> I wanted to create the empty directories on the backup i.e. run, dev, also 

Add something like this to the exclude-list:
/dev/*
/var/run/*
...
That'll copy the dir itself, but not its contents.

> directory links i.e. lib to lib64

I don't fully understand here. You have a '-a' (even a redundant '-l')
in the argument list - symlinks should be created on the target
location.

By the way, your sync cmd seems a bit odd:
-l is redundant if -a is specified
-C used while syncing a whole / might exclude some needed stuff
-H is what you usually want while syncing a whole /
--exclude items without any '/' might be dangerous (I suppose you meant
to exclude /var/run, /sys, /tmp, /boot etc. and not every file named
'run', 'sys', 'tmp' or 'boot' in the entire filesystem. Your current
cmd might 'exclude', for
instance, /usr/include/sys, /etc/runlevels/boot, /usr/src/linux*/arch/*/boot
and most likely more. Just a note for the case this isn't what you
actually want.)

 -rz
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