provides a quantitative study of nonnegative solutions to nonlinear diffusion equations of porous medium-type of the form $\partial_t u + {\mathcal L}u^m=0m>1{\mathcal L}$ belongs to a general class of linear operators, and the equation is posed in a bounded domain . As possible operators we include the three most common definitions of the fractional Laplacian in a bounded domain with zero Dirichlet conditions, and also a number of other nonlocal versions. In particular, can be a power of a uniformly elliptic operator with coefficients. Since the nonlinearity is given by with , the equation is degenerate parabolic. The basic well-posedness theory for this class of equations has been recently developed in [14,15]. Here we address the regularity theory: decay and positivity, boundary behavior, Harnack inequalities, interior and boundary regularity, and asymptotic behavior. All this is done in a quantitative way, based on sharp a priori estimates. Although our focus is on the fractional models, our results cover also the local case when is a uniformly elliptic operator, and provide new estimates even in this setting. A surprising aspect discovered in this paper is the possible presence of non-matching powers for the long-time boundary behavior. More precisely, when is a spectral power of the {Dirichlet} Laplacian inside a smooth domain, we can prove that:

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