RSync a whole Linux filesystem (sorta) - Pop-OS!

moveit.sh

# Move an installation of Pop-OS! from one disk to another.
# Useful guide if transferring data from a non encrypted install to an encrypted install.
# Create a fresh install of Pop-OS! in the new drive, and operatating from the live env do:

# unlock encrypted partitions
sudo udisksctl unlock -b /dev/<part>
# mount partitions
sudo udisksctl mount -b /dev/mapper/data-root # Or some other alias returned earlier

# REPEAT ABOVE FOR SOURCE AND DESTINATION

# Copy /etc/fstab from both systems to be able to merge them later
sudo cp /media/<src>/etc/fstab Desktop/fstab_src
sudo cp /media/<dst>/etc/fstab Desktop/fstab_dst

# Copy over files. Important: Do not foget the trailing slashes
# Note that /boot/ is ignored. The kernel will be "fresh"
sudo rsync -aAXv /media/<src>/ \
  --exclude={"/dev/*","/proc/*","/sys/*","/tmp/*","/run/*","/media/*","/lost+found","/boot/*"} \
  /media/<dst>/

# Merge both /etc/fstab files copied earlier to make sure the system will pick up the right partitions from the right disks
# Use fstab_dst (the one that was in the destination filesystem) as a base, and add the custom stuff you did (like external drive mounts) on the old installation.
sudo gedit Desktop/fstab_src Desktop/fstab_dst Desktop/fstab_new
sudo cp Desktop/fstab_new /media/<dst>/etc/fstab

# Broken? Maybe chroot can help https://support.system76.com/articles/login-from-live-disk/