core: Eliminate remaining usages of the global system instance

Removes all remaining usages of the global system instance. After this,
migration can begin to migrate to being constructed and managed entirely
by the various frontends.

src/core/cpu_manager.cpp

@@ -10,7 +10,6 @@
 #include "core/core.h"
 #include "core/core_timing.h"
 #include "core/cpu_manager.h"
-#include "core/gdbstub/gdbstub.h"
 #include "core/hle/kernel/kernel.h"
 #include "core/hle/kernel/physical_core.h"
 #include "core/hle/kernel/scheduler.h"