3

An rsync command that looks like of like this, rsync -av -e "ssh" --include="dir1" --include="dir2" --include="dir3" --include="file1" --include="file2" --include="file3" --exclude="*" user@server:/directory1/site/ /dir1, is not recursively copying the files. In other words, only the files and non-regular files in the /directory1/site directory are being copied and not the files in it's folders.

3

The rsync includes/excludes are weird. I strongly suggest you take some time and carefully read the INCLUDE/EXCLUDE PATTERN RULES section of the man page. Pay close attention to all the rules since some things simply won't work in what might seem like the obvious way.

a trailing "dir_name/***" will match both the directory (as if 
"dir_name/" had been specified) and everything in the directory 
(as if "dir_name/**" had been specified). This behavior was added
in version 2.6.7.

So if you wanted the entire contents of a directory you would use --include="dir3/***" instead of --include="dir3".

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