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/sd/Sd2Card.cpp

@@ -260,6 +260,11 @@ bool Sd2Card::init(uint8_t sckRateID, pin_t chipSelectPin) {
   // must supply min of 74 clock cycles with CS high.
   for (uint8_t i = 0; i < 10; i++) spiSend(0xFF);
 
+  // Initialization can cause the watchdog to timeout, so reinit it here
+  #if ENABLED(USE_WATCHDOG)
+    watchdog_reset();
+  #endif
+
   // command to go idle in SPI mode
   while ((status_ = cardCommand(CMD0, 0)) != R1_IDLE_STATE) {
     if (((uint16_t)millis() - t0) > SD_INIT_TIMEOUT) {
@@ -272,6 +277,11 @@ bool Sd2Card::init(uint8_t sckRateID, pin_t chipSelectPin) {
     crcSupported = (cardCommand(CMD59, 1) == R1_IDLE_STATE);
   #endif
 
+  // Initialization can cause the watchdog to timeout, so reinit it here
+  #if ENABLED(USE_WATCHDOG)
+    watchdog_reset();
+  #endif
+
   // check SD version
   for (;;) {
     if (cardCommand(CMD8, 0x1AA) == (R1_ILLEGAL_COMMAND | R1_IDLE_STATE)) {
@@ -292,6 +302,11 @@ bool Sd2Card::init(uint8_t sckRateID, pin_t chipSelectPin) {
     }
   }
 
+  // Initialization can cause the watchdog to timeout, so reinit it here
+  #if ENABLED(USE_WATCHDOG)
+    watchdog_reset();
+  #endif
+
   // initialize card and send host supports SDHC if SD2
   arg = type() == SD_CARD_TYPE_SD2 ? 0x40000000 : 0;
   while ((status_ = cardAcmd(ACMD41, arg)) != R1_READY_STATE) {