init files isn't just 'python' now and auto_open is removed.
Be more careful about where we stick init lines (see below).

Before, run.py was formatting all of the sign-in lines and
plot-calls. Now, these things happen in the code_translator.
Therefore, we need to actually insert lines into the code
we get back for the initializations to happen in a reasonable
order.
rerun all examples with run.py / test-publish.