GRE default prefs live in [gredir]/greprefs App default prefs live in [appdir]/defaults/pref
If you are not using the GRE, [gredir] and [appdir] are the same.
This should not affect existing embedding situations. However, if you currently ship a file [appdir]/defaults/pref/all.js you can probably remove most or all of this file, because appropriate defaults have been chosen in the GRE already.
If you have questions, feel free to post here or email me privately.
--BDS
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