RSYNC Does Not Delete Source Directories

The manpage even says:

--remove-source-files   sender removes synchronized files (non-dirs)

If you want to remove empty directories in your source, if there are still files left, do a:

find . -depth -type d -empty -delete

If it's just an empty source directory, a rmdir <directory> will of course suffice.

The behavior of --remove-source-files that you observe is exactly that specified by man rsync:

--remove-source-files

   This tells rsync to remove from the sending side the files (meaning non-directories) that are a part of the transfer and have been successfully duplicated on the receiving side.

There is no specific command to remove the directories, as these two discussions in StackExchange and ServerFault clearly show. The solution suggested there is to issue two separate commands:

 rsync -av --ignore-existing --remove-source-files source/ destination/ && \
 rsync -av --delete `mktemp -d`/ source/ 

The last piece of the command suggested in these two posts,

 rmdir source/

which is needed to remove the (now emptied) source directory has this form in these posts because the OPs and the answers are using rsync to move large amounts of files within the same machine. In your case you will have to do this manually.

Using "rm -rf" has an inherent race condition, you could namely delete files that were just created between the rsync and the rm invocations.

I prefer to use:

rsync --remove-source-files -a server:incoming/ incoming/ &&

ssh server find incoming -type d -delete

This will NOT remove the directories if they are not empty.