Josh Johnson has signed with the Padres for one year and $8 million. The Pirates evidently were "runners-up," and Johnson apparently rejected more money from other teams so that he could sign with the Padres. That's yet another advantage the Pirates don't have -- most players don't live anywhere near Pittsburgh, whereas lots of them do live in the Sun Belt.
That the Pirates apparently were serious contenders for Johnson might indicate that they're preparing for the possibility that A.J. Burnett won't return, but there's probably no way to know that for sure until Burnett signs, or announces he won't.