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/ctrl_access.c

@@ -642,5 +642,6 @@ U16 stream_stop(U8 id)
 
 //! @}
 
-#endif  // ACCESS_STREAM == true
-#endif
+#endif // ACCESS_STREAM
+
+#endif // ARDUINO_ARCH_SAM

Marlin/src/HAL/HAL_DUE/usb/sysclk.c

@@ -119,4 +119,4 @@ void sysclk_disable_usb(void)
 /**INDENT-ON**/
 /// @endcond
 
-#endif
+#endif // ARDUINO_ARCH_SAM

Marlin/src/HAL/HAL_DUE/usb/udc.c

@@ -1146,4 +1146,4 @@ bool udc_process_setup(void)
 
 //! @}
 
-#endif
+#endif // ARDUINO_ARCH_SAM

Marlin/src/HAL/HAL_DUE/usb/udi_cdc.c

@@ -1152,4 +1152,4 @@ iram_size_t udi_cdc_write_buf(const void* buf, iram_size_t size)
 
 //@}
 
-#endif
+#endif // ARDUINO_ARCH_SAM

Marlin/src/HAL/HAL_DUE/usb/udi_cdc_desc.c

@@ -255,5 +255,7 @@ UDC_DESC_STORAGE udc_config_t udc_config = {
 
 //@}
 //@}
-#endif
-#endif
+
+#endif // SDSUPPORT
+
+#endif // ARDUINO_ARCH_SAM

Marlin/src/HAL/HAL_DUE/usb/udi_composite_desc.c

@@ -187,5 +187,6 @@ UDC_DESC_STORAGE udc_config_t udc_config = {
 /**INDENT-ON**/
 //@}
 
-#endif
-#endif
+#endif // ARDUINO_ARCH_SAM
+
+#endif // SDSUPPORT

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

Marlin/src/HAL/HAL_DUE/usb/uotghs_device_due.c

@@ -2070,4 +2070,4 @@ static bool udd_ep_interrupt(void)
 
 //@}
 
-#endif
+#endif // ARDUINO_ARCH_SAM

Marlin/src/HAL/HAL_DUE/usb/uotghs_otg.h

@@ -238,5 +238,4 @@ void otg_dual_disable(void);
 }
 #endif
 
-
 #endif /* UOTGHS_OTG_H_INCLUDED */

Marlin/src/HAL/HAL_DUE/usb/usb_task.c

@@ -56,7 +56,7 @@
 static volatile bool main_b_cdc_enable = false;
 static volatile bool main_b_dtr_active = false;
 
-void HAL_idletask(void) {
+void usb_task_idle(void) {
   #if ENABLED(SDSUPPORT)
     // Attend SD card access from the USB MSD -- Prioritize access to improve speed
     int delay = 2;
@@ -107,8 +107,15 @@ void usb_task_cdc_set_dtr(const uint8_t port, const bool b_enable) {
 
   if (1200 == dwDTERate) {
     // We check DTR state to determine if host port is open (bit 0 of lineState).
-    if (!b_enable)
+    if (!b_enable) {
+
+      // Set RST pin to go low for 65535 clock cycles on reset
+      //  This helps restarting when firmware flash ends
+      RSTC->RSTC_MR = 0xA5000F01;
+
+      // Schedule delayed reset
       initiateReset(250);
+    }
     else
       cancelReset();
   }
@@ -290,7 +297,7 @@ bool usb_task_other_requests(void) {
   return true;
 }
 
-void HAL_init(void) {
+void usb_task_init(void) {
 
   uint16_t *ptr;
 

Marlin/src/HAL/HAL_DUE/usb/usb_task.h

@@ -49,6 +49,10 @@
 
 #include "usb_protocol_cdc.h"
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 /*! \brief Called by MSC interface
  * Callback running when USB Host enable MSC interface
  *
@@ -111,8 +115,20 @@ void usb_task_cdc_rx_notify(const uint8_t port);
  */
 void usb_task_cdc_config(const uint8_t port, usb_cdc_line_coding_t *cfg);
 
-/* The USB device interrupt
+/*! \brief The USB device interrupt
  */
 void USBD_ISR(void);
 
-#endif // _MAIN_H_
+/*! \brief USB task init
+ */
+void usb_task_init(void);
+
+/*! \brief USB task idle
+ */
+void usb_task_idle(void);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif // _USB_TASK_H_