This reverts commit 72cf2bdb87f09deff22e1085de3290126aa4ad05.

SYSCONF settings are getting cleared when they shouldn't be. Let's
revert the change until I get proper time to figure out why it's broken.

Some pieces of code are calling IsRunning because there's some
particular action that only makes sense when emulation is running, for
instance showing the state of the emulated CPU. IsRunning is appropriate
to use for this. Then there are pieces of code that are calling
IsRunning because there's some particular thing they must avoid doing
e.g. when the CPU thread is running or IOS is running. IsRunning isn't
quite appropriate for this. Such code should also be checking for the
states Starting and Stopping. Keep in mind that:

* When the state is Starting, the state can asynchronously change to
  Running at any time.
* When we try to stop the core, the state gets set to Stopping before we
  take any action to actually stop things.

This commit adds a new method Core::IsUninitialized, and changes all
callers of IsRunning and GetState that look to me like they should be
changed.

Core::GetState reads from four different pieces of state: s_is_stopping,
s_hardware_initialized, s_is_booting, and CPUManager::IsStepping.
I'm keeping that last one as is for now because there's code in Dolphin
that sets it directly, but we can unify the other three to make things
easier to reason about.

This commit also gets rid of s_is_started. This was previously used in
Core::IsRunningAndStarted to ensure true wouldn't be returned until the
CPU thread was started, but it wasn't used in Core::GetState, so
Core::GetState would happily return State::Running after we had
initialized the hardware but before we had initialized the CPU thread.
As far as I know, there are no callers that have any real need to know
whether the boot process is currently initializing the hardware or the
CPU thread. Perhaps once upon a time there was a desire to make the
apploader debuggable, but a long time has passed without anyone stepping
up to implement it, and the way CBoot::RunApploader is implemented makes
it rather difficult. So this commit makes all the functions in Core.cpp
consider the core to still be starting until the CPU thread is started.

On Windows:
wsi.render_window being set will set/save the initial geometry, which will cause sizing bugs until it's set again by the user resizing/repositioning.

UpdateData in AchievementsWindow now only updates the components being requested, massively improving the window's performance. The parameter is UpdatedItems in AchievementManager, which tracks which portions of the system have been updated for every update callback.