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From what people say about jQuery it does seem to be backwards compatible.
Maybe the issues we have are due to incompatibility in the plugins and possibly our own code, I think there is no magic solution here, but to debug the code.
We probably should isolate javascript used in askbot into a separate namespace, so that we could use whatever version we want, without competing with other code.
I don't know when this will be done, at this moment this is not the highest priority.