With the rsync command you should use an exclude-file (see --exclude option)
containing a list of directories and files not to be transferred like

./lost+found**
./run**
./dev/**
./sys/**
./tmp/**
etc (see rsync manual).

After transferring the files you may have to adapt files like /etc/fstab and the
configuration file for your boot-loader. Depending on your boot-loader you have
to install a new mbr (using grub-install or lilo with options like
"--boot-directory=DIR /dev/hdb", e.g., for grub).
-- 
Best regards,
Jörg-Volker.


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