how to backup user data?

[Kevin Kofler]

You can use SFTP to transfer the data from a running system, or you can backup the whole contents of the eMMC using dd (in the opposite direction you would use to flash a new image, but otherwise following the same instructions, i.e., booting the Phone with a JumpDrive microSD card and connecting it to the computer over USB) and then you can mount the contents of the image on the computer to get at the data (though it is a bit tricky because the image contains multiple partitions, unless you dd just the / partition (e.g. /dev/sdx1) to an image file rather than the whole device (e.g. /dev/sdx)).

As usual on GNU/Linux, you will mainly want to backup the contents of your home directory. Possibly also some stuff under /etc and/or /var.