Delay initialization of minecraft commands until after mod pre-init

This is a preparation PR to allow some features of https://github.com/MinecraftForge/MinecraftForge/pull/1220 

This PR delays the initialization of vanilla's commands, from before FML can startup its hooks into minecraft, to after the mod pre-initialization stage.

This will allow time for permission frameworks as specified in Forge pr 1220 to register themselves in the preinit stage, and thus will be available when the API registers permissions for vanilla commands.