Stanford: Minimal change for LPL Long run

* Adds flags for ungenerated_certs to allow cert runs which retain
  pre-existing certs, even when students fail by some new set of
  criteria, but which recreate certs for passing students, even when
  they previously had one.

@stvstnfrd and @jbau 
Maybe combine with the preceding line into an `elif` and save the additional level of indentation?