Return set_directions() to stepper.cpp (#12182)

Initial manual Z move can be negative if your stepper is inverted. Leads to bad situations for crashed or initially booted printers.

Marlin/src/module/stepper.cpp

 
   endstops.enable(true); // Start with endstops active. After homing they can be disabled
   sei();
+  set_directions(); // Init directions to last_direction_bits = 0  Keeps Z from being reversed
 }
 
 /**