in case you are worried about the two directories there might just be a misunderstanding. Master and slave both utilize two directories (in case you see more than two there might indeed be a problem). A synchronization of the index is done via file copy between master and slave. While the copying is in progress the index is not usable. For this reason the synchronization occurs in a offline copy. One the synchronization is complete the sync index (directory) becomes active. See FSMasterDirectoryProvider.java
for more details.