how do I upgrade sage 6.3 to 9.0?

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Ortolij's comment is a pretty acceptable answer.

I allow myself to add that upgrading such an antique may be painful, and that you might be better off removing the old version and installing the one you aim at.

Be axware, however, that the old (Sage) notebook is no longer maintainable, and that one of your last actins with your old Sage would be to export your Sage notebooks to Jupyter...

Be also awar that, from 9.1 onwards, Sage is based on Python 3. Sage 9.0 is the last Sage that can be build based on Python 2. There are some subtle (and some not-so-subtle (and some gross)) incompatibilities that may render your old code incompatible with a Python 3-based Sage...

HTH,