Disable and rename initial_repo_scan flag
When doing an migration from 2.X/1.X to 3.X or 4.X the initial_repo_scan was enabled by default. This is a really bad flag, and we should by default disable it.
I think by renaming it and making sure it's turned off, we can have a nicer migration path. And still expose it for people if they wish to enable this (somehow bad) functionality.