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perhaps a craigslist ad is different, but when people say they want a clean roommate, they mean they don't want to live with slobs.
isn't also possible that, as a single person, you may have developed some bad household habits, not having to pick up after yourself or clean your shower or etc? and as a non-stereotypical-single guy, they're just not into that?
it just seems too much like code for "clean" to mean chaste/hygienic/wholesome.
(though i also agree with the poster that said it might mean drug-free)
plus, with so much ambiguity, it also seems shortsighted to close off the potential match until you find out what it means...