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/HAL/HAL_DUE/HAL_Due.h

@@ -160,14 +160,15 @@ void toneInit();
 void tone(const pin_t _pin, const unsigned int frequency, const unsigned long duration=0);
 void noTone(const pin_t _pin);
 
-// Enable hooks into idle and setup for USB stack
+// Enable hooks into idle and setup for HAL
 #define HAL_IDLETASK 1
 #define HAL_INIT 1
+void HAL_idletask(void);
+void HAL_init(void);
+
 #ifdef __cplusplus
   extern "C" {
 #endif
-void HAL_idletask(void);
-void HAL_init(void);
 char *dtostrf (double __val, signed char __width, unsigned char __prec, char *__s);
 #ifdef __cplusplus
   }