Use o rsync com a opção -R
. Na página rsync(1)
man:
-R, --relative
Use relative paths. This means that the full path names speci‐
fied on the command line are sent to the server rather than just
the last parts of the filenames. This is particularly useful
when you want to send several different directories at the same
time. For example, if you used this command:
rsync -av /foo/bar/baz.c remote:/tmp/
... this would create a file named baz.c in /tmp/ on the remote
machine. If instead you used
rsync -avR /foo/bar/baz.c remote:/tmp/
then a file named /tmp/foo/bar/baz.c would be created on the
remote machine, preserving its full path. These extra path ele‐
ments are called "implied directories" (i.e. the "foo" and the
"foo/bar" directories in the above example).