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The Transparent Sync Guide
This guide is a repository of things you should or should not do with Transparent Sync.
If you use an <exclude>
with Transparent Sync, this will cause an odd situation where part of the tree comes from disk and a discontinuous tree comes from the database (the excluded children). This will cause errors and is a very weird place to put your database, so don't do it.
Since the disk becomes the master in TpSync, having overlapping configurations means that more than one thing is competing to be the master. That's going to cause weird behavior, say if you changed only one of the files, because only one of the files will end up really being the master.
Transparent Sync operates by reading from the serialization store directly. In other words transparent sync always acts like SerializedAsMasterEvaluator because disk is LITERALLY the master. So your custom evaluator behavior will be ignored.