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What Strong and I normally do is "[local stage path]/orm/4.3 -> [remote path]/orm" or "[local stage path]/orm/4.3/* -> [remote path]/orm/4.3". I've honestly never tried "[local stage path]/orm -> [remote path]". The first time I ran it, I used the wrong user account, so there was a permissions issue. I noticed that it was complaining about attempting an "rsync_delete on orm".
I think that makes sense. You're "sync'ing" the entire orm directory and it thinks you deleted the other subdirs. Is there a way to prevent that?