We study the late-time (t>0.5 days) X-ray afterglows of nearby (z<0.5) long Gamma-Ray Bursts (GRB) with Swift and identify a population of explosions with slowly decaying, super-soft (photon index Gamma_x>3) X-ray emission that is inconsistent with forward shock synchrotron radiation associated with the afterglow. These explosions also show larger-than-average intrinsic absorption (NH_x,i >6d21 cm-2) and prompt gamma-ray emission with extremely long duration (T_90>1000 s). Chance association of these three rare properties (i.e. large NH_x,i, super-soft Gamma_x and extreme duration) in the same class of explosions is statistically unlikely. We associate these properties with the turbulent mass-loss history of the progenitor star that enriched and shaped the circum-burst medium. We identify a natural connection between NH_x,i Gamma_x and T_90 in these sources by suggesting that the late-time super-soft X-rays originate from radiation reprocessed by material lost to the environment by the stellar progenitor before exploding, (either in the form of a dust echo or as reprocessed radiation from a long-lived GRB remnant), and that the interaction of the explosions shock/jet with the complex medium is the source of the extremely long prompt emission. However, current observations do not allow us to exclude the possibility that super-soft X-ray emitters originate from peculiar stellar progenitors with large radii that only form in very dusty environments.
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