hasMany serialization as object is opt-in

#1065 Made hasMany associations serialize as an object with index keys. This is a great fix for the case described there, but it changes the default and can cause problems.

This PR makes that object serialization opt-in with `encodeWithIndexes: true`.

In my case, I updated to the new JSON in some places, but I missed some. In one case, the app didn't even throw an error... just, a bunch of data got overwritten with blanks :disappointed: I hope that others don't have the same experience when updating to the latest version.

@arjeno, is the OK for you? I think your fix was important for the cases like the one you had, but I would like to keep the same default that batman.js has had from the start. Does this solution work for you, too?