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/watchdog_Due.cpp

@@ -23,17 +23,88 @@
 #ifdef ARDUINO_ARCH_SAM
 
 #include "../../inc/MarlinConfig.h"
+#include "../../Marlin.h"
+#include "watchdog_Due.h"
+
+// Override Arduino runtime to either config or disable the watchdog
+//
+// We need to configure the watchdog as soon as possible in the boot
+// process, because watchdog initialization at hardware reset on SAM3X8E
+// is unreliable, and there is risk of unintended resets if we delay
+// that initialization to a later time.
+void watchdogSetup(void) {
+
+  #if ENABLED(USE_WATCHDOG)
+
+    // 4 seconds timeout
+    uint32_t timeout = 4000;
+
+    // Calculate timeout value in WDT counter ticks: This assumes
+    // the slow clock is running at 32.768 kHz watchdog
+    // frequency is therefore 32768 / 128 = 256 Hz
+    timeout = (timeout << 8) / 1000;
+    if (timeout == 0)
+      timeout = 1;
+    else if (timeout > 0xFFF)
+      timeout = 0xFFF;
+
+    // We want to enable the watchdog with the specified timeout
+    uint32_t value =
+      WDT_MR_WDV(timeout) |               // With the specified timeout
+      WDT_MR_WDD(timeout) |               // and no invalid write window
+    #if !(SAMV70 || SAMV71 || SAME70 || SAMS70)
+      WDT_MR_WDRPROC   |                  // WDT fault resets processor only - We want
+                                          // to keep PIO controller state
+    #endif
+      WDT_MR_WDDBGHLT  |                  // WDT stops in debug state.
+      WDT_MR_WDIDLEHLT;                   // WDT stops in idle state.
+
+    #if ENABLED(WATCHDOG_RESET_MANUAL)
+      // We enable the watchdog timer, but only for the interrupt.
+
+      // Configure WDT to only trigger an interrupt
+      value |= WDT_MR_WDFIEN;             // Enable WDT fault interrupt.
+
+      // Disable WDT interrupt (just in case, to avoid triggering it!)
+      NVIC_DisableIRQ(WDT_IRQn);
+
+      // Initialize WDT with the given parameters
+      WDT_Enable(WDT, value);
+
+      // Configure and enable WDT interrupt.
+      NVIC_ClearPendingIRQ(WDT_IRQn);
+      NVIC_SetPriority(WDT_IRQn, 0); // Use highest priority, so we detect all kinds of lockups
+      NVIC_EnableIRQ(WDT_IRQn);
+
+    #else
+
+      // a WDT fault triggers a reset
+      value |= WDT_MR_WDRSTEN;
+
+      // Initialize WDT with the given parameters
+      WDT_Enable(WDT, value);
+
+    #endif
+
+    // Reset the watchdog
+    WDT_Restart(WDT);
+
+  #else
+
+    // Make sure to completely disable the Watchdog
+    WDT_Disable(WDT);
+
+  #endif
+}
 
 #if ENABLED(USE_WATCHDOG)
-
-  #include "watchdog_Due.h"
-
-  void watchdogSetup(void) {
-    // do whatever. don't remove this function.
+  // Initialize watchdog - On SAM3X, Watchdog was already configured
+  //  and enabled or disabled at startup, so no need to reconfigure it
+  //  here.
+  void watchdog_init(void) {
+    // Reset watchdog to start clean
+    WDT_Restart(WDT);
   }
-
-  void watchdog_init(void) { watchdogEnable(4000); }
-
 #endif // USE_WATCHDOG
 
 #endif