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Start the virtual machine and get to the command shell by pressing Ctrl-F1 like described here: Sage Appliance Online Docs

Log into the virtual machine as user gui. The user account running the web browser is called gui with password sage.

sagevm login: gui
Password: sage

This login should bring you in the /home/gui directory. You can list the contents of that directory with the command (short for list)

ls

remove (rm) files with the command

rm filename

Probably you can delete files also from the gui interface of the vm, but the commandline version should work in any case.