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There are intentionally vague broad steps, here just as a reminder to myself; best to look specific instructions for each of these steps up at restore time for the particular system you're restoring to.

A.) Backups should include all user data. Depending on who you ask, that's either:
1.) The entire filesystem except /dev/*, /proc/*, /sys/*, /tmp/*, /run/*, /mnt/*, /media/*, /lost+found (which can be pulled from a complete filesystem backup with rsync -avhP --exclude={"/dev/*","/proc/*","/sys/*","/tmp/*","/run/*","/mnt/*","/media/*","/lost+found"} /mnt/olddrive/ /mnt/netdrive/)
2.)/home, /etc (except /etc/passwd and /etc/groups, these have useful information to back up but may conflict if written to a new install), /usr/local, /opt, /root, /var (exluding /var/tmp, /var/run/, /var/lock, or /var/spool except you DO want /var/spool/cron/crontabs/)

B.) After copying all the above to the new or restored disk, you need to update /etc/fstab with the new disk UUIDs.

C.) Install GRUB Bootloader.

D.) If you're using LUKS encryption, set that…

Per numerous references around the web, to delete /path/to/directory-to-delete/:

 cd /path/to/ mkdir empty_dir rsync -a --delete empty_dir/ directory-to-delete/ rm -r empty_dir rm -r directory-to-delete 

Disclaimer: this is for my own reference, not recommended for your use. Use it at your own risk. If I am wrong—and I may be—these commands can do tremendous damage to your system.