Fix a regression reported at #9146

Fix a regression reported at #9146

This regression was introduced by me at 8b66f9ce. I did not take
into account that a call to a python script containing $$s is embedded
within a separate python script. Thus, when commandPrep() is called it
only sees the call to the outer python script, and does not see the
$$s contained in that python script. It therefore did not substitute
for it. This fix simply calls commandPrep() directly before writing
the embedded command.