Followup to #10102

* Automatically reset stepper timeout in manage_inactivity

Any code that adds moves to the planner can skip resetting the stepper timeout. We can let `idle` / `manage_inactivity` reset the timer whenever it detects any moves in the planner.

* blocks_queued => has_blocks_queued

- 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.

Fix #10098

[2.0.x] More complete Trinamic driver options

- Fix Autotune Thermal Protection
- Make 2 constants in autotune configurable

Thanks to Evgeny Kotsuba!

[2.0.x] Consolidate 3-point probing, auto delta probe radius

Based on #10131

[2.0.x] DUE - add full speed USB native port option