Comment #2 on issue 2389 by asmeurer: Semantic inconsistency between Basic.__contains__ and Tuple.__contains__
http://code.google.com/p/sympy/issues/detail?id=2389
Removing Basic.__contains__ would be a pretty big break. If you delete it and run the tests, for example, you get a ton of failures (all of which would be easy to fix, but the point is that it is used a lot at least in library code).
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