Upgrade SQL files don't always get run

While trying to debug why the 4.7.alpha1 sql wasn't running, Tim and I discovered that there's some particularly problematic logic in the upgrade code that will either load the sql for a particular rev or call the php function specific to that rev if it exists. So if the sql tpl doesn't exist it will cause the php function to be skipped. But if the php function exists it will cause the sql to get skipped unless the php function explicitly runs it. Most of the functions do remember to perform this obscure step, but a few don't.