I could override CGI::Application::query and set the __QUERY_OBJECT myself but that's not guaranteed to work if CGI::Application gets upgraded.
I really don't have a problem with changing C::A's behaviour on this issue if you want to create a patch (code, docs, and tests) that would do this. How does everyone else feel about this? Is there a real reason for C::A behaving like this?
My guess would be that it is so that you don't accidentally clobber the CGI object that has already been created for the request, and lose all the script input. If there was an optional parameter added that means, "yes, I know what I'm doing, really replace the existing query object with this new one", then perhaps it would be "safe" to do this.
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