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_timers_Due.cpp

@@ -96,6 +96,15 @@ void HAL_timer_start(const uint8_t timer_num, const uint32_t frequency) {
   IRQn_Type irq = TimerConfig[timer_num].IRQ_Id;
   uint32_t channel = TimerConfig[timer_num].channel;
 
+  // Disable interrupt, just in case it was already enabled
+  NVIC_DisableIRQ(irq);
+
+  // Disable timer interrupt
+  tc->TC_CHANNEL[channel].TC_IDR = TC_IDR_CPCS;
+
+  // Stop timer, just in case, to be able to reconfigure it
+  TC_Stop(tc, channel);
+
   pmc_set_writeprotect(false);
   pmc_enable_periph_clk((uint32_t)irq);
   NVIC_SetPriority(irq, TimerConfig [timer_num].priority);
@@ -103,12 +112,16 @@ void HAL_timer_start(const uint8_t timer_num, const uint32_t frequency) {
   // wave mode, reset counter on match with RC,
   TC_Configure(tc, channel, TC_CMR_WAVE | TC_CMR_WAVSEL_UP_RC | TC_CMR_TCCLKS_TIMER_CLOCK1);
 
+  // Set compare value
   TC_SetRC(tc, channel, VARIANT_MCK / 2 / frequency);
+
+  // And start timer
   TC_Start(tc, channel);
 
   // enable interrupt on RC compare
   tc->TC_CHANNEL[channel].TC_IER = TC_IER_CPCS;
 
+  // Finally, enable IRQ
   NVIC_EnableIRQ(irq);
 }