When you synchronize directories with rsync you have to pay attention to use (or not use) trailing /.

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Example:

# without trailing slash
$ mkdir -p a/foo/bar/baz
$ mkdir b
$ rsync -a a b
$ find b
b
b/a
b/a/foo
b/a/foo/bar
b/a/foo/bar/baz

# with trailing slash
$ mkdir -p a/foo/bar/baz
$ mkdir b
$ rsync -a a/ b/
$ find b
b
b/foo
b/foo/bar
b/foo/bar/baz