include_root_in_json for all but ActiveResource 3.1

Please review @csaunders @jduff 
what happen?
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Various versions of ActiveResource (3.0, 3.1, 3.2, 4.0) made changes to json encode/decoding with respect to whether the root element was included. The latest gem push included some changes from February that removed and simplified the monkeypatching, but 4.0 had not been released or tested at the time the changes were made.
what do?
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This PR just sets `ShopifyAPI::Base.include_root_in_json` to true for all ActiveResource versions other than 3.1 (for which a patched `encode` function exists). It also updates CHANGELOG to reflect the changes absorbed over the last year.
what next?
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We want to release 3.1.1 of the gem ASAP to prevent users from grabbing 3.1.0 and seeing code 400 errors all over the place. The way we support multiple versions of ActiveResource through conditional code paths can be cleaned up by putting functionality in modules that are included depending on the value of `ActiveResource::VERSION`. We'll work on that cleanup and more in 3.1.2.