Rsync: General file/folder synchronization

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http://serverfault.com – I have a file server, which is in-charge of pulling a folder tree from multiple workstations on a daily basis. My current method for this is by using rsync, (which works pretty well provided directory names and/or files remain the same) however, when files are renamed or moved about within subdir1, rsync will copy them over to the server, creating duplicates. I have to manually find and delete extraneous files/folders that had been left on the server during previous syncs. Note that I cannot use rsync's --delete flag because any sync from a workstation will then mirror that particular folder (HowTos)