Use "-f" to select filesystem mode, followed by the command to execute.
Optionally put ":" at the start of a filename to indicate that it's on the
remote device, if it would otherwise be ambiguous.
Examples:
$ pyboard.py -f ls
$ pyboard.py -f cat main.py
$ pyboard.py -f cp :main.py . # get from device
$ pyboard.py -f cp main.py : # put to device
$ pyboard.py -f rm main.py