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/usb/udi_msc.c

@@ -1127,5 +1127,6 @@ bool udi_msc_trans_block(bool b_read, uint8_t * block, iram_size_t block_size,
 
 //@}
 
-#endif
-#endif
+#endif // SDSUPPORT
+
+#endif // ARDUINO_ARCH_SAM