It seems like this could get really spammy and it's not informative enough to help people track down the usage. We could use a utility like the [one Python has for deprecations](http://docs.python.org/2/library/warnings.html#warnings.warn). Ideally, the warning message would include the key ("setValue called to set preference fooBarBaz, use PreferencesManager.set instead"), be displayed with a stack trace and only be displayed once. I think this would be a handy utility to have generally. The utility would basically just need to keep track of the messages shown during that run of Brackets and to not display those messages again.