Fix the automatic mysql_upgrade in 1.2.X

Dave & I tried to get postConfigure to automatically run mysql_upgrade during an upgrade, but couldn't get it to stick. As of 1.2.1, postConfigure does run mysql_upgrade, and it seems to be successful, but after the entire upgrade process is finished, it seems that at least the CS tables were not upgraded. Attempting to drop a CS table results in a crash in mysqld, which is the symptom of an un-upgraded table. Andrew suspects it may be that CS was not fully up by the time the upgrade happened. To check whether that is the case, we could just add a pause just before mysql_upgrade is run.

This ticket covers getting the automatic mysql_upgrade to work, and removing the instruction to run it manually in the upgrade documentation.