{Initialize,Shutdown}WiiRoot should only be responsible for setting the
SESSION_WII_ROOT or managing the temporary NAND directory.
Move all the content manipulation out of these functions to ensure
separation of concerns and call them after/before WiiRoot init/shutdown
to make sure they operate on the correct root.
Dolphin is able to generate one with all correct default settings, so
we don't need to ship with a pre-generated SYSCONF and worry about
syncing default settings.
Additionally, this commit changes SysConf to work with session SYSCONFs
so that Dolphin is able to generate a default one even for Movie/TAS.
Which SYSCONF needs to be touched is explicitly specified to avoid
confusion about which file SysConf is managing.
(Another notable change is that the Wii root functions are moved into
Core to prevent Common from depending on Core.)
