  Observations from the radio to the gamma-ray wavelengths indicate that
supernova remnant (SNR) shocks are sites of effective particle acceleration. It
has been proposed that the presence of dense clumps in the environment where
supernovae explode might have a strong impact in shaping the hadronic gamma-ray
spectrum. Here we present a detailed numerical study about the penetration of
relativistic protons into clumps which are engulfed by a SNR shock, taking into
account the magneto-hydrodynamical properties of the background plasma. We show
that the spectrum of protons inside clumps is much harder than that in the
diffuse inter-clump medium and we discuss the implications for the formation of
the spectrum of hadronic gamma rays, which does not reflect anymore the
acceleration spectrum of protons, resulting substantially modified inside the
clumps due to propagation effects. For the Galactic SNR RX J1713.7-3946, we
show that a hadronic scenario including dense clumps inside the remnant shell
is able to reproduce the broadband gamma-ray spectrum from GeV to TeV energies.
Moreover, we argue that small clumps crossed by the shock could provide a
natural explanation to the non-thermal X-ray variability observed in some hot
spots of RX J1713.7-3946. Finally we discuss the detectability of gamma-ray
emission from clumps with the upcoming Cherenkov Telescope Array and the
possible detection of the clumps themselves through molecular lines.
