This appears to be a bug. Would you like to file a JIRA issue?
In the ServerSynchronizer.synchronizeConfigSpecificDir method, the call
to getFileName passes in SyncLevel.DIRECTORY rather than
SyncLevel.RECURSIVE, which means that only the files at the top level of
the config specific directory are synchronized rather than all files
under the directory.
Unfortunately, there isn't any workaround for this other than fixing the
code.
Or can you include the libraries in your application?
Tom