Fixes T13284. See that task for substantial discussion. There are currently two cases where we'll skip over commits which we should publish:
- if a branch is not permanent, then later made permanent; or
- in some cases, the first time we examine branches in a repository.
In both cases, this error is one-shot and things work correctly going forward. The root cause is conflation between the states "this ref currently permanent" and "this ref was permanent the last time we updated refs".
Separate these pieces of state and cover all these cases. Also introduce a "--rebuild" flag to fix the state of bad commits.