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/module/temperature.h

@@ -202,6 +202,11 @@ class Temperature {
 
   private:
 
+    #if EARLY_WATCHDOG
+      // If temperature controller is running
+      static bool inited;
+    #endif
+
     #if ENABLED(TEMP_SENSOR_1_AS_REDUNDANT)
       static uint16_t redundant_temperature_raw;
       static float redundant_temperature;