Various fixes for DUE... (#10152)

- Watchdog reset during SD Card initialization.
- Move `DebugMonitor` to `DebugMonitor_Due.cpp`.
- Since the watchdog is enabled on boot do extra resets during init.
- Have `thermalManager` do watchdog reset before its ISR starts to prevent reset.
- Ensure that timers are stopped before reprogramming them to address tone issues.
- Improve SAM3XE reset when reflashed through the native port.

Marlin/src/Marlin.cpp

@@ -648,9 +648,6 @@ void setup() {
 
   #ifdef HAL_INIT
     HAL_init();
-    #if defined(ARDUINO_ARCH_SAM) && PIN_EXISTS(BEEPER) && ENABLED(SPEAKER)
-      toneInit();
-    #endif
   #endif
 
   #if ENABLED(MAX7219_DEBUG)