Hi Ronald,

I don't think that you can just copy files over because many of the links won't work.
It is a while since I set my system up but I think this is how I did it. (below)
Provided your hard drive/SSD is not full with data you can create an image of only the data rather than the empty space on the drive with GParted which is a free app in Linux. Even 125GB SDs are pretty cheap as a back up or just save the image to a hard drive on your PC. You could create more than one partition on your drive and keep your base programs on the one and all your FITS files (if you save direct to the local drive). That way you only need to back up the smaller partition that reflects the system. You can back up the data (FITS files with just copy and paste).
Take a look at GParted it is a great program!
I think that there is an option in the Raspberry Pi SD creator program to image on the data on the SD/SSD/Hard drive too although I don't use this option currently. It is likely that someone more technically competent than I knows a better way.

Mike

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