The main work to cite is:
Towards a Curated Collection of Code Clones Ewan Tempero 7th International Workshop on Software Clones (IWSC2013). May 2013The BibTeX entry is at the bottom of this page. A preprint (what was submitted to IWSC) is available as PDF.
The preferred citation is to use the IWSC paper and identify the version used. If that is not appropriate for some reason, then the citation to use to identify a particular release used in a study is:
Qualitas Research Group, Qualitas Corpus Clone Collection Version <versionid>, qualitascorpus.com/clones. The University of Auckland, <month> <year>.where <versionid> is the release date (using ISO 8601) given for the particular release used and <month> and <year> are the month and year of the release date.
Qualitas Research Group, Qualitas Corpus Clone Collection Version 20130501 qualitascorpus.com/clones. The University of Auckland, May 2013.
@inproceedings{Tempero:IWSC:2013,
author = {Tempero, Ewan},
title = {Towards a Curated Collection of Code Clones},
booktitle = {7th International Workshop on Software Clones},
month = may,
year = {2013},
}