How were urolithins discovered and named?
The identification of urolithins as products of human metabolism of ellagic acid was reported by Cerda et al. in the European Journal of Nutrition in 2004. The full reference is
Cerda, B., Espin, J.C., Parra, S., Martinez, P. and Tomas-Barberan, F.A. (2004) The potent in vitro antioxidant ellagitannins from pomegranate juice are metabolised into bioavailable but poor antioxidant hydroxy-6H-dibenzopyran-6-one derivatives by the colonic microflora of healthy humans. Eur J Nut 43:205-220.
However, these researchers did not name the compounds as urolithins. Rather, they note that the compounds

have also been found as constituents of ‘clover stone’, a type
of renal calculus found in sheep which can also ingest large
amounts of ellagitannins[26]. In fact, the metabolite d
(3,8-dihydroxy-6H-dibenzo[b,d]pyran-6-one) has been previously named
as ‘urolithin  B’ [22, 26].

That explanation seems sufficient to understand the source of the name, but if you are interested in the specifics of the original discovery, reference 26 is to the Dictionary of Natural Products published in 1992 by Chapman &amp; Hall, which is available only by subscription. Perhaps someone with access to that Dictionary can look up the entry on urolithin and provide more info.
UPDATE: Since this answer has received a decent amount of attention, I dug a bit deeper to find the references for the first isolation and naming of the compounds (thereby actually answering the question).
In 1963 at the 430th meeting of the Biochemical Society in Oxford, England, Nottle and Pope first reported isolating two compounds that they named &quot;urolithin A&quot; and &quot;urolithin B&quot;. Their report was published among the proceedings of the meeting in the Biochemical Journal, which are available for free from the journal here. The full reference is
Nottle, M.C. and Pope, G.S. Two Constituents of 'CloverStone', a Type of Urinary Calculus Found in Sheep in Proceedings of The Biochemical Society. Biochem J (1963) 89 (1): 1P–67P.
The Nottle and Pope report is on p. 67P. In that report, however, the structures of the urolithins were not described, as they had not yet been determined. In a subsequent paper, Pope reported the structures of the urolithins, noting that they were actually previously known compounds (specifically urolithin A is identical to pigment I of castoreum, isolated from beaver scent glands), but despite the compounds already being known, Pope and others continued to use the new name, which seems to have stuck. That report is also freely available from the Biochemical Journal here. The full reference is
Pope, G.S. (1964) Isolation of Two Benzocoumarins from 'Clover Stone', a Type of Renal Calculus Found in Sheep. Biochem J 93:474.