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Johan, you can run Sage at the shell prompt, just as you run GAP. Then of course everything is very similar to using Python, GAP or any other interpreted language. You can put your Sage code in text files, with extension .sage, load them, and off you go!

In case, your Sage worksheets are still most probably in your Linux account directory, in the subdirectory .sage/sage_notebook.sagenb/home/admin/ It should be possible to recover what's there, if needed.